WorldWideScience

Sample records for macromolecule crystal quality

  1. Biological Macromolecule Crystallization Database

    Science.gov (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  2. An Overview of Biological Macromolecule Crystallization

    Science.gov (United States)

    Krauss, Irene Russo; Merlino, Antonello; Vergara, Alessandro; Sica, Filomena

    2013-01-01

    The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality. PMID:23727935

  3. Discovery of Reversible Crystallization of Macromolecules

    Science.gov (United States)

    Wunderlich, Bernhard

    2004-03-01

    For 10 years "reversing melting" was observed with temperature-modulated differential scanning calorimetry, TMDSC. This reversing melting is the first harmonic response beyond that caused by the heat capacity of a metastable, semicrystalline macromolecular sample. Before one can identify "reversible melting," the calorimeter response must be corrected for loss of linearity, stationarity, frequency, amplitude, and instrument lag, or proper experiment-design must avoid these problems. Using quasi-isothermal TMDSC, the following observations were made [Prog. Polymer Sci. 28 (2003) 383-450]: Equilibrium crystals of polymers may melt at the equilibrium melting-temperature, but crystallization needs supercooling, even in the presence of crystal nuclei, making the overall process irreversible. Metastable, folded-chain crystals of the same molecules also melt irreversibly, however, may have some specific reversibility. Flexible, linear molecules of up to 10 nm length may melt fully reversibly. Macromolecules of less flexibility may lose the ability to melt reversibly. Decoupling of molecular segments, molecular nucleation, segregation of molar masses, rigid amorphous fractions, effects of equilibrium point defects in crystals and glasses, and transition-less ordering and solidification will be discussed in some detail. Supported by NSF, Polymers Program, DMR-0312233, and the Div. of Mat. Sci., BES, of DOE at ORNL, managed by UT-Battelle, LLC, for the U.S. Department of Energy, DOE-AC05-00OR22725.

  4. Digital X-ray camera for quality evaluation three-dimensional topographic reconstruction of single crystals of biological macromolecules

    Science.gov (United States)

    Borgstahl, Gloria (Inventor); Lovelace, Jeff (Inventor); Snell, Edward Holmes (Inventor); Bellamy, Henry (Inventor)

    2008-01-01

    The present invention provides a digital topography imaging system for determining the crystalline structure of a biological macromolecule, wherein the system employs a charge coupled device (CCD) camera with antiblooming circuitry to directly convert x-ray signals to electrical signals without the use of phosphor and measures reflection profiles from the x-ray emitting source after x-rays are passed through a sample. Methods for using said system are also provided.

  5. Crystallization of Biological Macromolecules in Microgravity

    Science.gov (United States)

    Snell, Edward H.; Chayen, N. E.; Helliwell, J. R.

    2000-01-01

    An overview of microgravity crystallization explaining why microgravity is used, factors which affect crystallization, the method of crystallization and the environment itself. Also covered is how best to make use of microgravity and what the future might hold.

  6. Crystallization of Biological Macromolecules in Microgravity

    Science.gov (United States)

    Snell, Edward H.; Chayen, N. E.; Helliwell, J. R.

    2000-01-01

    An overview of microgravity crystallization explaining why microgravity is used, factors which affect crystallization, the method of crystallization and the environment itself. Also covered is how best to make use of microgravity and what the future might hold.

  7. Crystallization of biological macromolecules in a reduced gravity environment

    Science.gov (United States)

    Meehan, E. J., Jr.

    1979-01-01

    A battery of micro techniques were developed which allow the screening of a large number of conditions using only a small amount of the macromolecule. The need to develop methodologies for growing large crystals required for neutron diffraction studies is discussed.

  8. Liquid Between Macromolecules in Protein Crystals: Static Versus Dynamics

    Science.gov (United States)

    Chernov, A. A.

    2005-01-01

    Protein crystals are so fragile that they often can not be handled by tweezers. Indeed, measurements of the Young modulus, E, of lysozyme crystals resulted in E approx. equals 0.1 - 1 GPa, the lower figures, 0.1 - 0.5 GPa, being obtained from triple point bending of as-grown and not cross-linked crystals sitting in solution. The bending strength was found to be approx.10(exp -2) E. On the other hand, ultrasound speed and Mandelstam-Raman-Brilloin light scattering experiments led to much higher figures, E approx. equals 2.7 GPa. The lower figures for E were found from static or low frequency crystal deformations measurements, while the higher moduli are based on high frequency lattice vibrations, 10(exp 7) - 10(exp 10) 1/s. The physical reason for the about an order of magnitude discrepancy is in different behavior of water filling space between protein molecules. At slow lattice deformation, the not-bound intermolecular water has enough time to flow from the compressed to expanded regions of the deformed crystal. At high deformation frequencies in the ultra- and hypersound waves, the water is confined in the intermolecular space and, on that scale, behaves like a solid, thus contributing to the elastic crystal moduli. In this case, the reciprocal crystal modulus is expected to be an average of the water protein and water compressibilities (reciprocal compressibilities): the bulk modulus for lysozyme is 26 GPa, for water it is 7 GPa. Anisotropy of the crystal moduli comes from intermolecular contacts within the lattice while the high frequency hardness comes from the bulk of protein molecules and water bulk moduli. These conclusions are based on the analysis of liquid flow in porous medium to be presented.

  9. MASSIF-1: a beamline dedicated to the fully automatic characterization and data collection from crystals of biological macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Bowler, Matthew W., E-mail: mbowler@embl.fr [European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, F-38042 Grenoble (France); Université Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, F-38042 Grenoble (France); Nurizzo, Didier, E-mail: mbowler@embl.fr; Barrett, Ray; Beteva, Antonia; Bodin, Marjolaine [European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble (France)

    2015-10-03

    MASSIF-1 (ID30A-1) is a new beamline dedicated to the completely automatic characterization and data collection from crystals of biological macromolecules. MASSIF-1 (ID30A-1) is an ESRF undulator beamline operating at a fixed wavelength of 0.969 Å (12.8 keV) that is dedicated to the completely automatic characterization of and data collection from crystals of biological macromolecules. The first of the ESRF Upgrade MASSIF beamlines to be commissioned, it has been open since September 2014, providing a unique automated data collection service to academic and industrial users. Here, the beamline characteristics and details of the new service are outlined.

  10. Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments.

    Science.gov (United States)

    Offermann, Lesa R; He, John Z; Mank, Nicholas J; Booth, William T; Chruszcz, Maksymilian

    2014-03-01

    The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Our findings indicate that almost 40 % of entries deposited to the Protein Data Bank (PDB) reporting crystallization conditions contain at least one carboxylic acid. In order to analyze the role of carboxylic acids in macromolecular crystallization, a large-scale analysis of the successful crystallization experiments reported to the PDB was performed. The PDB is currently the largest source of crystallization data, however it is not easily searchable. These complications are due to a combination of a free text format, which is used to capture information on the crystallization experiments, and the inconsistent naming of chemicals used in crystallization experiments. Despite these difficulties, our approach allows for the extraction of over 47,000 crystallization conditions from the PDB. Initially, the selected conditions were investigated to determine which carboxylic acids or their salts are most often present in crystallization solutions. From this group, selected sets of crystallization conditions were analyzed in detail, assessing parameters such as concentration, pH, and precipitant used. Our findings will lead to the design of new crystallization screens focused around carboxylic acids.

  11. MASSIF-1: a beamline dedicated to the fully automatic characterization and data collection from crystals of biological macromolecules

    Science.gov (United States)

    Bowler, Matthew W.; Nurizzo, Didier; Barrett, Ray; Beteva, Antonia; Bodin, Marjolaine; Caserotto, Hugo; Delagenière, Solange; Dobias, Fabian; Flot, David; Giraud, Thierry; Guichard, Nicolas; Guijarro, Mattias; Lentini, Mario; Leonard, Gordon A.; McSweeney, Sean; Oskarsson, Marcus; Schmidt, Werner; Snigirev, Anatoli; von Stetten, David; Surr, John; Svensson, Olof; Theveneau, Pascal; Mueller-Dieckmann, Christoph

    2015-01-01

    MASSIF-1 (ID30A-1) is an ESRF undulator beamline operating at a fixed wavelength of 0.969 Å (12.8 keV) that is dedicated to the completely automatic characterization of and data collection from crystals of biological macromolecules. The first of the ESRF Upgrade MASSIF beamlines to be commissioned, it has been open since September 2014, providing a unique automated data collection service to academic and industrial users. Here, the beamline characteristics and details of the new service are outlined. PMID:26524320

  12. 生物大分子结晶技术研究进展%Progress in Research of Technologies for Crystallization of Biological Macromolecules

    Institute of Scientific and Technical Information of China (English)

    徐乐慧; 洪鸣凰; 赵文杰; 任国宾

    2011-01-01

    获得具有高分辨率的晶体是目前生物大分子结构测定的主要瓶颈,生物大分子的结晶是一个复杂的物理化学过程,涉及多方面的影响因素.本文综述了近年来生物大分子结晶的热点方法和技术.%Obtaining the high-resolution crystal structure has become a bottleneck for structure determination of biological macromolecules. The crystallization of biological macromolecules is a complicated process influenced by many parameters. The recent technologies for preparing crystal of biological macromolecules as well as techniques for controlling the crystallization process are reviewed.

  13. 生物大分子结晶过程的动力学%The Kinetics of Crystallization Process of Biological Macromolecule

    Institute of Scientific and Technical Information of China (English)

    桂林; 李琳; 胡松青; 陈玲; 范治国; 李坚斌

    2006-01-01

    In this paper ,the crystallization process of biological macromolecules was presented, and the mechanisms and kinetics of crystallization were analyzed.%阐述了生物大分子结晶的一般过程,分析了结晶的机制和动力学.

  14. The Effect of Solution Parameters on Lysozyme Nucleation Rates and Crystal Quality

    Science.gov (United States)

    Judge, R. A.; Snell, E. H.

    1998-01-01

    In the pursuit of strongly diffracting high quality macromolecule crystals of suitable volume, this study investigates how the formation of macromolecules in solution and their growth characteristics effect crystal volume and diffracting quality. We systematically investigated the effect of solution conditions on lysozyme nucleation rates and the volume of crystals produced. Batch crystallization plates were used in combination with a video microscope system to measure nucleation rates and crystal volume. As expected from classical nucleation theory, crystal numbers were found to increase with increases in temperature and supersaturation. Small changes in solution pH, at constant supersaturation values were found, however, to dramatically effect the number of crystals nucleated in the wells varying from 1000s to 10s in the pH range 4.0 to 5.2. Having optimized the conditions required to produce an appropriate number of crystals of a suitable volume for X-ray analysis, a large number of uniform crystals were produced under exactly the same conditions. In the X-ray analysis of more than 50 such crystals there was found a wide variation in crystal lattice parameters and data quality. The variation in X-ray quality crystal samples is thought to be related to the growth rate variation caused by growth rate dispersion seen in lysozyme crystal growth experiments.

  15. Simultaneous X-ray diffraction from multiple single crystals of macromolecules

    DEFF Research Database (Denmark)

    Paithankar, Karthik S.; Sørensen, Henning Osholm; Wright, Jonathan P.

    2011-01-01

    The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedu...

  16. Microgravity crystallization of macromolecules: An interim report and proposal for continued research

    Science.gov (United States)

    Goldberg, Benjamin E.

    1986-01-01

    An initial investigation exploring the effects of gravity on the crystallization of macromolecular systems has been completed. Monodisperse poly(ethylene), molecular weight 48,000 was melted and recrystallized under gravitational conditions: 0, 1, and 2 g. No correlations to gravitational environment were noted for the 20 C/min melt, as monitored with a photodensitometer system. However, post-crystallization testing of the recrystallized samples revealed thicker samples with more regions of large, well defined spherulites for the zero gravity crystallization environment. The results of the post-crystallization analysis have been reviewed and the results related to nucleation concerns. Finally, birefringence data, consistent with, but not explained by, the nucleation scenarios is detailed, and further investigations are proposed.

  17. Fully automatic characterization and data collection from crystals of biological macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander; Nurizzo, Didier, E-mail: nurizzo@esrf.fr [European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble (France); Bowler, Matthew W., E-mail: nurizzo@esrf.fr [European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble (France); Université Grenoble Alpes–EMBL–CNRS, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble (France); European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble (France)

    2015-07-31

    A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention. Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.

  18. Crystalline Hybrid Polyphenylene Macromolecules from Octaalkynylsilsesquioxanes, Crystal Structures, and a Potential Route to 3-D Graphenes

    Energy Technology Data Exchange (ETDEWEB)

    Roll, Mark F; Kampf, Jeffrey W.; Laine, Richard M

    2011-05-10

    We report here the Diels–Alder reaction of octa(diphenylacetylene)silsesquioxane [DPA₈OS] with tetraphenylcyclopentadienone or tetra(p-tolyl)cyclopentadienone to form octa(hexaphenylbenzene)octasilsesquioxane, (Ph₆C₆)₈OS, or octa(tetratolyldiphenylbenzene)octasilsesquioxane, (p-Tolyl₄Ph₂C₆)₈OS. Likewise, tetra(p-tolyl)cyclopentadienone reacts with octa(p-tolylethynylphenyl)OS to form octa(pentatolylphenylbenzene)octasilsesquioxane (p-Tolyl₅PhC₆)₈OS. These compounds, with molecular weights of 4685–5245 Da, were isolated and characterized using a variety of analytical methods. The crystal structure of DPA₈OS offers a 3 nm³ unit cell with Z = 1. The crystal structure of (Ph₆C₆)₈OS was determined to have a triclinic unit cell of 11 nm³ with Z = 1. The latter structure is believed to be the largest discrete molecular structure reported with 330 carbons. Efforts to dehydrogenatively cyclize (Scholl reaction) the hexaarylbenzene groups to form 3-D octgraphene compounds are described.

  19. Can Solution Supersaturation Affect Protein Crystal Quality?

    Science.gov (United States)

    Gorti, Sridhar

    2013-01-01

    The formation of large protein crystals of "high quality" is considered a characteristic manifestation of microgravity. The physical processes that predict the formation of large, high quality protein crystals in the microgravity environment of space are considered rooted in the existence of a "depletion zone" in the vicinity of crystal. Namely, it is considered reasonable that crystal quality suffers in earth-grown crystals as a result of the incorporation of large aggregates, micro-crystals and/or large molecular weight "impurities", processes which are aided by density driven convective flow or mixing at the crystal-liquid interface. Sedimentation and density driven convection produce unfavorable solution conditions in the vicinity of the crystal surface, which promotes rapid crystal growth to the detriment of crystal size and quality. In this effort, we shall further present the hypothesis that the solution supersaturatoin at the crystal surface determines the growth mechanism, or mode, by which protein crystals grow. It is further hypothesized that protein crystal quality is affected by the mechanism or mode of crystal growth. Hence the formation of a depletion zone in microgravity environment is beneficial due to inhibition of impurity incorporatoin as well as preventing a kinetic roughening transition. It should be noted that for many proteins the magnitude of neither protein crystal growth rates nor solution supersaturation are predictors of a kinetic roughening transition. That is, the kinetic roughening transition supersaturation must be dtermined for each individual protein.

  20. Electrospray crystallization for high-quality submicron-sized crystals

    NARCIS (Netherlands)

    Radacsi, N.; Stankiewicz, A.I.; Creyghton, Y.L.M.; Heijden, A.E.D.M. van der; Horst, J.H. ter

    2011-01-01

    Nano- and submicron-sized crystals are too small to contain inclusions and are, therefore, expected to have a higher internal quality compared to conventionally sized particles (several tens to hundreds of microns). Using electrospray crystallization, nano- and submicron-sized crystals can be easily

  1. Can Supersaturation Affect Protein Crystal Quality?

    Science.gov (United States)

    Gorti, Sridhar

    2013-01-01

    In quiescent environments (microgravity, capillary tubes, gels) formation of a depletion zone is to be expected, due either to limited sedimentation, density driven convection or a combination of both. The formation of a depletion zone can: Modify solution supersaturation near crystal; Give rise to impurity partitioning. It is conjectured that both supersaturation and impurity partitioning affect protein crystal quality and size. Further detailed investigations on various proteins are needed to assess above hypothesis.

  2. Ion specificities of artificial macromolecules.

    Science.gov (United States)

    Liu, Lvdan; Kou, Ran; Liu, Guangming

    2016-12-21

    Artificial macromolecules are well-defined synthetic polymers, with a relatively simple structure as compared to naturally occurring macromolecules. This review focuses on the ion specificities of artifical macromolecules. Ion specificities are influenced by solvent-mediated indirect ion-macromolecule interactions and also by direct ion-macromolecule interactions. In aqueous solutions, the role of water-mediated indirect ion-macromolecule interactions will be discussed. The addition of organic solvents to aqueous solutions significantly changes the ion specificities due to the formation of water-organic solvent complexes. For direct ion-macromolecule interactions, we will discuss specific ion-pairing interactions for charged macromolecules and specific ion-neutral site interactions for uncharged macromolecules. When the medium conditions change from dilute solutions to crowded environments, the ion specificities can be modified by either the volume exclusion effect, the variation of dielectric constant, or the interactions between ions, macromolecules, and crowding agents.

  3. Organized monolayers of biological macromolecules on Au(111) surfaces

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Chi, Qijin; Nielsen, Jens Ulrik

    2002-01-01

    Single-crystal electrochemistry and scanning tunneling microscopy directly in aqueous electrolyte solution (in situ STM) are established in physical electrochemistry but new in studies of adsorption and interfacial electrochemistry of biological macromolecules. These high-resolution techniques have...

  4. Searching for the Best Protein Crystals: Synchrotron Based Measurements of Protein Crystal Quality

    Science.gov (United States)

    Borgstahl, Gloria; Snell, Edward H.; Bellamy, Henry; Pangborn, Walter; Nelson, Chris; Arvai, Andy; Ohren, Jeff; Pokross, Matt

    1999-01-01

    We are developing X-ray diffraction methods to quantitatively evaluate the quality of protein crystals. The ultimate use for these crystal quality will be to optimize crystal growth and freezing conditions to obtain the best diffraction data. We have combined super fine-phi slicing with highly monochromatic, low divergence synchrotron radiation and the ADSC Quantum 4 CCD detector at the Stanford Synchrotron Radiation laboratory beamline 1.5 to accurately measure crystal mosaicity. Comparisons of microgravity versus earth-grown insulin crystals using these methods will be presented.

  5. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    KAUST Repository

    Saidaminov, Makhsud I.

    2015-07-06

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at elevated temperatures. The crystals can be both size- and shape-controlled by manipulating the different crystallization parameters. Despite the rapidity of the method, the grown crystals exhibit transport properties and trap densities comparable to the highest quality MAPbX3 reported to date. The phenomenon of inverse or retrograde solubility and its correlated inverse temperature crystallization strategy present a major step forward for advancing the field on perovskite crystallization.

  6. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    Science.gov (United States)

    Saidaminov, Makhsud I.; Abdelhady, Ahmed L.; Murali, Banavoth; Alarousu, Erkki; Burlakov, Victor M.; Peng, Wei; Dursun, Ibrahim; Wang, Lingfei; He, Yao; Maculan, Giacomo; Goriely, Alain; Wu, Tom; Mohammed, Omar F.; Bakr, Osman M.

    2015-07-01

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br- or I-) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at elevated temperatures. The crystals can be both size- and shape-controlled by manipulating the different crystallization parameters. Despite the rapidity of the method, the grown crystals exhibit transport properties and trap densities comparable to the highest quality MAPbX3 reported to date. The phenomenon of inverse or retrograde solubility and its correlated inverse temperature crystallization strategy present a major step forward for advancing the field on perovskite crystallization.

  7. Analysis of macromolecules, ligands and macromolecule-ligand complexes

    Science.gov (United States)

    Von Dreele, Robert B [Los Alamos, NM

    2008-12-23

    A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

  8. A Course on Macromolecules.

    Science.gov (United States)

    Horta, Arturo

    1985-01-01

    Describes a senior-level course that: (1) focuses on the structure and reactions of macromolecules; (2) treats industrial polymers in a unified way; and (3) uses analysis of conformation and conformational statistics as a unifying approach. Also discusses course topics, including polysaccharides, proteins, nucleic acids, and others. (JN)

  9. Crystal quality analysis and improvement using x-ray topography

    Science.gov (United States)

    Maj, J. A.; Goetze, K.; Macrander, A. T.; Zhong, Y. C.; Huang, X. R.; Maj, L.

    2008-08-01

    The Topography X-ray Laboratory of the Advanced Photon Source (APS) at Argonne National Laboratory operates as a collaborative effort with APS users to produce high performance crystals for APS X-ray beamline experiments. For many years the topography laboratory has worked closely with an on-site optics shop to help ensure the production of crystals with the highest quality, most stress-free surface finish possible. It has been instrumental in evaluating and refining methods used to produce high quality crystals. Topographical analysis has shown to be an effective method to quantify and determine the distribution of stresses, to help identify methods that would mitigate the stresses and improve the Rocking curve, and to create CCD images of the crystal. This paper describes the topography process and offers methods for reducing crystal stresses in order to substantially improve the crystal optics.

  10. High-quality single crystals for neutron experiments

    Indian Academy of Sciences (India)

    Geetha Balakrishnan

    2008-10-01

    To make headway on any problem in physics, high-quality single crystals are required. In this talk, special emphasis will be placed on the crystal growth of various oxides (superconductors and magnetic materials), borides and carbides using the image furnaces at Warwick. The floating zone method of crystal growth used in these furnaces produces crystals of superior quality, circumventing many of the problems associated with, for example, flux growth from the melt. This method enables the growth of large volumes of crystal, a prerequisite especially for experiments using neutron beams. Some examples of experimental results from crystals grown at Warwick, selected from numerous in-house studies and our collaborative research projects with other UK and international groups will be discussed.

  11. Crystal quality analysis and improvement using x-ray topography.

    Energy Technology Data Exchange (ETDEWEB)

    Maj, J.; Goetze, K.; Macrander, A.; Zhong, Y.; Huang, X.; Maj, L.; Univ. of Chicago

    2008-01-01

    The Topography X-ray Laboratory of the Advanced Photon Source (APS) at Argonne National Laboratory operates as a collaborative effort with APS users to produce high performance crystals for APS X-ray beamline experiments. For many years the topography laboratory has worked closely with an on-site optics shop to help ensure the production of crystals with the highest quality, most stress-free surface finish possible. It has been instrumental in evaluating and refining methods used to produce high quality crystals. Topographical analysis has shown to be an effective method to quantify and determine the distribution of stresses, to help identify methods that would mitigate the stresses and improve the Rocking curve, and to create CCD images of the crystal. This paper describes the topography process and offers methods for reducing crystal stresses in order to substantially improve the crystal optics.

  12. Construction with macromolecules

    Directory of Open Access Journals (Sweden)

    Stefan Hecht

    2005-03-01

    Full Text Available The generation of nanosized features via the bottom-up organization of individual atoms and molecules represents one of the most rapidly emerging fields in modern science and technology. In order to gain general and modular access to nanostructures, a construction kit consisting of molecular building blocks with defined nanoscale dimensions, shape, and functionality is required. While nature has developed a hierarchical strategy to construct sophisticated and complex nanostructures, chemistry is just starting to explore artificial macromolecules as a means to synthesize specific nano-objects. In this review, recent advances in achieving control over conformation within macromolecules and the interconnection of conformationally defined subunits by either covalent bonds or self-assembly are discussed in analogy to natural structure evolution.

  13. High-quality Crystal Filter – Design and Realization

    Directory of Open Access Journals (Sweden)

    D. M. Dujković

    2013-11-01

    Full Text Available Analog oscillators and filters are still very important devices in modern telecommunication and measurement equipment. Quartz crystal units are used for high-quality oscillators and filters, due to their extremely stable resonant frequency and Q-factor. In this paper the design and realization of a high-quality bandpass quartz crystal filter with a possible application to antenna circuitry is described.

  14. Fabrication of High Quality Three-Dimensional Photonic Crystals

    Institute of Scientific and Technical Information of China (English)

    HU Xiao-Yong; LIU Yuan-Hao; CHENG Bing-Ying; ZHANG Dao-Zhong; MENG Qing-Bo

    2004-01-01

    High quality colloidal photonic crystals made from polystyrene spheres with diameter 240nm are fabricated by the vertical deposition method. The scanning electron microscopy (SEM) and the transmittance spectrum are used to characterize the properties of the photonic crystal. The SEM images show that there are few lattice defects. The transmittance of the photonic crystal is above 75% in the pass band at 700nm and is lower than 5% at the centre of the band gap, respectively. It is found that proper concentration is a very important factor to fabricate the photonic crystal when the diameter of the spheres is lower than 300nm.

  15. Macromolecular Crystallization in Microgravity

    Science.gov (United States)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural

  16. Crystal Quality, the Long and the Short of It

    Science.gov (United States)

    Snell, Eddie H.

    2004-01-01

    The term "crystal quality" is ambiguous and implies different meanings to different crystallographers. For the physical crystallographer who aims to understand long-range aspects of crystal growth mosaicity is one of the leading measures of perfection. For the structural crystallographer and those seeking to understand growth at a short-range, molecular level, the detail in the resulting structure is a key goal. Different quality measures have been developed due to different needs. Each of the measures has advantages and each has limitations. In this talk a sample of these measures will be discussed with particular emphasis applied to their application in the analysis of microgravity grown crystals. The advantages and limitations of each will be discussed. Ultimately, the choice of crystal quality measurement lies in the nature of the question asked. It is scfill to remember that beauty is often in the eye of the beholder.

  17. Sperm macromolecules associated with bull fertility.

    Science.gov (United States)

    Kaya, Abdullah; Memili, Erdoğan

    2016-06-01

    Bull fertility, ability of the sperm to fertilize and activate the egg that sustain embryo development, is vitally important for effective and efficient production of cattle. Fertility is a complex trait with low heritability. Despite recent advances in genomic selection and possibility of enormous paternal benefits to profitable cattle production, there exist no reliable tests for evaluating semen quality and predicting bull fertility. This review focuses on sperm macromolecules such as transcripts, proteins and the epigenome, i.e., the functional genome that are associated with bull fertility. Generating new information in these systems is important beyond agriculture because such progress advances the fundamental science of the mammalian male gamete while at the same time introduces biotechnology into livestock production. Sperm macromolecules and epigenome markers associated with bull fertility can be used alone or in combination with the current SNP microarrays to determine sperm quality and to indicate bull fertility.

  18. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    OpenAIRE

    Saidaminov, Makhsud I.; Abdelhady, Ahmed L.; Murali, Banavoth; Alarousu, Erkki; Burlakov, Victor M.; Peng, Wei; Dursun, Ibrahim; Wang, Lingfei; He, Yao; Maculan, Giacomo; Goriely, Alain; Wu, Tom; Mohammed, Omar F.; Bakr, Osman M.

    2015-01-01

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3 +, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at e...

  19. Diffusion of macromolecules through sclera.

    Science.gov (United States)

    Miao, Heng; Wu, Bi-Dong; Tao, Yong; Li, Xiao-Xin

    2013-02-01

    To quantify the in vitro permeability coefficient over different topographical locations of porcine sclera to macromolecules with different molecular weight. Fresh equatorial and posterior superotemporal porcine sclera was mounted in a two-chamber diffusion apparatus, and its permeability to fluorescein isothiocyanate (FITC)-conjugated dextrans ranging in molecular weight from 40 kDa to 150 kDa was determined by fluorescence spectrophotometry. The sclera was processed as frozen sections and viewed with a fluorescence microscope. The thickness of the area and the thickness that macromolecules enriched in the surface of sclera were measured. The permeability coefficient (Pc) of porcine sclera to macromolecules was significantly higher (40 kDa, p = 0.028; 70 kDa, p = 0.033; 150 kDa, p = 0.007) in equatorial region than posterior, which could be attributed to the significant difference of thickness (p macromolecules enriched in the scleral surface was thicker for those with larger MW (p macromolecules. Larger macromolecules are more likely to accumulate in scleral surface. The difference between topographical locations may have pharmacokinetic implications when considering transscleral diffusion of macromolecules. © 2012 The Authors. Acta Ophthalmologica © 2012 Acta Ophthalmologica Scandinavica Foundation.

  20. Crystal quality and inhibitor binding by aspartic proteinases; preparation of high quality crystals of mouse renin

    Science.gov (United States)

    Badasso, M.; Sibanda, B. L.; Cooper, J. B.; Dealwis, C. G.; Wood, S. P.

    1992-08-01

    Renin from mouse submandibular glands has been highly purified and co-crystallized with a synthetic nonapeptide fragment of rat angiotensionogen in which the scissile Leu-Leu bond has been modified as a hydroxyethylene mimic of the transition state. The strong diffraction from these crystals compared to the native form is discussed in relation to the behaviour of other members of the aspartic proteinase family in crystallisation.

  1. Physicochemical Properties of Ion Pairs of Biological Macromolecules.

    Science.gov (United States)

    Iwahara, Junji; Esadze, Alexandre; Zandarashvili, Levani

    2015-09-30

    Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic moieties are important for proteins and nucleic acids to perform their function. Although numerous three-dimensional structures show ion pairs at functionally important sites of biological macromolecules and their complexes, the physicochemical properties of the ion pairs are not well understood. Crystal structures typically show a single state for each ion pair. However, recent studies have revealed the dynamic nature of the ion pairs of the biological macromolecules. Biomolecular ion pairs undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. This dynamic behavior is reasonable in light of the fundamental concepts that were established for small ions over the last century. In this review, we introduce the physicochemical concepts relevant to the ion pairs and provide an overview of the recent advancement in biophysical research on the ion pairs of biological macromolecules.

  2. Macromolecular crystallization in microgravity

    Energy Technology Data Exchange (ETDEWEB)

    Snell, Edward H [Biophysics Group, NASA Marshall Space Flight Center, Code XD42, Huntsville, AL 35812 (United States); Helliwell, John R [Department of Chemistry, The University of Manchester, Manchester, M13 9PL (United Kingdom)

    2005-04-01

    Density difference fluid flows and sedimentation of growing crystals are greatly reduced when crystallization takes place in a reduced gravity environment. In the case of macromolecular crystallography a crystal of a biological macromolecule is used for diffraction experiments (x-ray or neutron) so as to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal then the greater the molecular structure detail that can be extracted. It is this structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences, with major potential in understanding disease pathologies. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyse the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry and mathematics meet to enable insight to the fundamentals of life. As the reader will see, there is a great deal of physics involved when the microgravity environment is applied to crystallization, some of it known, and undoubtedly much yet to

  3. Macromolecules in Undergraduate Physical Chemistry.

    Science.gov (United States)

    Mattice, Wayne L.

    1981-01-01

    Suggests the topic of macromolecules and synthetic polymers be included in undergraduate courses. Two macromolecular systems (polyethylene in a state unperturbated by long-range interactions and a polypeptide undergoing a helix-coil transition) are described which are suitable for inclusion in the statistical mechanics section of physical…

  4. Ion binding to biological macromolecules.

    Science.gov (United States)

    Petukh, Marharyta; Alexov, Emil

    2014-11-01

    Biological macromolecules carry out their functions in water and in the presence of ions. The ions can bind to the macromolecules either specifically or non-specifically, or can simply to be a part of the water phase providing physiological gradient across various membranes. This review outlines the differences between specific and non-specific ion binding in terms of the function and stability of the corresponding macromolecules. Furthermore, the experimental techniques to identify ion positions and computational methods to predict ion binding are reviewed and their advantages compared. It is indicated that specifically bound ions are relatively easier to be revealed while non-specifically associated ions are difficult to predict. In addition, the binding and the residential time of non-specifically bound ions are very much sensitive to the environmental factors in the cells, specifically to the local pH and ion concentration. Since these characteristics differ among the cellular compartments, the non-specific ion binding must be investigated with respect to the sub-cellular localization of the corresponding macromolecule.

  5. DNA compaction by nonbinding macromolecules

    NARCIS (Netherlands)

    Vries, de R.J.

    2012-01-01

    Compaction of DNA by nonbinding macromolecules such as uncharged flexible polymer chains and negatively charged globular proteins is thought to have various applications in biophysics, for example in the formation of a nucleoid structure in bacteria. A simple experimental model that has been very

  6. DNA compaction by nonbinding macromolecules

    NARCIS (Netherlands)

    Vries, de R.J.

    2012-01-01

    Compaction of DNA by nonbinding macromolecules such as uncharged flexible polymer chains and negatively charged globular proteins is thought to have various applications in biophysics, for example in the formation of a nucleoid structure in bacteria. A simple experimental model that has been very we

  7. INFLUENCE OF MACROMOLECULES ON CHEMICAL TRANSPORT

    Science.gov (United States)

    Macromolecules in the pore fluid influence the mobility of hydrophobic compounds through soils. his study evaluated the significance of macromolecules in facilitating chemical transport under laboratory conditions. Partition coefficients between 14C-labeled hexachlorobenzene and ...

  8. Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

    Science.gov (United States)

    Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

  9. Effect of Crucibles on Qualities of Self-Seeded Aluminium Nitride Crystals Grown by Sublimation

    Institute of Scientific and Technical Information of China (English)

    HAN Qi-Feng; WANG Yu-Qi; DUAN Cheng-Hong; QIU Kai; JI Chang-Jian; LI Xin-Hua; ZHONG Fei; YIN Zhi-Jun; CAO Xian-Cun; ZHOU Xiu-Ju

    2007-01-01

    Self-seeded aluminium nitride (AIN)crystals are grown in tungsten and hot pressed boron nitride(HPBN)crucibles With different shapes by a sublimation method.The qualities of the AIN crystals are characterized by high-resolution transmission electronic microscopy(HRTEM),scanning electron microscopy(SEM)and MicroRaman spectroscopy.The results indicate that the better quality crystals can be collected in.conical tungsten crucible.

  10. The radiation chemistry of macromolecules

    CERN Document Server

    1973-01-01

    The Radiation Chemistry of Macromolecules, Volume II is a collection of papers that discusses radiation chemistry of specific systems. Part 1 deals with radiation chemistry of substituted vinyl polymers, particularly polypropylene (PP) as its structure is intermediate between polyethylene and polyisobutylene. This part also discusses polypropylene oxide (PPOx) for it can be prepared in the atactic, isotactic, and optically active forms. One paper focuses on the fundamental chemical processes and the changes in physical properties that give rise to many different applications of polystyrene. An

  11. Localization of intracrystalline organic macromolecules in mollusk shells

    Science.gov (United States)

    Suzuki, Michio; Okumura, Taiga; Nagasawa, Hiromichi; Kogure, Toshihiro

    2011-12-01

    As a crucial first step for understanding the organic-inorganic interaction in biomineralization of mollscan shells, localization of the intracrystalline organic macromolecules in biogenic calcium carbonate crystals of the nacreous, prismatic ( Pinctada fucata) and foliated ( Cellana toreuma) microstructures were investigated using Fresnel contrast analysis in a transmission electron microscope. Spherular Fresnel contrasts in the crystals correspond to organic substances, which was confirmed by the detection of 1s→π * (CC) transition peak at 284 eV in electron energy loss spectroscopy. Nano-sized (5-10 nm) spherules in the aragonite tablets constituting the nacreous layer of P. fucata specifically concentrate in the vicinity of the interlamellar membrane between the aragonite tablets. The dominant sizes of the organic macromolecules extracted by dissolving the aragonite tablets in the nacreous layer of P. fucata were estimated using the gel-filtration analysis to be roughly 10 and 4 nm, which dimensionally corresponds to the sizes observed by Fresnel contrast imaging in the tablets. These results will serve for understanding the functions of intracrystalline organic macromolecules in mollusk shells.

  12. Investigation of the influence of crystal quality on Borrmann spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kalaydzhyan, Aram

    2012-12-15

    The goal of thesis is to apply the dynamical theory of X-ray diffraction for perfect crystals to mosaic crystals, which are composed of slightly misoriented blocks. For this purpose statistical methods were used for the description of crystal defects. This concept was combined with the diffraction theory and implemented in code. This program was used for numerical simulations of diffraction processes in transmission geometry by plane barium titanate crystals. The computed dependencies on defects for Borrmann spectroscopy satisfy the initial expectations for medium orders of crystal defects qualitatively.

  13. Crystal growth of high-quality ZrB 2 single crystals using the floating-zone method

    Science.gov (United States)

    Hori, Kenji; Inoue, Shinji; Isogami, Mineo

    2008-01-01

    High-quality ZrB 2 single crystals with diameters of 13 mm and lengths of 45 mm were grown from boron-rich molten zones (boron 80 mol%), using the RF heated floating-zone method. The (0 0 0 1) single crystals were also grown using seed crystals. Control of temperature gradients on the growing interfaces was performed by arranging ceramic cylinders around the growing crystals and the feed rods. This made it possible to grow high-quality ZrB 2 single crystals free of defects such as lineage structures observed in X-ray topographies of cross-sections. In the central areas (3 mm square) of the grown crystals, the full-widths at half-maximum (FWHM) of the X-ray rocking curve (( 10-1¯0) diffraction) were improved to 24.5-42.4 arc sec compared with the crystals obtained until now. The ZrB 2 obtained seems to be quite suitable for substrates of GaN.

  14. Configurational diffusion of coal macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Guin, J.A.; Curtis, C.W.; Tarrer, A.R.; Kim, S.; Hwang, D.; Chen, C.C.; Chiou, Z.

    1991-01-01

    The objective of our research was to obtain fundamental information regarding the functional dependence of the diffusion coefficient of coal molecules on the ratio of molecule to pore diameter. That is, the objective of our study was to examine the effect of molecule size and configuration on hindered diffusion of coal macromolecules through as porous medium. To best accomplish this task, we circumvented the complexities of an actual porous catalyst by using a well defined porous matrix with uniform capillaric pores, i.e., a track-etched membrane. In this way, useful information was obtained regarding the relationship of molecular size and configuration on the diffusion rate of coal derived macromolecules through a pore structure with known geometry. Similar studies were performed using a pellet formed of porous alumina, to provide a link between the idealized membranes and the actual complex pore structure of real catalyst extrudates. The fundamental information from our study will be useful toward the tailoring of catalysts to minimize diffusional influences and thereby increase coal conversion and selectivity for desirable products. (VC)

  15. Effect of Crystal Quality on HCP-BCC Phase Transition in Solid 4He

    CERN Document Server

    Mikhin, N; Rudavskii, E; Vekhov, Y; Mikhin, Nikolay; Polev, Andrey; Rudavskii, Eduard; Vekhov, Yegor

    2006-01-01

    The kinetics of HCP-BCC structure phase transition is studied by precise pressure measurement technique in 4He crystals of different quality. An anomalous pressure behavior in bad quality crystals under constant volume conditions is detected just after HCP-BCC structure phase transition. A sharp pressure drop of 0.2 bar was observed at constant temperature. The subsequent pressure kinetics is a non-monotonic temperature function. The effect observed can be explained if we suppose that microscopic liquid droplets appear on the HCP-BCC interphase region in bad quality crystals. After the interphase region disappearance, these droplets are crystallized with pressure reduction. It is shown that this effect is absent in high quality thermal-treated crystals.

  16. Dermal and transdermal delivery of pharmaceutically relevant macromolecules.

    Science.gov (United States)

    Münch, S; Wohlrab, J; Neubert, R H H

    2017-10-01

    The skin offers an attractive way for dermal and transdermal drug delivery that is why the drug still needs certain qualities to transcend the outermost layer of the skin, the stratum corneum. The requirements are: drugs with a maximum molecular weight of 1kDa, high lipophilicity and a certain polarity. This would restrict the use of a transdermal delivery of macromolecules, which would make the drug more effective in therapeutic administration. Various studies have shown that macromolecules without support do not penetrate the human skin. This effect can be achieved using physical and chemical methods, as well as biological peptides. The most popular physical method is the use of microneedles to create micropores in the skin and release the active agent in different sections. But also, other methods have been tested. Microjets, lasers, electroporation, sonophoresis and iontophoresis are also promising methods to successfully deliver dermal and transdermal macromolecules. Additionally, there are different penetration enhancer groups and biological peptides, which are also considered to be interesting approaches of enabling macromolecules to travel along the skin. All these methods will be described and evaluated in this review article. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Templated and self-limiting calcite formation directed by coccolith organic macromolecules.

    Science.gov (United States)

    Gal, Assaf; Wirth, Richard; Barkay, Zahava; Eliaz, Noam; Scheffel, André; Faivre, Damien

    2017-07-06

    The formation of intricately shaped crystalline minerals by organisms is orchestrated by specialized biomacromolecules. The macromolecules associated with coccoliths, nanometer-sized calcite crystal arrays produced by marine microalgae, can form a distinct calcium-rich phase via macromolecular recognition. Here, we show that this calcium-rich phase can be mineralized into a thin film of single-crystalline calcite by the balanced addition of carbonate ions. Such a crystallization process provides a strategy to direct crystalline products via local interactions between soluble macromolecules and compatible templates.

  18. MEASURING THE SHAPES OF MACROMOLECULES – AND WHY IT MATTERS

    Directory of Open Access Journals (Sweden)

    Jie Li

    2013-09-01

    Full Text Available The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing numerical and analytical approaches that solve these problems. We cover in more details our own work in this field, focusing on the alpha shape theory as it provides a unifying mathematical framework that enable the analytical calculations of the surface area and volume of a macromolecule represented as a union of balls, the detection of pockets and cavities in the molecule, and the quantification of contacts between the atomic balls. We have shown that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity. We conclude with a brief description of new challenges for the alpha shape theory in modern structural biology.

  19. Measuring the shapes of macromolecules – and why it matters

    Directory of Open Access Journals (Sweden)

    Jie Li

    2013-09-01

    Full Text Available The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing numerical and analytical approaches that solve these problems. We cover in more details our own work in this field, focusing on the alpha shape theory as it provides a unifying mathematical framework that enable the analytical calculations of the surface area and volume of a macromolecule represented as a union of balls, the detection of pockets and cavities in the molecule, and the quantification of contacts between the atomic balls. We have shown that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity. We conclude with a brief description of new challenges for the alpha shape theory in modern structural biology.

  20. Measuring the shapes of macromolecules - and why it matters.

    Science.gov (United States)

    Li, Jie; Mach, Paul; Koehl, Patrice

    2013-01-01

    The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing numerical and analytical approaches that solve these problems. We cover in more details our own work in this field, focusing on the alpha shape theory as it provides a unifying mathematical framework that enable the analytical calculations of the surface area and volume of a macromolecule represented as a union of balls, the detection of pockets and cavities in the molecule, and the quantification of contacts between the atomic balls. We have shown that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity. We conclude with a brief description of new challenges for the alpha shape theory in modern structural biology.

  1. Conformations of Macromolecules and their Complexes from Heterogeneous Datasets

    CERN Document Server

    Schwander, P; Ourmazd, A

    2014-01-01

    We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.

  2. A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel.

    Science.gov (United States)

    Cao, Hui-Ling; Sun, Li-Hua; Li, Jian; Tang, Lin; Lu, Hui-Meng; Guo, Yun-Zhu; He, Jin; Liu, Yong-Ming; Xie, Xu-Zhuo; Shen, He-Fang; Zhang, Chen-Yan; Guo, Wei-Hong; Huang, Lin-Jun; Shang, Peng; He, Jian-Hua; Yin, Da-Chuan

    2013-10-01

    High-quality crystals are key to obtaining accurate three-dimensional structures of proteins using X-ray diffraction techniques. However, obtaining such protein crystals is often a challenge. Several containerless crystallization techniques have been reported to have the ability to improve crystal quality, but it is unknown which is the most favourable way to grow high-quality protein crystals. In this paper, a quality comparison of protein crystals which were grown under three containerless conditions provided by diamagnetic levitation, silicone oil and agarose gel was conducted. A control experiment on a vessel wall was also simultaneously carried out. Seven different proteins were crystallized under the four conditions, and the crystal quality was assessed in terms of the resolution limit, the mosaicity and the Rmerge. It was found that the crystals grown under the three containerless conditions demonstrated better morphology than those of the control. X-ray diffraction data indicated that the quality of the crystals grown under the three containerless conditions was better than that of the control. Of the three containerless crystallization techniques, the diamagnetic levitation technique exhibited the best performance in enhancing crystal quality. This paper is to our knowledge the first report of improvement of crystal quality using a diamagnetic levitation technique. Crystals obtained from agarose gel demonstrated the second best improvement in crystal quality. The study indicated that the diamagnetic levitation technique is indeed a favourable method for growing high-quality protein crystals, and its utilization is thus potentially useful in practical efforts to obtain well diffracting protein crystals.

  3. Relaxation Dynamics of Semiflexible Fractal Macromolecules

    Directory of Open Access Journals (Sweden)

    Jonas Mielke

    2016-07-01

    Full Text Available We study the dynamics of semiflexible hyperbranched macromolecules having only dendritic units and no linear spacers, while the structure of these macromolecules is modeled through T-fractals. We construct a full set of eigenmodes of the dynamical matrix, which couples the set of Langevin equations. Based on the ensuing relaxation spectra, we analyze the mechanical relaxation moduli. The fractal character of the macromolecules reveals itself in the storage and loss moduli in the intermediate region of frequencies through scaling, whereas at higher frequencies, we observe the locally-dendritic structure that is more pronounced for higher stiffness.

  4. Bond Tension in Tethered Macromolecules.

    Science.gov (United States)

    Sheiko, Sergei S; Panyukov, Sergey; Rubinstein, Michael

    2011-06-14

    The paper presents scaling analysis of mechanical tension generated in densely branched macromolecules tethered to a solid substrate with a short linker. Steric repulsion between branches results in z-fold amplification of tension in the linker, where z is the number of chain-like arms. At large z ~ 100-1000, the generated tension may exceed the strength of covalent bonds and sever the linker. Two types of molecular architectures were considered: polymer stars and polymer "bottlebrushes" tethered to a solid substrate. Depending on the grafting density, one distinguishes the so-called mushroom, loose grafting, and dense grafting regimes. In isolated (mushroom) and loosely tethered bottlebrushes, the linker tension is by a factor of [Formula: see text] smaller than the tension in a tethered star with the same number of arms z. In densely tethered stars, the effect of interchain distance (d) and number of arms (z) on the magnitude of linker tension is given by f ≅ f0z(3/2)(b/d) for stars in a solvent environment and f ≅ f0z(2) (b/d)(2) for dry stars, where b is the Kuhn length and f0 ≅ kBT/b is intrinsic bond tension. These relations are also valid for tethered bottlebrushes with long side chains. However, unlike molecular stars, bottlebrushes demonstrate variation of tension along the backbone f ≅ f0s z(1/2) / d as a function of distance s from the free end of the backbone. In dense brushes [Formula: see text] with z ≅ 1000, the backbone tension increases from f ≅ f0 = 1 pN at the free end of the backbone (s ≅ b) to its maximum f ≅ zf0 ≅ 1 nN at the linker to the substrate (s ≅ zb).

  5. Macromolecule-Assisted de novo Protein Folding

    Science.gov (United States)

    Choi, Seong Il; Son, Ahyun; Lim, Keo-Heun; Jeong, Hotcherl; Seong, Baik L.

    2012-01-01

    In the processes of protein synthesis and folding, newly synthesized polypeptides are tightly connected to the macromolecules, such as ribosomes, lipid bilayers, or cotranslationally folded domains in multidomain proteins, representing a hallmark of de novo protein folding environments in vivo. Such linkage effects on the aggregation of endogenous polypeptides have been largely neglected, although all these macromolecules have been known to effectively and robustly solubilize their linked heterologous proteins in fusion or display technology. Thus, their roles in the aggregation of linked endogenous polypeptides need to be elucidated and incorporated into the mechanisms of de novo protein folding in vivo. In the classic hydrophobic interaction-based stabilizing mechanism underlying the molecular chaperone-assisted protein folding, it has been assumed that the macromolecules connected through a simple linkage without hydrophobic interactions and conformational changes would make no effect on the aggregation of their linked polypeptide chains. However, an increasing line of evidence indicates that the intrinsic properties of soluble macromolecules, especially their surface charges and excluded volume, could be important and universal factors for stabilizing their linked polypeptides against aggregation. Taken together, these macromolecules could act as folding helpers by keeping their linked nascent chains in a folding-competent state. The folding assistance provided by these macromolecules in the linkage context would give new insights into de novo protein folding inside the cell. PMID:22949867

  6. Modeling the Color Image and Video Quality on Liquid Crystal Displays with Backlight Dimming

    DEFF Research Database (Denmark)

    Korhonen, Jari; Mantel, Claire; Burini, Nino

    2013-01-01

    Objective image and video quality metrics focus mostly on the digital representation of the signal. However, the display characteristics are also essential for the overall Quality of Experience (QoE). In this paper, we use a model of a backlight dimming system for Liquid Crystal Display (LCD...

  7. Alignment of synaptic vesicle macromolecules with the macromolecules in active zone material that direct vesicle docking.

    Science.gov (United States)

    Harlow, Mark L; Szule, Joseph A; Xu, Jing; Jung, Jae Hoon; Marshall, Robert M; McMahan, Uel J

    2013-01-01

    Synaptic vesicles dock at active zones on the presynaptic plasma membrane of a neuron's axon terminals as a precondition for fusing with the membrane and releasing their neurotransmitter to mediate synaptic impulse transmission. Typically, docked vesicles are next to aggregates of plasma membrane-bound macromolecules called active zone material (AZM). Electron tomography on tissue sections from fixed and stained axon terminals of active and resting frog neuromuscular junctions has led to the conclusion that undocked vesicles are directed to and held at the docking sites by the successive formation of stable connections between vesicle membrane proteins and proteins in different classes of AZM macromolecules. Using the same nanometer scale 3D imaging technology on appropriately stained frog neuromuscular junctions, we found that ∼10% of a vesicle's luminal volume is occupied by a radial assembly of elongate macromolecules attached by narrow projections, nubs, to the vesicle membrane at ∼25 sites. The assembly's chiral, bilateral shape is nearly the same vesicle to vesicle, and nubs, at their sites of connection to the vesicle membrane, are linked to macromolecules that span the membrane. For docked vesicles, the orientation of the assembly's shape relative to the AZM and the presynaptic membrane is the same vesicle to vesicle, whereas for undocked vesicles it is not. The connection sites of most nubs on the membrane of docked vesicles are paired with the connection sites of the different classes of AZM macromolecules that regulate docking, and the membrane spanning macromolecules linked to these nubs are also attached to the AZM macromolecules. We conclude that the luminal assembly of macromolecules anchors in a particular arrangement vesicle membrane macromolecules, which contain the proteins that connect the vesicles to AZM macromolecules during docking. Undocked vesicles must move in a way that aligns this arrangement with the AZM macromolecules for docking

  8. Preparation of high-quality poly-Si films by a solid phase crystallizing method

    CERN Document Server

    Yao Ruo He

    2002-01-01

    A solid phase crystallizing method has been developed to grow a Si crystal at temperatures as low as 550 degree C. Using this method, a high-quality thin-film polycrystalline silicon (Poly-Si) was obtained. The largest grain size, examined with X-ray diffraction spectroscopy and scanning electron microscopy images of recrystallized samples, is approximately 1 mu m for substrate temperature at 300 degree C and annealed at 550 degree C for 3 hours

  9. Quality assessment of layer-structured semiconductor single crystals by nuclear quadruple resonance method

    Science.gov (United States)

    Samila, Andriy; Khandozhko, Alexander; Lastivka, Galina; Politansky, Leonid; Khandozhko, Victor

    2015-11-01

    A method for quality assessment of layer-structured semiconductor single crystals (InSe, GaSe, GaS) grown in evacuated ampoules by the Bridgman technique is proposed. For this purpose, nuclear quadruple resonance method with a consecutive scanning of the entire sample volume and evaluation of crystal perfection by the resulting spectra is used. Effective interaction between high-frequency field and crystal and, accordingly, restriction of scanning area of sample under study is provided with the use of a two-way saddle-shaped coil for a nuclear quadruple resonance spectrometer.

  10. Diffusion of Au in ZnSe and its dependence on crystal quality

    Science.gov (United States)

    Slotte, J.; Salonen, R.; Ahlgren, T.; Rauhala, E.; Keinonen, J.; Räisänen, J.; Uusimaa, P.; Salokatve, A.; Pessa, M.; Laakso, A.

    1999-01-01

    Diffusion of gold in zinc selenide has been studied by using a 12C and 4He ion backscattering technique. The samples were thin films grown by molecular beam epitaxy on bulk GaAs (100) substrates and on GaAs (100) epitaxial layers followed by evaporation of gold and annealing in the temperature range 400-800 °C. The surface properties of the samples were studied with scanning electron microscopy and atomic force microscopy. The crystal quality of the samples was studied with 4He ion channeling. The gold diffusion was found to depend significantly on the crystal quality of the ZnSe. An empirical model for calculating the diffusion coefficient for different crystal quality ZnSe is presented.

  11. Molecular Imprinting of Macromolecules for Sensor Applications.

    Science.gov (United States)

    Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

    2017-04-19

    Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.

  12. Recent Patents in Pulmonary Delivery of Macromolecules.

    Science.gov (United States)

    Ray, Animikh; Mandal, Abhirup; Mitra, Ashim K

    2015-01-01

    Pulmonary delivery is a non-invasive form of delivery that holds tremendous therapeutic promise for topical and systemic administration of several macromolecules. Oral administration of macromolecules has several limitations such as low bioavailability, degradation of drug before reaching circulation and insufficient absorption across intestinal membrane. Administration of macromolecules such as proteins, peptides and nucleic acids via inhalation offers great potential due to the avoidance of first pass metabolism, higher surface area and rapid clinical response. However, delivery of reproducible, uniform and safe doses of inhaled particles remains a major challenge for clinical translation. Recent advances in the fields of biotechnology and particle engineering led to progress in novel pulmonary drug delivery systems. Moreover, significant developments in carriers and delivery devices prevent denaturation of macromolecules and control their release within the lungs. This article reviews the advances in pulmonary drug delivery systems by focusing on the recent patents in delivery of macromolecules. Furthermore, recent patents in gene delivery to the lungs have also been discussed. List of patents included in this review is comprehensive in terms of pulmonary delivery of therapeutics. It includes inventions related to proteins and peptides, DNA therapeutics, siRNA and other genetic materials with therapeutic applications. The diseases targeted by these therapeutic molecules are varied including but not limited to different forms of cancer, respiratory diseases etc.

  13. Macromolecular crowding: Macromolecules friend or foe.

    Science.gov (United States)

    Mittal, Shruti; Chowhan, Rimpy Kaur; Singh, Laishram Rajendrakumar

    2015-09-01

    Cellular interior is known to be densely crowded due to the presence of soluble and insoluble macromolecules, which altogether occupy ~40% of the total cellular volume. This results in altered biological properties of macromolecules. Macromolecular crowding is observed to have both positive and negative effects on protein folding, structure, stability and function. Significant data has been accumulated so far on both the aspects. However, most of the review articles so far have focused on the positive aspect of macromolecular crowding and not much attention has been paid on the deleterious aspect of crowding on macromolecules. In order to have a complete knowledge of the effect of macromolecular crowding on proteins and enzymes, it is important to look into both the aspects of crowding to determine its precise role under physiological conditions. To fill the gap in the understanding of the effect of macromolecular crowding on proteins and enzymes, this review article focuses on the deleterious influence of crowding on macromolecules. Macromolecular crowding is not always good but also has several deleterious effects on various macromolecular properties. Taken together, the properties of biological macromolecules in vivo appears to be finely regulated by the nature and level of the intracellular crowdedness in order to perform their biological functions appropriately. The information provided here gives an understanding of the role played by the nature and level of cellular crowdedness in intensifying and/or alleviating the burden of various proteopathies. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. General Differential Contact Identities for Macromolecules.

    Science.gov (United States)

    Landy, Jonathan; Pincus, P A; Jho, YongSeok

    2015-10-16

    We discuss general Maxwell identities relating a macromolecule's charge, the forces acting at its surface, and the osmotic pressure of the solution in which it sits. The identities are closely related to the contact value relations that hold for certain special geometries, but are more general. In particular, the Maxwell identities can be applied to any macromolecule geometry, and they hold both within and outside of mean-field theory. Examples illustrate that combining the identities with approximate treatments of screening can often return simple, accurate osmotic pressure estimates.

  15. Large-area high-quality 2D ultrathin Mo2C superconducting crystals

    Science.gov (United States)

    Xu, Chuan; Wang, Libin; Liu, Zhibo; Chen, Long; Guo, Jingkun; Kang, Ning; Ma, Xiu-Liang; Cheng, Hui-Ming; Ren, Wencai

    2015-11-01

    Transition metal carbides (TMCs) are a large family of materials with many intriguing properties and applications, and high-quality 2D TMCs are essential for investigating new physics and properties in the 2D limit. However, the 2D TMCs obtained so far are chemically functionalized, defective nanosheets having maximum lateral dimensions of ~10 μm. Here we report the fabrication of large-area high-quality 2D ultrathin α-Mo2C crystals by chemical vapour deposition (CVD). The crystals are a few nanometres thick, over 100 μm in size, and very stable under ambient conditions. They show 2D characteristics of superconducting transitions that are consistent with Berezinskii-Kosterlitz-Thouless behaviour and show strong anisotropy with magnetic field orientation; moreover, the superconductivity is also strongly dependent on the crystal thickness. Our versatile CVD process allows the fabrication of other high-quality 2D TMC crystals, such as ultrathin WC and TaC crystals, which further expand the large family of 2D materials.

  16. Fabricating centimeter-scale high quality factor two-dimensional periodic photonic crystal slabs.

    Science.gov (United States)

    Lee, Jeongwon; Zhen, Bo; Chua, Song-Liang; Shapira, Ofer; Soljačić, Marin

    2014-02-10

    We present a fabrication route for centimeter-scale two-dimensional defect-free photonic crystal slabs with quality factors bigger than 10,000 in the visible, together with a unique way to quantify their quality factors. We fabricate Si(3)N(4) photonic crystal slabs, and perform an angle-resolved reflection measurement. This measurement data is used to retrieve the quality factors of the slabs by fitting it to a model based on temporal coupled-mode theory. The macroscopic nature of the structure and the high quality factors of their resonances could open up new opportunities for realizing efficient macroscale optoelectronic devices such as sensors, lasers, and energy harvesting systems.

  17. Growth of Large High-Quality Type-Ⅱ a Diamond Crystals

    Institute of Scientific and Technical Information of China (English)

    WANG Xian-Cheng; MA Hong-An; ZANG Chuan-Yi; TIAN Yu; LI Shang-Sheng; JIA Xiao-Peng

    2005-01-01

    @@ Large high-quality type-Ⅱ a diamond crystals in size of about 4.0mm have been grown under the condition of 5.5 GPa and 1200-1300 ℃ by using the temperature gradient method in a domestic cubic anvil high-pressure apparatus. The Fe55Co16Ni25 alloy (KOV) is used as the solvent metal, and Ti with the content 1.5wt.% of the solvent metal is selected as the nitrogen getter to reduce the impurity of nitrogen in the diamond crystal.To avoid the impurities and cave in the crystal, the growth rate of the initial stage of the growing process is controlled within 0.45mg/h and the ring carbon source of the size φ8mm-φ6mm×3 mm is used to gnow large diamond crystals.

  18. Rapid growth of a large-scale(600 mm aperture) KDP crystal and its optical quality

    Institute of Scientific and Technical Information of China (English)

    Guohui; Li; Guozong; Zheng; Yingkun; Qi; Peixiu; Yin; En; Tang; Fei; Li; Jing; Xu; Taiming; Lei; Xiuqin; Lin; Min; Zhang; Junye; Lu; Jinbo; Ma; Youping; He; Yuangen; Yao

    2014-01-01

    Potassium dihydrogen phosphate(KDP) single crystals are the only nonlinear crystals currently used for electro-optic switches and frequency converters in inertial confinement fusion research, due to their large dimension and exclusive physical properties. Based on the traditional solution-growth process, large bulk KDP crystals, usually with sizes up to600 × 600 mm2 so as to make a frequency doubler for the facility requirement loading highly flux of power laser, can be grown in standard Holden-type crystallizers, without spontaneous nucleation and visible defects, one to two orders of magnitude faster than by conventional methods. Pure water and KDP raw material with a few ion impurities such as Fe,Cr, and Al(less than 0.1 ppm) were used. The rapid-growth method includes extreme conditions such as temperature range from 60 to 35℃ , overcooling up to 5℃ , growth rates exceeding 10 mm/day, and crystal size up to 600 mm. The optical parameters of KDP crystals were determined. The optical properties of crystals determined indicate that they are of favorable quality for application in the facility.

  19. Evaluation of the Quality of Sapphire Using X-Ray Rocking Curves and Double-Crystal X-Ray Topography

    Science.gov (United States)

    1994-05-01

    hard, high-strength, chemically resistant optical windows; and sub- srates for the growth of epitaxial films. The quality of a sapphire crystal can... crystal diffractometer. Single- crystal sapphire may be grown by a variety of different methods, of which the more common are Verneuil (flame fusion...Linear features (L), which may represent slight variations in lattice parameter along the crystal growth front, or dislocation networks, ad small

  20. The Place of Macromolecules in Freshman Chemistry

    Science.gov (United States)

    Wunderlich, Bernhard

    1973-01-01

    Discusses the inclusion of knowledge on macromolecules into a freshman chemistry course which emphasizes topics in organic chemistry, polymer science and biochemistry, atoms, chemical thermodynamics, and inorganic chemistry. Indicates that the program is the only way to keep chemistry education up to date. (CC)

  1. Macromolecule diffusion and confinement in prokaryotic cells

    NARCIS (Netherlands)

    Mika, Jacek T.; Poolman, Bert

    We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the mobility and thus the diffusion coefficients (D) of molecules, which is not trivial in small cells. The

  2. Macromolecule diffusion and confinement in prokaryotic cells

    NARCIS (Netherlands)

    Mika, Jacek T.; Poolman, Bert

    2011-01-01

    We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the mobility and thus the diffusion coefficients (D) of molecules, which is not trivial in small cells. The

  3. Macromolecule diffusion and confinement in prokaryotic cells

    NARCIS (Netherlands)

    Mika, Jacek T.; Poolman, Bert

    2011-01-01

    We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the mobility and thus the diffusion coefficients (D) of molecules, which is not trivial in small cells. The

  4. Responsive inverse opal hydrogels for the sensing of macromolecules.

    Science.gov (United States)

    Couturier, Jean-Philippe; Sütterlin, Martin; Laschewsky, André; Hettrich, Cornelia; Wischerhoff, Erik

    2015-05-26

    Dual responsive inverse opal hydrogels were designed as autonomous sensor systems for (bio)macromolecules, exploiting the analyte-induced modulation of the opal's structural color. The systems that are based on oligo(ethylene glycol) macromonomers additionally incorporate comonomers with various recognition units. They combine a coil-to-globule collapse transition of the LCST type with sensitivity of the transition temperature toward molecular recognition processes. This enables the specific detection of macromolecular analytes, such as glycopolymers and proteins, by simple optical methods. While the inverse opal structure assists the effective diffusion even of large analytes into the photonic crystal, the stimulus responsiveness gives rise to strong shifts of the optical Bragg peak of more than 100 nm upon analyte binding at a given temperature. The systems' design provides a versatile platform for the development of easy-to-use, fast, and low-cost sensors for pathogens.

  5. Protein Adsorption Behavior of Synthetic Macromolecules Based on Quartz Crystal Macrobaiance%基于QCM-D技术的合成高分子对蛋白的吸附行为

    Institute of Scientific and Technical Information of China (English)

    张奕; 曾戎; 周长忍

    2009-01-01

    The surface topography, hydrophobicity, hydrated process and protein adsorption behavior of poly (lactic acid), polycarbonate and polymethylmethacrylate were investigated with the quartz crystal microbalance (QCM) with dissipation monitoring and atomic force microscopy (AFM) techniques. The result reveals that: with the hydrophobicity of film increased, protein adsorbed amount increases while viscoelastic property of protein layer adsorbed decreases. There are two types of protein adsorbed on the surface: one is reversible, another is irreversible. The reversible part will be resolved into phosphate buffered solution(PBS) after rinsing, however the irreversible part will remain on the films with the changed conformation and more rigid property. Langmuir model is found to fit with the protein adsorption dynamics curves well. The result shows that adsorption rate constant increases with the hydrophobicity of films.%采用AFM(原子力显微镜)和QCM-D(带损耗测量的石英晶体微天平)等技术研究了聚乳酸、聚碳酸酯和聚甲基丙烯酸甲酯三种合成高分子材料经旋转成膜后的袁面形貌、亲疏水性、水合过程及蛋白吸附行为.结果发现,薄膜的疏水性越强,蛋白吸附量越多,蛋白层的粘弹性越小;且吸附在材料表面的蛋白分为可逆吸附和不可逆吸附两部分,可逆部分可被PBS(磷酸盐缓冲溶液)洗脱,而不可逆吸附蛋白由于在疏水力作用下构象发生变化,变得致密无法脱附,粘弹性比发生可逆吸附的蛋白更小.用Langmuir吸附速率方程可较好地拟合薄膜的蛋白吸附动力学曲线,发现薄膜疏水性越强,白蛋白吸附速率越快.

  6. Macromolecules Inquiry: Transformation of a Standard Biochemistry Lab

    Science.gov (United States)

    Unsworth, Elizabeth

    2014-01-01

    Identification of macromolecules in food is a standard introductory high school biology lab. The intent of this article is to describe the conversion of this standard cookbook lab into an inquiry investigation. Instead of verifying the macromolecules found in food, students use their knowledge of the macromolecules in food to determine the…

  7. The use of ionic liquids as crystallization additives allowed to overcome nanodrop scaling up problems: A success case for producing diffraction-quality crystals of a nitrate reductase

    Science.gov (United States)

    Coelho, Catarina; Trincão, José; João Romão, Maria

    2010-02-01

    The native structure of the heterodimeric periplasmic nitrate reductase (NapAB) from Cupriavidus ( C.) necator was solved at 1.5 Å resolution, using one single crystal obtained at the robot facility at the EMBL, Grenoble. The reaction mechanism for this family of proteins was recently revised, based on new crystallographic evidence, and new structural studies are required to clarify this new mechanistic implication. Several nanodrop crystallization trials yielded microcrystals of the C. necator NapAB. However, scale-up attempts systematically failed and did not yield any suitable crystals. Only with the use of ionic liquids (IL) were we able to grow, in a reproducible manner, larger crystals, which diffracted X-rays to 1.7 Å resolution. By using the IL [C 4mim]Cl as a crystallization additive, we achieved reproducibility in obtaining good quality crystals. Although no IL molecules could be identified in the electron density maps, the crystals grown in the presence and absence of IL have large differences in cell constants. This is the first report of the use of IL for a difficult crystallization problem. The procedure now reported can be applied for crystal optimization such as size increase or improvement of fine needles, as well as for scaling-up crystallization conditions from nanolitre to microlitre drop volumes.

  8. Growth and characterization of large, high quality MoSe2 single crystals

    Science.gov (United States)

    Bougouma, Moussa; Batan, Abdelkrim; Guel, Boubié; Segato, Tiriana; Legma, Jean B.; Reniers, Francois; Delplancke-Ogletree, Marie-Paule; Buess-Herman, Claudine; Doneux, Thomas

    2013-01-01

    MoSe2 single crystals were grown by chemical vapor transport using TeCl4 as transport agents in the temperature gradient 1020-980 °C. They were characterized by scanning electron microscopy (SEM), optical microscopy, image analysis coupled with SEM, microanalysis by SEM-EDX, X-ray fluorescence, inductively coupled plasma (ICP), X-ray photoelectron spectroscopy (XPS) and electrical conductivity. The characterizations showed that single crystals are perfectly homogeneous, stoichiometric and have very few defects and clean surfaces with areas in the range of 35-100 mm2. Single crystals grown by TeCl4 showed a high electrical conductivity. Their properties were highly dependent on the quality of the polycrystalline powders used for the growth.

  9. Persistence Length of DNA Macromolecule with Kinks

    CERN Document Server

    Simonov, Kyrylo

    2014-01-01

    The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular macromolecule structure cause significant bending of the double helix, or kinks. In this paper an approach for Kratky-Porod model to calculate persistence length of DNA macromolecule with kinks is developed. The presented approach considers kinks of arbitrary configuration, including two basic types of kinks, type 1 - sharp kink caused by unstacking a single base pair step, and type 2 - intrinsic-induced kink that involves several base pairs. Within developed approach analytical expressions for persistence length, coil size and gyration radius of kinky double helix were obtained.

  10. Behavior of macromolecules in adsorbed layers

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A model for describing the behavior of macromolecules in adsorbed layers is developed by introducing a concept of distribution density of layer thickness U based on stochastic process and probabilistic statistics. The molecular behavior of layers adsorbed on clay particle surfaces is discussed; the random distribution and its statistics of the layer thickness are given by incorporating experimental results with an ionic polyelectrolyte with the molecular weight of 1.08×106 and chain charged density of 0.254.

  11. Quality improvement of CdMnTe:In single crystals by an effective post-growth annealing

    Science.gov (United States)

    Yu, Pengfei; Xu, Yadong; Luan, Lijun; Du, Yuanyuan; Zheng, Jiahong; Li, Hui; Jie, Wanqi

    2016-10-01

    In this paper, an effective annealing method in which CdMnTe:In (CMT:In) single crystals were coated with CMT powders of the same composition was used to improve the crystal quality of CMT:In crystals. The results indicated that the density of Te inclusions decreased as the annealing time increased. The resistivity and IR transmittance of annealed CMT:In crystals were enhanced obviously. The resistivity of 120 h annealed crystal increased even two orders of magnitude. The reduction of full-width at-half-maximum (FWHM) and the increase of the intensity of X-ray rocking curve indicated an improvement of the crystal quality. PL measurements also showed the crystal quality improved after annealing. No characteristic peak of 241Am γ-ray could be observed in the detector fabricated with as-grown crystal. Remarkably, for the detector fabricated with annealed crystals, the peak of 241Am γ-ray appeared. And the energy resolution and μτ value were improved as the annealing time increased. Specially, 120 h annealed CMT:In crystal with 10.11% energy resolution and 1.20×10-3 cm2/V μτ value has the best detector performance.

  12. Magnetotransport Properties in High-Quality Ultrathin Two-Dimensional Superconducting Mo2C Crystals.

    Science.gov (United States)

    Wang, Libin; Xu, Chuan; Liu, Zhibo; Chen, Long; Ma, Xiuliang; Cheng, Hui-Ming; Ren, Wencai; Kang, Ning

    2016-04-26

    Ultrathin transition metal carbides are a class of developing two-dimensional (2D) materials with superconductivity and show great potentials for electrical energy storage and other applications. Here, we report low-temperature magnetotransport measurements on high-quality ultrathin 2D superconducting α-Mo2C crystals synthesized by a chemical vapor deposition method. The magnetoresistance curves exhibit reproducible oscillations at low magnetic fields for temperature far below the superconducting transition temperature of the crystals. We interpret the oscillatory magnetoresistance as a consequence of screening currents circling around the boundary of triangle-shaped terraces found on the surface of ultrathin Mo2C crystals. As the sample thickness decreases, the Mo2C crystals exhibit negative magnetoresistance deep in the superconducting transition regime, which reveals strong phase fluctuations of the superconducting order parameters associated with the superconductor-insulator transition. Our results demonstrate that the ultrathin superconducting Mo2C crystals provide an interesting system for studying rich transport phenomena in a 2D crystalline superconductor with enhanced quantum fluctuations.

  13. Induced growth of high quality ZnO thin films by crystallized amorphous ZnO

    Institute of Scientific and Technical Information of China (English)

    Wang Zhi-Jun; Song Li-Jun; Li Shou-Chun; Lu You-Ming; Tian Yun-Xia; Liu Jia-Yi; Wang Lian-Yuan

    2006-01-01

    This paper reports the induced growth of high quality ZnO thin film by crystallized amorphous ZnO. Firstly amorphous ZnO was prepared by solid-state pyrolytic reaction, then by taking crystallized amorphous ZnO as seeds (buffer layer), ZnO thin films have been grown in diethyene glycol solution of zinc acetate at 80℃. X-ray Diffraction curve indicates that the films were preferentially oriented [001] out-of-plane direction of the ZnO. Atomic force microscopy and scanning electron microscopy were used to evaluate the surface morphology of the ZnO thin film. Photoluminescence spectrum exhibits a strong ultraviolet emission while the visible emission is very weak. The results indicate that high quality ZnO thin film was obtained.

  14. High quality factor nanophotonic resonators in bulk rare-earth doped crystals

    CERN Document Server

    Zhong, Tian; Kindem, Jonathan M; Miyazono, Evan; Faraon, Andrei

    2015-01-01

    Numerous bulk crystalline materials exhibit attractive nonlinear and luminescent properties for classical and quantum optical applications. A chip-scale platform for high quality factor optical nanocavities in these materials will enable new optoelectronic devices and quantum light-matter interfaces. In this article, photonic crystal nanobeam resonators fabricated using focused ion beam milling in bulk insulators, such as rare-earth doped yttrium orthosilicate and yttrium vanadate, are demonstrated. Operation in the visible, near infrared, and telecom wavelengths with quality factors up to 27,000 and optical mode volumes close to one cubic wavelength is measured. These devices enable new nanolasers, on-chip quantum optical memories, single photon sources, and non-linear devices at low photon numbers based on rare-earth ions. The techniques are also applicable to other luminescent centers and crystals.

  15. Beam quality investigation in Nd:YAG crystal fiber amplifier pumped at >110w

    Science.gov (United States)

    Rodin, Aleksej M.; Aleknavicius, Aidas; Michailovas, Andrejus; Dementjev, Aleksandr S.

    2015-02-01

    We present results of beam quality investigation in Nd:YAG crystal fiber amplifier seeded by ns, sub-ns and ps laser pulses counter-propagating to continuous pump of refractive index at zero stresses and zero strains is found for YAG type cubic crystals. Using plane strain approximation the analytical expression for thermal radial and tangential changes of refractive index is found, and the relation between different expressions for so-called photoelastic constants Cr,θ is established. The methods of numerical calculation of rays and Gaussian beam propagation in a graded-index medium of active element are developed. The error in widely used formula for M2 of Gaussian beam with quartic phase aberration is corrected. It is shown that beam quality degradation can be explained by active thermal lens in power amplifier when changes of transverse beam shape or beam width during amplification are taken into account.

  16. Identifiability, reducibility, and adaptability in allosteric macromolecules.

    Science.gov (United States)

    Bohner, Gergő; Venkataraman, Gaurav

    2017-05-01

    The ability of macromolecules to transduce stimulus information at one site into conformational changes at a distant site, termed "allostery," is vital for cellular signaling. Here, we propose a link between the sensitivity of allosteric macromolecules to their underlying biophysical parameters, the interrelationships between these parameters, and macromolecular adaptability. We demonstrate that the parameters of a canonical model of the mSlo large-conductance Ca(2+)-activated K(+) (BK) ion channel are non-identifiable with respect to the equilibrium open probability-voltage relationship, a common functional assay. We construct a reduced model with emergent parameters that are identifiable and expressed as combinations of the original mechanistic parameters. These emergent parameters indicate which coordinated changes in mechanistic parameters can leave assay output unchanged. We predict that these coordinated changes are used by allosteric macromolecules to adapt, and we demonstrate how this prediction can be tested experimentally. We show that these predicted parameter compensations are used in the first reported allosteric phenomena: the Bohr effect, by which hemoglobin adapts to varying pH. © 2017 Bohner and Venkataraman.

  17. Shape transformation of lipid vesicles induced by diffusing macromolecules.

    Science.gov (United States)

    Góźdź, W T

    2011-01-14

    The attachment of macromolecules to the surface of a lipid vesicle may cause its deformations such as budding or creation of cylindrical protrusions. Diffusion of the macromolecules in the membranes may cause its shape transformations. The process of shrinking the protrusions due to diffusion of the macromolecules is investigated. It is assumed that macromolecules modify locally the spontaneous curvature and bending rigidity of the lipid membrane. Both spontaneous curvature and bending rigidities depend on the concentration of membrane components. It has been shown that cylindrical protrusions are created when the macromolecules which induce large spontaneous curvature are accumulated at a piece of the vesicle surface. It has been observed that here the elastic constants influence very little the evolution of the vesicle shape caused by diffusing macromolecules and the most important is the value the spontaneous curvature imposed by the macromolecules.

  18. Crystal quality of two-dimensional gallium telluride and gallium selenide using Raman fingerprint

    Directory of Open Access Journals (Sweden)

    Jannatul Susoma

    2017-01-01

    Full Text Available We have established Raman fingerprint of GaTe and GaSe to investigate their crystal quality. As unencapsulated, they both oxidise in ambient conditions which can be detected in their Raman analysis. X-ray photoelectron spectroscopy (XPS analysis shows a good agreement with Raman analysis. 50-nm-thick Al2O3 encapsulation layer deposited by atomic layer deposition (ALD inhibits degradation in ambient conditions.

  19. Growth of large size lithium niobate single crystals of high quality by tilting-mirror-type floating zone method

    Energy Technology Data Exchange (ETDEWEB)

    Sarker, Abdur Razzaque, E-mail: razzaque_ru2000@yahoo.com [Department of Physics, University of Rajshahi (Bangladesh)

    2016-05-15

    Large size high quality LiNbO{sub 3} single crystals were grown successfully by tilting-mirror-type floating zone (TMFZ) technique. The grown crystals were characterized by X-ray diffraction, etch pits density measurement, Impedance analysis, Vibrating sample magnetometry (VSM) and UV-Visible spectrometry. The effect of mirror tilting during growth on the structural, electrical, optical properties and defect density of the LiNbO{sub 3} crystals were investigated. It was found that the defect density in the crystals reduced for tilting the mirror in the TMFZ method. The chemical analysis revealed that the grown crystals were of high quality with uniform composition. The single crystals grown by TMFZ method contains no low-angle grain boundaries, indicating that they can be used for high efficiency optoelectronic devices. (author)

  20. Development of the Influence of Magnetic Field on Polymer Crystallization%磁场影响高聚物结晶的研究进展

    Institute of Scientific and Technical Information of China (English)

    刘丽; 高翔; 陆王君

    2012-01-01

    The magnetic effects on the biological macromolecules solution crystallization,have been widely studied for many years.The research showed that the magnetic method is a novel way to control the process of solution crystallization of macromolecules and can improve the quality of the single crystal.By contrast,the effects on the bulk crystallization of polymer have been seldom reported in the past years.In this article,the development of the magnetic effects on macromolecules and bulk polymer crystallization has been discussed,including the influence on the crystal morphology,kinetics of crystallization and related theories,etc.%磁场对生物大分子溶液结晶的影响已被广泛研究。研究表明,磁场可以作为调控大分子溶液结晶形貌和晶体结构的新方法。近年,磁场对本体聚合物结晶的影响已备受关注。文中从稳恒磁场对生物大分子和本体聚合物结晶形态、结晶动力学的影响以及相关理论等方面,综述了近年来稳恒磁场作用下,生物大分子溶液结晶与本体结晶的研究现状。

  1. Liquid phase crystallized silicon on glass: Technology, material quality and back contacted heterojunction solar cells

    Science.gov (United States)

    Haschke, Jan; Amkreutz, Daniel; Rech, Bernd

    2016-04-01

    Liquid phase crystallization has emerged as a novel approach to grow large grained polycrystalline silicon films on glass with high electronic quality. In recent years a lot of effort was conducted by different groups to determine and optimize suitable interlayer materials, enhance the crystallographic quality or to improve post crystallization treatments. In this paper, we give an overview on liquid phase crystallization and describe the necessary process steps and discuss their influence on the absorber properties. Available line sources are compared and different interlayer configurations are presented. Furthermore, we present one-dimensional numerical simulations of a rear junction device, considering silicon absorber thicknesses between 1 and 500 µm. We vary the front surface recombination velocity as well as doping density and minority carrier lifetime in the absorber. The simulations suggest that a higher absorber doping density is beneficial for layer thicknesses below 20 µm or when the minority carrier lifetime is short. Finally, we discuss possible routes for device optimization and propose a hybride cell structure to circumvent current limitations in device design.

  2. Fabrication of high-quality three-dimensional photonic crystal heterostructures

    Institute of Scientific and Technical Information of China (English)

    Liu Zheng-Qi; Feng Tian-Hua; Dai Qiao-Feng; Wu Li-Jun; Lan Sheng

    2009-01-01

    Three-dimensional photonic crystal (PC) heterostructures with high quality are fabricated by using a pressure controlled isothermal heating vertical deposition technique. The formed heterostructures have higher quality, such as deeper band gaps and sharper band edges, than the heterostructures reported so far. Such a significant improvement in quality is due to the introduction of a thin TiO2 buffer layer between the two constitutional PCs. It is revealed that the disorder caused by lattice mismatch is successfully removed if the buffer layer is used once. As a result, the formed heterostructures possess the main features in the band gap of constitutional PCs. The crucial role of the thin buffer layer is also verified by numerical simulations based on the finite-difference time-domain technique.

  3. Bonding quality of Yb:Y3Al5O12/Y3Al5O12 composite crystals

    Institute of Scientific and Technical Information of China (English)

    Bourdet; GILBET; J; C; CHANTELOUP

    2008-01-01

    The Yb:Y3Al5O12/Y3Al5O12 (Yb:YAG/YAG) composite crystals were prepared by thermal bonding method with different technological parameters. The bonding in-terface of the composite crystals were observed by optical microscope, scanning electron microscope, and atom force microscope. The light scattering experiments for bonding interface of the composite crystals were measured by the laser and transmission spectra. All experiments show that high-quality Yb:YAG/YAG com-posite crystals without space transition layer and light scattering on the bonding interface can be obtained by thermal bonding method under appropriate technological parameters.

  4. Improvement of the quality factor of single crystal diamond mechanical resonators

    Science.gov (United States)

    Liao, Meiyong; Toda, Masaya; Sang, Liwen; Teraji, Tokuyuki; Imura, Masataka; Koide, Yasuo

    2017-02-01

    Single-crystal diamond (SCD) has the potential to boost microelectromechanical system (MEMS) with unprecedented performance in terms of its intrinsic mechanical, chemical, and electronic properties, especially in the applications under extreme conditions. On the basis of the analysis of the energy dissipation in diamond mechanical resonators, the authors report on the marked improvement of the quality factor of SCD-MEMS resonators. Ion implantation assisted lift-off technique (IAL) is utilized to fabricate the SCD resonators. The quality factor of the resonator fabricated from the ion-damaged SCD layer alone is as low as 100-300 owing to the bulk or surface defects. The growth of homoepitaxial layers on the ion-implanted SCD substrates significantly improves the quality factor by more than 100 times. Cantilevers made of SCD epilayers of different thicknesses are examined. It is found that the quality factor increases with increasing the epilayer thickness. The maximum quality factor of the SCD cantilevers fabricated by the IAL technique reaches 3.9 × 104. A bilayer model is proposed to describe the variation of the quality factor.

  5. Crystal growth of proteins, nucleic acids, and viruses in gels.

    Science.gov (United States)

    Lorber, Bernard; Sauter, Claude; Théobald-Dietrich, Anne; Moreno, Abel; Schellenberger, Pascale; Robert, Marie-Claire; Capelle, Bernard; Sanglier, Sarah; Potier, Noëlle; Giegé, Richard

    2009-11-01

    Medium-sized single crystals with perfect habits and no defect producing intense and well-resolved diffraction patterns are the dream of every protein crystallographer. Crystals of biological macromolecules possessing these characteristics can be prepared within a medium in which mass transport is restricted to diffusion. Chemical gels (like polysiloxane) and physical gels (such as agarose) provide such an environment and are therefore suitable for the crystallisation of biological macromolecules. Instructions for the preparation of each type of gel are given to urge crystal growers to apply diffusive media for enhancing crystallographic quality of their crystals. Examples of quality enhancement achieved with silica and agarose gels are given. Results obtained with other substances forming gel-like media (such as lipidic phases and cellulose derivatives) are presented. Finally, the use of gels in combination with capillary tubes for counter-diffusion experiments is discussed. Methods and techniques implemented with proteins can also be applied to nucleic acids and nucleoprotein assemblies such as viruses.

  6. Growth of high-quality hexagonal ErMnO3 single crystals by the pressurized floating-zone method

    Science.gov (United States)

    Yan, Z.; Meier, D.; Schaab, J.; Ramesh, R.; Samulon, E.; Bourret, E.

    2015-01-01

    Hexagonal manganites are among the most intensively studied multiferroics, exhibit unusual geometrically driven ferroelectricity and magnetoelectric couplings, and form domains and domain walls with intriguing functional properties. In order to study these electronic correlation phenomena and develop a comprehensive understanding about the underlying physics, the availability of high-quality single-crystals is crucial. In particular, different members of the RMnO3 (R=Sc, Y, In, Dy to Lu) family require different growth condition in order to achieve stoichiometric single-phase crystals. Here, we report on the growth of high-quality ErMnO3 single crystals with dimensions of 5 mm in diameter and up to 60 mm in length using the pressurized floating-zone technique. We present Laue diffraction, piezoresponse force microscopy, and conductive atomic force microscopy data, reflecting the quality of our single crystals regarding the structure, as well as electronic properties on the level of domains and domain walls.

  7. Influence of colloidal particle transfer on the quality of self-assembling colloidal photonic crystal under confined condition

    Institute of Scientific and Technical Information of China (English)

    赵永强; 李娟; 刘秋艳; 董文钧; 陈本永; 李超荣

    2015-01-01

    The relationship between colloidal particle transfer and quality of colloidal photonic crystal (CPC) is investigated by comparing colloidal particle self-assembling under the vertical channel (VC) and horizontal channel (HC) conditions. Both the theoretical analyses and the experimental measurements indicate that crystal quality depends on the stability of mass transfer. For the VC, colloidal particle transfer takes place in a stable laminar flow, which is conducive to forming high-quality crystal. In contrast, it happens in an unstable turbulent flow for the HC. Crystals with cracks and uneven surface formed under the HC condition can be seen from the images of field emission scanning electron microscope (SEM) and three-dimensional (3D) laser scanning microscope (LSM), respectively.

  8. Flexibility and Stability of Metal Coordination Macromolecules.

    Science.gov (United States)

    Jiang, Heyan; Geng, Diya; Liu, Dapeng; Lanigan, Nicholas; Wang, Xiaosong

    2017-06-16

    The effect of chain structure on flexibility and stability of macromolecules containing weak P-Fe metal coordination bonds is studied. Migration insertion polymerization (MIP) of FpCX Fp (1) and PR2 CY PR2 (2) (Fp: CpFe(CO)2 ; CX and CY : alkyl spacers; P: phosphine; R: phenyl or isopropyl) generates P(1/2), in which the P-Fe and Fe-P bonds with opposite bonding direction are alternatively arranged in the backbone. On the other hand, P(FpCX P) synthesized from AB-type monomers (FpCX P) has P-Fe bonds arranged in the same direction. P(1/2) is more rigid and stable than P(FpCX P), which is attributed to the chain conformation resulting from the P-Fe bonding direction. In addition, the longer spacers render P(1/2) relatively flexible; the phenyl substituents, as compared with the isopropyl groups, improves the rigidity, thermal, and solution stability of P(1/2). It is therefore possible to incorporate weak metal coordination bonds into macromolecules with improved stability and adjustable flexibility for material processing. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Hybrid Opto-electric Manipulation of Macromolecules

    Science.gov (United States)

    Wereley, Steve

    2013-11-01

    Recently our research group has developed an innovative method for capturing, concentrating, manipulating and sorting populations of micro- and nanometer-scaled entities-particles, cells, macro-molecules, etc. These populations range from individual particles to thousands of particles (Lab-on-a-Chip, 2008; Microfluidics and Nanofluidics, 2008) while the sizes range from microns to nanometers. This novel technique combines features of optical trapping and dielectrophoresis in an innovative, dynamic way using a simple parallel plate electrode configuration. Transparent electrodes comprised of Indium Tin Oxide (ITO) on glass substrates are used to generate an electric field in the fluid while at the same time allowing light into and out of the fluid. Near-IR optical illumination causes subtle localized heating, creating an electric permittivity gradient that in turn drives a microscopic toroidal vortex. The vortex efficiently transports particles to a preferred location, usually the surface of the electrode. Recent advances have extended have allowed us to apply this technique to macromolecules (DNA, proteins) as well as nanoscale particles (quantum dots, nanowires and PSL particles).

  10. Microgravity protein crystal growth; results and hardware development

    Science.gov (United States)

    DeLucas, Lawrence J.; Smith, Graig D.; Carter, Daniel C.; Snyder, Robert S.; McPherson, A.; Koszelak, S.; Bugg, Charles E.

    1991-02-01

    Protein crystal growth experiments have been performed on a series of US shuttle missions. Crystallographic studies of proteins and nucleic acids have played key roles in establishing the structural foundations of molecular biology and biochemistry and for revealing structure/function relationships that are of major importance in understanding how macromolecules operate in biological systems. A number of major advances in the technology involved in determining protein structures have shortened the time span involved in structure determination. The major bottleneck in the widespread application of protein crystallography is the ability to produce high quality crystals that are suitable for a complete structural analysis. Evidence from several investigations indicates that crystals of superior quality can be obtained in a microgravity environment. This paper summarizes results obtained from a series of US shuttle missions and describes new hardware currently being developed for future shuttle missions.

  11. Transmission electron microscopy for the evaluation and optimization of crystal growth

    Energy Technology Data Exchange (ETDEWEB)

    Stevenson, Hilary P.; Lin, Guowu; Barnes, Christopher O.; Sutkeviciute, Ieva; Krzysiak, Troy; Weiss, Simon C.; Reynolds, Shelley; Wu, Ying; Nagarajan, Veeranagu; Makhov, Alexander M.; Lawrence, Robert; Lamm, Emily; Clark, Lisa; Gardella, Timothy J.; Hogue, Brenda G.; Ogata, Craig M.; Ahn, Jinwoo; Gronenborn, Angela M.; Conway, James F.; Vilardaga, Jean-Pierre; Cohen, Aina E.; Calero, Guillermo

    2016-04-26

    The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.

  12. Shear dependent nonlinear vibration in a high quality factor single crystal silicon micromechanical resonator

    Science.gov (United States)

    Zhu, H.; Shan, G. C.; Shek, C. H.; Lee, J. E.-Y.

    2012-07-01

    The frequency response of a single crystal silicon resonator under nonlinear vibration is investigated and related to the shear property of the material. The shear stress-strain relation of bulk silicon is studied using a first-principles approach. By incorporating the calculated shear property into a device-level model, our simulation closely predicts the frequency response of the device obtained by experiments and further captures the nonlinear features. These results indicate that the observed nonlinearity stems from the material's mechanical property. Given the high quality factor (Q) of the device reported here (˜2 × 106), this makes it highly susceptible to such mechanical nonlinear effects.

  13. High-quality single-crystal growth and unique electronic states in cerium and uranium compounds

    Science.gov (United States)

    Onuki, Yoshichika; Settai, Rikio; Sugiyama, Kiyohiro; Inada, Yoshihiko; Takeuchi, Tetsuya; Haga, Yoshinori; Yamamoto, Etsuji; Harima, Hisatomo; Yamagami, Hiroshi

    2007-03-01

    We have grown many kinds of high-quality single crystals of cerium and uranium compounds and studied the Fermi surface properties via the de Haas-van Alphen experiments and energy band calculations. The quasi-two-dimensional electronic states are clarified in some compounds such as USb2, CeCoIn5, UPtGa5 and most likely UIr. In a ferromagnet CeRh3B2, we have found unique electronic states with quasi-one-dimensional character.

  14. Growth of optical-quality anthracene crystals doped with dibenzoterrylene for controlled single photon production

    Energy Technology Data Exchange (ETDEWEB)

    Major, Kyle D., E-mail: kyle.major11@imperial.ac.uk; Lien, Yu-Hung; Polisseni, Claudio; Grandi, Samuele; Kho, Kiang Wei; Clark, Alex S.; Hwang, J.; Hinds, E. A., E-mail: ed.hinds@imperial.ac.uk [Centre for Cold Matter, Department of Physics, Blackett Laboratory, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom)

    2015-08-15

    Dibenzoterrylene (DBT) molecules within a crystalline anthracene matrix show promise as quantum emitters for controlled, single photon production. We present the design and construction of a chamber in which we reproducibly grow doped anthracene crystals of optical quality that are several mm across and a few μm thick. We demonstrate control of the DBT concentration over the range 6–300 parts per trillion and show that these DBT molecules are stable single-photon emitters. We interpret our data with a simple model that provides some information on the vapour pressure of DBT.

  15. Advances in industrial prospective of cellulosic macromolecules enriched banana biofibre resources: A review.

    Science.gov (United States)

    Pappu, Asokan; Patil, Vikas; Jain, Sonal; Mahindrakar, Amit; Haque, Ruhi; Thakur, Vijay Kumar

    2015-08-01

    Biological macromolecules enriched resources are rapidly emerging as sustainable, cost effective and environmental friendly materials for several industrial applications. Among different biological macromolecules enriched resources, banana fibres are one of the unexplored high potential bio-resources. Compared to various natural fibres such as jute, coir, palm etc., the banana fibres exhibits a better tensile strength i.e. 458 MPa with 17.14 GPa tensile modulus. Traditionally used petroleum based synthetic fibres have been proven to be toxic, non-biodegradable and energy intensive for manufacturing. Cellulosic banana fibres are potential engineering materials having considerable scope to be used as an environmental friendly reinforcing element for manufacturing of polymer based green materials. This paper summarizes the world scenario of current production of biological macromolecules rich banana residues and fibres; major user's of banana fibres. The quality and quantity of biological macromolecules especially the cellulose, hemicellulose, lignin, wax, engineering and mechanical properties of banana biofibre resources are reported and discussed. Subsequently, the findings of the recent research on bio resource composites, materials performance and opportunities have been discussed which would be a real challenge for the tomorrow world to enhance the livelihood environmental friendly advancement. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. A liquid crystal display with consistent moving image quality regardless of viewing angles

    Science.gov (United States)

    Kim, Jong-Man; Kim, Seung-Ryul; Kim, Jongbin; Kim, Minkoo; Lee, Seung-Woo

    2014-08-01

    This paper proposes a new overdrive (OD) technology to precisely compensate for the viewing angle dependent characteristics of LCDs. This paper reports that optical response of liquid crystal displays (LCDs) is considerably dependent on viewing angles for the first time. The new OD technology applies different OD look-up tables (LUTs) depending on the viewing angles. In addition, we combine a new OD technology with an eye tracker that is usually adopted for autostereoscopic 3D LCD systems. The application results show that a new OD technology improves the motion image quality perfectly regardless of viewing angles. We expect that our proposed method will definitely enable the LCD products to have consistent motion image quality regardless of viewing angles.

  17. Influence of Dielectric Loss on Quality Factors of Photonic Crystal Microcavity Modes

    Institute of Scientific and Technical Information of China (English)

    XIONG Zhi-Gang; LI Zhi-Yuan; ZHANG Dao-Zhong

    2008-01-01

    We numerically investigate the quMity factors of two-dimensionM (2D) photonic crystal (PC) microcavities using an auxiliary differential equations (ADE) technique in the context of finite-difference time-domain (FDTD)method. The microcavities are formed by point defects in the air hole lattice hexagonedly patterned in ZnO (zinc oxide) matrix. The quality factors of these microcavities are limited primarily by the absorption of the background dielectric. We show that the ratio between the quality factors of microcavities in lossy and lossless background dielectric depends on the overlap between the field of cavity modes and the absorbing background dielectric in addition to the magnitude of absorption. These results will be helpful when designing and optimizing photonie erystal microcavities formed in lossy medium.

  18. A technique for measuring the quality of an elliptically bent pentaerythritol [PET(002)] crystal.

    Science.gov (United States)

    Haugh, M J; Jacoby, K D; Barrios, M A; Thorn, D; Emig, J A; Schneider, M B

    2016-11-01

    We present a technique for determining the X-ray spectral quality from each region of an elliptically curved PET(002) crystal. The investigative technique utilizes the shape of the crystal rocking curve which changes significantly as the radius of curvature changes. This unique quality information enables the spectroscopist to verify where in the spectral range that the spectrometer performance is satisfactory and where there are regions that would show spectral distortion. A collection of rocking curve measurements for elliptically curved PET(002) has been built up in our X-ray laboratory. The multi-lamellar model from the XOP software has been used as a guide and corrections were applied to the model based upon measurements. But, the measurement of RI at small radius of curvature shows an anomalous behavior; the multi-lamellar model fails to show this behavior. The effect of this anomalous RI behavior on an X-ray spectrometer calibration is calculated. It is compared to the multi-lamellar model calculation which is completely inadequate for predicting RI for this range of curvature and spectral energies.

  19. A technique for measuring the quality of an elliptically bent pentaerythritol [PET(002)] crystal

    Science.gov (United States)

    Haugh, M. J.; Jacoby, K. D.; Barrios, M. A.; Thorn, D.; Emig, J. A.; Schneider, M. B.

    2016-11-01

    We present a technique for determining the X-ray spectral quality from each region of an elliptically curved PET(002) crystal. The investigative technique utilizes the shape of the crystal rocking curve which changes significantly as the radius of curvature changes. This unique quality information enables the spectroscopist to verify where in the spectral range that the spectrometer performance is satisfactory and where there are regions that would show spectral distortion. A collection of rocking curve measurements for elliptically curved PET(002) has been built up in our X-ray laboratory. The multi-lamellar model from the XOP software has been used as a guide and corrections were applied to the model based upon measurements. But, the measurement of RI at small radius of curvature shows an anomalous behavior; the multi-lamellar model fails to show this behavior. The effect of this anomalous RI behavior on an X-ray spectrometer calibration is calculated. It is compared to the multi-lamellar model calculation which is completely inadequate for predicting RI for this range of curvature and spectral energies.

  20. Technical and radiological image quality comparison of different liquid crystal displays for radiology

    Directory of Open Access Journals (Sweden)

    Dams FE

    2014-10-01

    Full Text Available Francina EM Dams,2 KY Esther Leung,1 Pieter HM van der Valk,2 Marc CJM Kock,2 Jeroen Bosman,1 Sjoerd P Niehof1 1Medical Physics and Technology, 2Department of Radiology, Albert Schweitzer Hospital, Dordrecht, The Netherlands Background: To inform cost-effective decisions in purchasing new medical liquid crystal displays, we compared the image quality in displays made by three manufacturers. Methods: We recruited 19 radiologists and residents to compare the image quality of four liquid crystal displays, including 3-megapixel Barco®, Eizo®, and NEC® displays and a 6-megapixel Barco display. The evaluators were blinded to the manufacturers' names. Technical assessments were based on acceptance criteria and test patterns proposed by the American Association of Physicists in Medicine. Radiological assessments were performed on images from the American Association of Physicists in Medicine Task Group 18. They included X-ray images of the thorax, knee, and breast, a computed tomographic image of the thorax, and a magnetic resonance image of the brain. Image quality was scored on an analog scale (range 0–10. Statistical analysis was performed with repeated-measures analysis of variance. Results: The Barco 3-megapixel display passed all acceptance criteria. The Eizo and NEC displays passed the acceptance criteria, except for the darkest pixel value in the grayscale display function. The Barco 6-megapixel display failed criteria for the maximum luminance response and the veiling glare. Mean radiological assessment scores were 7.8±1.1 (Barco 3-megapixel, 7.8±1.2 (Eizo, 8.1±1.0 (NEC, and 8.1±1.0 (Barco 6-megapixel. No significant differences were found between displays. Conclusion: According to the tested criteria, all the displays had comparable image quality; however, there was a three-fold difference in price between the most and least expensive displays. Keywords: data display, humans, radiographic image enhancement, user-computer interface

  1. Controlled doping by self-assembled dendrimer-like macromolecules.

    Science.gov (United States)

    Wu, Haigang; Guan, Bin; Sun, Yingri; Zhu, Yiping; Dan, Yaping

    2017-02-01

    Doping via self-assembled macromolecules might offer a solution for developing single atom electronics by precisely placing individual dopants at arbitrary location to meet the requirement for circuit design. Here we synthesize dendrimer-like polyglycerol macromolecules with each carrying one phosphorus atom in the core. The macromolecules are immobilized by the coupling reagent onto silicon surfaces that are pre-modified with a monolayer of undecylenic acid. Nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) are employed to characterize the synthesized macromolecules and the modified silicon surfaces, respectively. After rapid thermal annealing, the phosphorus atoms carried by the macromolecules diffuse into the silicon substrate, forming dopants at a concentration of 10(17) cm(-3). Low-temperature Hall effect measurements reveal that the ionization process is rather complicated. Unlike the widely reported simple ionization of phosphorus dopants, nitrogen and carbon are also involved in the electronic activities in the monolayer doped silicon.

  2. Controlled doping by self-assembled dendrimer-like macromolecules

    Science.gov (United States)

    Wu, Haigang; Guan, Bin; Sun, Yingri; Zhu, Yiping; Dan, Yaping

    2017-02-01

    Doping via self-assembled macromolecules might offer a solution for developing single atom electronics by precisely placing individual dopants at arbitrary location to meet the requirement for circuit design. Here we synthesize dendrimer-like polyglycerol macromolecules with each carrying one phosphorus atom in the core. The macromolecules are immobilized by the coupling reagent onto silicon surfaces that are pre-modified with a monolayer of undecylenic acid. Nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) are employed to characterize the synthesized macromolecules and the modified silicon surfaces, respectively. After rapid thermal annealing, the phosphorus atoms carried by the macromolecules diffuse into the silicon substrate, forming dopants at a concentration of 1017 cm‑3. Low-temperature Hall effect measurements reveal that the ionization process is rather complicated. Unlike the widely reported simple ionization of phosphorus dopants, nitrogen and carbon are also involved in the electronic activities in the monolayer doped silicon.

  3. The crystalline quality distribution in CdZnTe single crystal correlated to the interface shape during growth

    Energy Technology Data Exchange (ETDEWEB)

    Azoulay, M.; Rotter, S.; Gafni, G. (Soreq Nuclear Research Center, Yavne (Israel)); Roth, M. (School of Applied Science and Technology, Hebrew Univ. of Jerusalem (Israel))

    1992-02-01

    Crystalline quality of CdZnTe single crystals grown by the vertical gradient freeze (VGF) method has been evaluated using the double crystal rocking curve (DCRC) analysis and etch pits density (EPD) measurements. The full width at half maximum (HWHM) values of the DCRCs vary within 40% while the EPD values range from 2 to 8 x 10{sup 4} cm{sup -2} along the crystal growth axis. Best results are obtained for the central part of the crystals, where the growth interface exhibits a nearly planar shape. The results obtained have been used for practical implications with regard to the use of CdZnTe crystals as a substrate material for HgCdTe thin films growth. (orig.).

  4. Quality control on pre-serial Bridgman production of PbWO{sub 4} scintillating crystals by means of photoelasticity

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldi, D., E-mail: d.rinaldi@univpm.i [Dipartimento di Fisica e Ingegneria dei Materiali e del Territorio, Universita Politecnica delle Marche, via Brecce Bianche, 60131 Ancona (Italy); INFN section of Perugia (Italy); Ciriaco, A. [Dipartimento di Fisica e Ingegneria dei Materiali e del Territorio, Universita' Politecnica delle Marche, via Brecce Bianche, 60131 Ancona (Italy); Lebeau, M. [CERN PH department, 1211 Geneva 23 (Switzerland); Paone, N. [Dipartimento di Meccanica, Universita' Politecnica delle Marche, via Brecce Bianche, 60131 Ancona (Italy)

    2010-04-11

    Residual internal stresses in PbWO{sub 4} (PWO) scintillating crystals grown by Bridgman method have been systematically studied. Residual stresses induced during growth play an important role in production yield. Cracking probability during mechanical processing as well as stable mechanical properties in finished crystal are closely related to internal stress levels. A regular production of good-quality crystals requires a fast and easy feed-back on growth parameters. Samples from a pre-serial production were analyzed in order to give the producer a quality feed-back for process optimization. By means of photoelasticity, we measured residual stress distribution in several sections along the growth axis and for typical positions in every section. The stress analysis revealed defects occurring during the crystallization process, attributed to dislocations, lattice disorientation and poly-crystallinity. This work had been prompted by the need for quality monitoring of a pre-serial production of PWO for the CMS experiment at CERN's LHC. Mapping stress levels inside the ingot volume and proposing a synthetic parameter to be used as a quality indicator, the resulting analysis should contribute to parameter optimization and improve the growth performance. The proposed method may be useful in conventional crystal production.

  5. Growth of high quality mercurous halide single crystals by physical vapor transport method for AOM and radiation detection applications

    Science.gov (United States)

    Amarasinghe, Priyanthi M.; Kim, Joo-Soo; Chen, Henry; Trivedi, Sudhir; Qadri, Syed B.; Soos, Jolanta; Diestler, Mark; Zhang, Dajie; Gupta, Neelam; Jensen, Janet L.; Jensen, James

    2016-09-01

    Single crystals of mercurous halide were grown by physical vapor transport method (PVT). The orientation and the crystalline quality of the grown crystals were determined using high resolution x-ray diffraction (HRXRD) technique. The full width at half maximum (FWHM) of the grown mercurous bromide crystals was measured to be 0.13 degrees for (004) reflection, which is the best that has been achieved so far for PVT grown mercurous halide single crystals. The extended defects of the crystals were also analyzed using high resolution x-ray diffraction topography. Preliminary studies were carried out to evaluate the performance of the crystals on acousto-optic modulator (AOM) and gamma-ray detector applications. The results indicate the grown mercurous halide crystals are excellent materials for acousto-optic modulator device fabrication. The diffraction efficiencies of the fabricated AOM device with 1152 and 1523 nm wavelength lasers polarizing parallel to the acoustic wave were found to be 35% and 28%, respectively. The results also indicate the grown crystals are a promising material for gamma-ray detector application with a very high energy resolution of 1.86% FWHM.

  6. Crystal Quality and Light Output Power of GaN-Based LEDs Grown on Concave Patterned Sapphire Substrate.

    Science.gov (United States)

    Wu, YewChung Sermon; Isabel, A Panimaya Selvi; Zheng, Jian-Hsuan; Lin, Bo-Wen; Li, Jhen-Hong; Lin, Chia-Chen

    2015-04-22

    The crystal quality and light output power of GaN-based light-emitting diodes (LEDs) grown on concave patterned sapphire substrate (CPSS) were investigated. It was found that the crystal quality of GaN-based LEDs grown on CPSS improved with the decrease of the pattern space (percentage of c-plane). However, when the pattern space decreased to 0.41 μm (S0.41-GaN), the GaN crystallinity dropped. On the other hand, the light output power of GaN-based LEDs was increased with the decrease of the pattern space due to the change of the light extraction efficiency.

  7. Design of slotted high quality factor photonic-crystal nanocavities embedded in electro-optic polymers

    Science.gov (United States)

    Nakadai, Masahiro; Konoike, Ryotaro; Tanaka, Yoshinori; Asano, Takashi; Noda, Susumu

    2017-09-01

    We improve design quality factors of slotted photonic crystal nanocavities embedded in electro-optic polymers (EOPs), which enables control of resonant wavelengths without the use of light-absorbing free carriers. We form nanocavities by modifying single- and double-slotted line-defect waveguides with lattice-constant modulations analytically determined based on dispersions of the waveguides. A double-slotted nanocavity achieves a fourfold increase in Q factor (36 million) compared to a single-slotted nanocavity with similar modulation of lattice constants. Both structures can realize large concentration of light in the EOP region (50%), and resonant wavelength modulations of ∼0.01% are expected with applied voltage of 2 V.

  8. High quality factor two dimensional GaN photonic crystal cavity membranes grown on silicon substrate

    Science.gov (United States)

    Vico Triviño, N.; Rossbach, G.; Dharanipathy, U.; Levrat, J.; Castiglia, A.; Carlin, J.-F.; Atlasov, K. A.; Butté, R.; Houdré, R.; Grandjean, N.

    2012-02-01

    We report on the achievement of freestanding GaN photonic crystal L7 nanocavities with embedded InGaN/GaN quantum wells grown by metal organic vapor phase epitaxy on Si (111). GaN was patterned by e-beam lithography, using a SiO2 layer as a hard mask, and usual dry etching techniques. The membrane was released by underetching the Si (111) substrate. Micro-photoluminescence measurements performed at low temperature exhibit a quality factor as high as 5200 at ˜420 nm, a value suitable to expand cavity quantum electrodynamics to the near UV and the visible range and to develop nanophotonic platforms for biofluorescence spectroscopy.

  9. Second Harmonic Light Scattering from Macromolecules: Collagen.

    Science.gov (United States)

    Roth, Shmuel

    In this work we present the theory and practice of optical second harmonic generation (SHG) as applied to rat-tail tendon collagen. Our work is the first quantitative application of SHG to biological systems. The angular dependence of SHG is found to display a sharp, intense, forward peak superimposed on a broad background. The sharp peak is shown to imply long-range polar order, while the broad background corresponds to that predicted for the random "up"/"down" array of collagen fibrils seen with the electron microscope. The dependence of fibril diameter distribution on age and state of hydration is measured. Our experiments also reveal information concerning the structure of the fibrils and their arrangement in the tendon. The degree of polar order, the coherence length of tendon for harmonic generation and the absolute magnitude of the nonlinear susceptibility of the collagen fibril are also determined. The biological significance of these findings and the many advantages of SHG for the structural study of biological macromolecules and tissues are discussed.

  10. Encoding of Primary Structures of Biological Macromolecules Within a Data Mining Perspective

    Institute of Scientific and Technical Information of China (English)

    Mondher Maddouri; Mourad Elloumi

    2004-01-01

    An encoding method has a direct effect on the quality and the representation of the discovered knowledge in data mining systems. Biological macromolecules are encoded by strings of characters, called primary structures. Knowing that data mining systems usually use relational tables to encode data, we have then to reencode these strings and transform them into relational tables. In this paper, we do a comparative study of the existing static encoding methods, that are based on the Biologist know-how, and our new dynamic encoding one,that is based on the construction of Discriminant and Minimal Substrings (DMS). Different classification methods are used to do this study. The experimental results show that our dynamic encoding method is more efficient than the static ones, to encode biological macromolecules within a data mining perspective.

  11. The CMS Electromagnetic Calorimeter: Results on Crystal Measurements, Quality Control and Data Management in the Rome Regional Center

    CERN Document Server

    Costantini, S

    2004-01-01

    The barrel of the CMS electromagnetic calorimeter is currently under construction and will contain 61200 PbWO4 crystals. Half of them are being fully characterized for dimensions, optical properties and light yield in the INFN-ENEA Regional Center near Rome. We describe the setup of an automatic quality control system for the crystal measurements and the present results on their qualification, as well as the REDACLE project, which has been developed to control and ease the production process. As it will not be possible to precalibrate the whole calorimeter,the crystal measurements and quality checks performed at the Regional Center will be crucial to provide a basis for fast in-situ calibration with particles. REDACLE is at the same time a fast database and a data management system, where the database and the workflow structures are decoupled, in order to obtain the best flexibility.

  12. Growth of High Quality Semi-Insulating InP Single Crystal by Suppression of Compensation Defects

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Deep level defects in as-grown and annealed SI-InP samples were investigated by thermally stimulated current spectroscopy. Correlations between electrical property, compensation ratio, thermal stability and deep defect concentration in SI-InP were revealed. An optimized crystal growth condition for high quality SI-InP was demonstrated based on the experimental results.

  13. Sandwich complex-containing macromolecules: property tunability through versatile synthesis.

    Science.gov (United States)

    Abd-El-Aziz, Alaa S; Agatemor, Christian; Etkin, Nola

    2014-03-01

    Sandwich complexes feature unique properties as the physical and electronic properties of a hydrocarbon ligand or its derivative are integrated into the physical, electronic, magnetic, and optical properties of a metal. Incorporation of these complexes into macromolecules results in intriguing physical, electrical, and optical properties that were hitherto unknown in organic-based macromolecules. These properties are tunable through well-designed synthetic strategies. This review surveys many of the synthetic approaches that have resulted in tuning the properties of sandwich complex-containing macromolecules. While the past two decades have seen an ever-growing number of research publications in this field, gaps remain to be filled. Thus, we expect this review to stimulate research interest towards bridging these gaps, which include the insolubility of some of these macromolecules as well as expanding the scope of the sandwich complexes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Ligand Binding to Macromolecules: Allosteric and Sequential Models of Cooperativity.

    Science.gov (United States)

    Hess, V. L.; Szabo, Attila

    1979-01-01

    A simple model is described for the binding of ligands to macromolecules. The model is applied to the cooperative binding by hemoglobin and aspartate transcarbamylase. The sequential and allosteric models of cooperative binding are considered. (BB)

  15. Effect of anionic macromolecules on intestinal permeability of furosemide.

    Science.gov (United States)

    Valizadeh, Hadi; Fahimfar, Hadi; Ghanbarzadeh, Saeed; Islambulchilar, Ziba; Zakeri-Milani, Parvin

    2015-02-01

    Furosemide is an anionic molecule and has very low absorption in gastro intestinal tract. The aim of this study was to investigate the effect of anionic macromolecules on the intestinal permeability of Furosemide. The intestinal permeability of Furosemide was determined using single-pass intestinal perfusion technique in rats. Briefly a jejunal segment of ∼10 cm was isolated and cannulated in both ends for inlet and outlet solution. The perfusate was collected every 10 min and samples were analyzed using the RP-HPLC method. Test samples containing furosemide and two anionic macromolecules, sodium carboxy methyl cellulose and sodium alginate, at different concentrations were used. The obtained data showed that existence of Sodium carboxy methyl cellulose significantly increased the Peff values in all three investigated concentrations (p macromolecules at specific concentrations could alter the permeability of anionic drugs across the biological membranes. Donnan phenomenon and chelating property of macromolecules could be attributed to the observed effect.

  16. A general method to study equilibrium partitioning of macromolecules

    DEFF Research Database (Denmark)

    The distribution of macromolecules between a confined microscopic solution and a macroscopic bulk solution plays an important role in understanding separation processes such as Size Exclusion Chromatography (SEC). In this study, we have developed an efficient computational algorithm for obtaining...

  17. Improving Protein Crystal Quality by the Without-Oil Microbatch Method: Crystallization and Preliminary X-ray Diffraction Analysis of Glutathione Synthetase from Pseudoalteromonas haloplanktis

    Directory of Open Access Journals (Sweden)

    Antonella Albino

    2011-09-01

    Full Text Available Glutathione synthetases catalyze the ATP-dependent synthesis of glutathione from L-γ-glutamyl-L-cysteine and glycine. Although these enzymes have been sequenced and characterized from a variety of biological sources, their exact catalytic mechanism is not fully understood and nothing is known about their adaptation at extremophilic environments. Glutathione synthetase from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhGshB has been expressed, purified and successfully crystallized. An overall improvement of the crystal quality has been obtained by adapting the crystal growth conditions found with vapor diffusion experiments to the without-oil microbatch method. The best crystals of PhGshB diffract to 2.34 Å resolution and belong to space group P212121, with unit-cell parameters a = 83.28 Å, b = 119.88 Å, c = 159.82 Å. Refinement of the model, obtained using phases derived from the structure of the same enzyme from Escherichia coli by molecular replacement, is in progress. The structural determination will provide the first structural characterization of a psychrophilic glutathione synthetase reported to date.

  18. Electrically assisted delivery of macromolecules into the corneal epithelium

    OpenAIRE

    HAO, JINSONG; Li, S. Kevin; Liu, Chia-Yang; Kao, Winston W. Y.

    2009-01-01

    Electrically assisted delivery is noninvasive and has been investigated in a number of ocular drug delivery studies. The objectives of this study were to examine the feasibility of electrically assisted delivery of macromolecules such as small interfering RNA (siRNA) into the corneal epithelium, to optimize the iontophoresis and electroporation methods, and to study the mechanisms of corneal iontophoresis for macromolecules. Anodal and cathodal iontophoresis, electroporation and their combina...

  19. Submillimeter wave spectroscopy of biological macromolecules

    Science.gov (United States)

    Globus, Tatiana

    2005-03-01

    The recently emergence of submillimeter-wave or terahertz (THz) spectroscopy of biological molecules has demonstrated the capability to detect low-frequency internal molecular vibrations involving the weakest hydrogen bonds of the DNA base pairs and/or non-bonded interactions. These multiple bonds, although having only ˜ 5% of the strength of covalent bonds, stabilize the structure of bio-polymers, by holding the two strands of the DNA double helix together, or polypeptides together in different secondary structure conformations. There will be a review of THz-frequency transmission (absorption) results for biological materials obtained from Fourier Transform Infrared (FTIR) spectroscopy during the last few years^1,2. Multiple resonances, due to low frequency vibrational modes within biological macromolecules, have been unambiguously demonstrated in qualitative agreement with theoretical prediction, thereby confirming the fundamental physical nature of observed resonance features. The discovery of resonance character of interaction between THz radiation and biological materials opens many possible applications for THz spectroscopy technique in biological sensing and biomedicine using multiple resonances as distinctive spectral fingerprints. However, many issues still require investigation. Kinetics of interactions with radiation at THz has not been studied and vibrational lifetimes have not been measured directly as a function of frequency. The strength of resonant modes of bio-molecules in aqueous environment and strong dependence of spectra on molecular orientation need explanation. Vibrational modes have not been assigned to specific motions within molecules. THz spectroscopy of bio-polymers makes it only in first steps. 1. T. Globus, D. Woolard, M. Bykhovskaia, B. Gelmont, L. Werbos, A. Samuels. International Journal of High Speed Electronics and Systems (IJHSES), 13, No. 4, 903-936 (2003). 2. T. Globus, T. Khromova, D. Woolard and B. Gelmont. Proceedings of

  20. Electrically assisted delivery of macromolecules into the corneal epithelium.

    Science.gov (United States)

    Hao, Jinsong; Li, S Kevin; Liu, Chia-Yang; Kao, Winston W Y

    2009-12-01

    Electrically assisted delivery is noninvasive and has been investigated in a number of ocular drug delivery studies. The objectives of this study were to examine the feasibility of electrically assisted delivery of macromolecules such as small interfering RNA (siRNA) into the corneal epithelium, to optimize the iontophoresis and electroporation methods, and to study the mechanisms of corneal iontophoresis for macromolecules. Anodal and cathodal iontophoresis, electroporation and their combinations were the methods examined with mice in vivo. Cyanine 3 (Cy3)-labeled glyceraldehyde-3-phosphate dehydrogenase (GAPDH) siRNA and fluorescein isothiocyanate (FITC)-labeled dextran of different molecular weights (4-70 kDa) were the macromolecules studied. Microscopy and histology after cryostat sectioning were used to analyze and compare the delivery of the macromolecules to the cornea. Iontophoresis was effective in delivering siRNA and dextran up to 70 kDa into the cornea. The electroporation method studied was less effective than that of iontophoresis. Although both iontophoresis and electroporation alone can deliver the macromolecules into the cornea, these methods alone were not as effective as the combination of iontophoresis and electroporation (iontophoresis followed by electroporation). The significant enhancement of dextran delivery in anodal iontophoresis suggests that electroosmosis can be a significant flux-enhancing mechanism during corneal iontophoresis. These results illustrate the feasibility of electrically assisted delivery of macromolecules such as siRNA into the cornea.

  1. Characterization of grown-in dislocations in high-quality glucose isomerase crystals by synchrotron monochromatic-beam X-ray topography

    Science.gov (United States)

    Suzuki, Ryo; Koizumi, Haruhiko; Kojima, Kenichi; Fukuyama, Seijiro; Arai, Yasutomo; Tsukamoto, Katsuo; Suzuki, Yoshihisa; Tachibana, Masaru

    2017-06-01

    High quality glucose isomerase (GI) single crystals are grown by using chemical cross-linked seed crystals. The crystal structure is an orthorhombic system in which the molecular arrangement is close to a body-centered cubic (bcc) one. The crystal defects, especially dislocations, in GI crystals are experimentally characterized by synchrotron monochromatic-beam X-ray topography. Two straight dislocations are clearly observed, which originate from the interface between the cross-linked seed crystal and the grown crystal. From the invisibility criterion of the dislocation images, it is experimentally identified that they are close to be of pure edge character with the Burgers vector of [1 1 bar 1] which is typical one in bcc metal crystals. Moreover, bead-like contrasts along the dislocation images and the equal-thickness fringes, related to Pendellösung fringes, at crystal edges are clearly observed, which have never been observed in other protein crystals so far. These contrasts can attributed to the dynamical diffraction effect which has been often observed in high-quality crystals such as Si. Thus it seems that the perfection of GI crystals shown in this paper is extremely high compared with other protein crystals reported so far.

  2. Gallium nitride L3 photonic crystal cavities with an average quality factor of 16 900 in the near infrared

    Energy Technology Data Exchange (ETDEWEB)

    Vico Triviño, Noelia; Carlin, Jean-François; Butté, Raphaël; Grandjean, Nicolas [Institute of Condensed Matter Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Minkov, Momchil, E-mail: momchil.minkov@epfl.ch; Savona, Vincenzo [Laboratory of Theoretical Physics of Nanosystems, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Urbinati, Giulia; Galli, Matteo [Dipartimento di Fisica, Università di Pavia, via Bassi 6, 27100 Pavia (Italy)

    2014-12-08

    Photonic crystal point-defect cavities were fabricated in a GaN free-standing photonic crystal slab. The cavities are based on the popular L3 design, which was optimized using an automated process based on a genetic algorithm, in order to maximize the quality factor. Optical characterization of several individual cavity replicas resulted in an average unloaded quality factor Q = 16 900 at the resonant wavelength λ∼1.3 μm, with a maximal measured Q value of 22 500. The statistics of both the quality factor and the resonant wavelength are well explained by first-principles simulations including fabrication disorder and background optical absorption.

  3. Gallium nitride L3 photonic crystal cavities with an average quality factor of 16,900 in the near infrared

    CERN Document Server

    Triviño, Noelia Vico; Urbinati, Giulia; Galli, Matteo; Carlin, Jean-François; Butté, Raphaël; Savona, Vincenzo; Grandjean, Nicolas

    2014-01-01

    Photonic crystal point-defect cavities were fabricated in a GaN free-standing photonic crystal slab. The cavities are based on the popular L3 design, which was optimized using an automated process based on a genetic algorithm, in order to maximize the quality factor. Optical characterization of several individual cavity replicas resulted in an average unloaded quality factor Q = 16,900 at the resonant wavelength {\\lambda} $\\sim 1.3$ {\\mu}m, with a maximal measured Q value of 22,500. The statistics of both the quality factor and the resonant wavelength are well explained by first-principles simulations including fabrication disorder and background optical absorption.

  4. Growth of high quality single crystals of Bi2Se3 topological insulator via solid state reaction method

    Science.gov (United States)

    Yadav, Anil K.; Majhi, Kunjalata; Banerjee, Abhishek; Devi, Poonam; Ganesan, R.; Mishra, P.; Lohani, H.; Sekhar, B. R.; Kumar, P. S. Anil

    2016-05-01

    Recently discovered, Topological Insulators (TIs) have garnered enormous amount of attention owing to its unique surface properties which has potential applications in the field of spintronics and other modern technologies. For all this, it should require a very good quality samples. There are a number of techniques suggested by people for the growth of good quality TIs. Here, we are reporting the growth of high quality single crystals of Bi2Se3 (a TI) by slow cooling solid-state reaction method. X-ray diffraction measurements performed on a cleaved flake of single crystal Bi2Se3 showed up with proper orientations of the crystal planes. High energy X-ray diffraction has been performed to confirm the stoichiometry of the compound and also recorded Laue patterns prove the single crystalline nature of Bi2Se3. Moreover, angle resolved photo-emission spectroscopy (ARPES) carried out on a flat crystal flake shows distinct Dirac dispersion of surface bands at the gamma point clarifying it as a 3D topological insulator.

  5. High quality (InNb)0.1Ti0.9O2 single crystal grown using optical floating zone method

    Science.gov (United States)

    Liu, Ziyi; Song, Yongli; Wang, Xianjie; Su, Yantao; Liu, Zhiguo; Sui, Yu

    2016-07-01

    A crack-free (InNb)0.1Ti0.9O2 single crystal of 4 mm in diameter and 30 mm in length was successfully grown by the optical floating zone method. The polycrystalline feed and seed rods for growing the (InNb)0.1Ti0.9O2 single crystal were prepared by solid-state reaction method. The oxygen partial pressure significantly affected the crystal quality of the material. As shown in reflecting polarizing microphotographs, crystals grown in air have fewer grain boundaries than those grown in pure oxygen; some air-grown crystals are completely free of grain boundaries. Compared to pure TiO2 crystal, the (Nb+In) co-doped TiO2 crystal required a lower growth rate of 5 mm/h to ensure high quality.

  6. Magnetic Control of Convection during Protein Crystallization

    Science.gov (United States)

    Ramachandran, N.; Leslie, F. W.

    2004-01-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular Crystals for diffraction analyses has been the central focus for bio-chemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and Sedimentation as is achieved in "microgravity", we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, f o d o n of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with counteracts on for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility

  7. Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

    Science.gov (United States)

    Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

    2000-01-01

    A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

  8. An automatic device for the quality control of large-scale crystal's production

    CERN Document Server

    Baccaro, S; Castellani, M; Cecilia, A; Dafinei, I; Diemoz, M; Guerra, S; Longo, E; Montecchi, M; Organtini, G; Pellegrini, F

    2001-01-01

    In 1999, the construction of the electromagnetic calorimeter of the Compact Muon Solenoid (CMS) experiment started. Half of the barrel calorimeter made of 61200 lead tungstate (PWO) crystals will be assembled and tested in the Regional Centre of INFN-ENEA in Rome, Italy. Before assembling, all 30600 PWO crystals will be qualified for scintillation and radiation hardness characteristics by a specially built Automatic Crystal Control System. The measuring techniques for crystal qualification and performances of the automatic system will be discussed in this work. (11 refs).

  9. Investigation on quality of cubic GaN/GaAs (100) by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    徐大鹏; 王玉田; 杨辉; 郑联喜; 李建斌; 段俐宏; 吴荣汉

    1999-01-01

    Cubic GaN was grown on GaAs (100) by low pressure metal organic chemical vapor deposition (MOCVD). X-ray diffraction, scanning electron microscope (SEM) and photoluminescence (PL) spectra were performed to characterize the quality of the GaN film. The PL spectra of cubic GaN thin films being thicker than 1.5 μm were reported. Triple-crystal diffraction to analyze orientation distributions and strain of the thin films was also demonstrated.

  10. Tailoring liquid crystalline lipid nanomaterials for controlled release of macromolecules.

    Science.gov (United States)

    Bisset, Nicole B; Boyd, Ben J; Dong, Yao-Da

    2015-11-10

    Lipid-based liquid crystalline materials are being developed as drug delivery systems. However, the use of these materials for delivery of large macromolecules is currently hindered by the small size of the water channels in these structures limiting control over diffusion behaviour. The addition of the hydration-modulating agent, sucrose stearate, to phytantriol cubic phase under excess water conditions incrementally increased the size of these water channels. Inclusion of oleic acid enabled further control of swelling and de-swelling of the matrix via a pH triggerable system where at low pH the hexagonal phase is present and at higher pH the cubic phase is present. Fine control over the release of various sized model macromolecules is demonstrated, indicating future application to controlled loading and release of large macromolecules such as antibodies. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. A general method to study equilibrium partitioning of macromolecules

    DEFF Research Database (Denmark)

    The distribution of macromolecules between a confined microscopic solution and a macroscopic bulk solution plays an important role in understanding separation processes such as Size Exclusion Chromatography (SEC). In this study, we have developed an efficient computational algorithm for obtaining...... the equilibrium partition coefficient (pore-to-bulk concentration ratio) and the concentration profile inside the confining geometry. The algorithm involves two steps. First, certain characteristic structure properties of the studied macromolecule are obtained by sampling its configuration space, and second those...... data are used for the computation of partition coefficient and concentration profile for any confinement size. Our algorithm is versatile to the model and type of the macromolecule studied, and is capable of handling three types of confining geometries (slit, rectangular channel and rectangular box...

  12. Intellective high-precision macromolecule resistance temperature/humidity instrument

    Science.gov (United States)

    Liu, Guixiong; Zhou, Qinhe; Kuang, Yongcong; Xu, Jing; Zeng, Zhixin

    2001-09-01

    Considering that the resistance of macromolecule resistor varies in a wide range and humidity sensor component is sensitive to temperature as well, a intelligent high- precision macromolecule resistance temperature/humidity instrument was proposed in this paper, the instrument is based on the integration of frequency-and-period-measuring method, and sensing characteristic calculation and compensation using interpolation. Practical applications show that the instrument has the advantages of high precision, simple peripheral circuit, low cost, suitability for remote measurement, strong ability of anti-interference and wide operation range.

  13. ASPHERICITY AND PROLATENESS OF LINEAR AND CIRCULAR MACROMOLECULES

    Institute of Scientific and Technical Information of China (English)

    WEI Gaoyuan

    1995-01-01

    The shape asymmetry of gaussian models of linear and circular macromolecules has been numerically invesigated in terms of asphericity and prolateness parameters. These parameters are found to decrease with increasing length for the macromolecule either confined to a plane or in three dimensions. The effect of dimensionality on these parameters is visible only for low dimensions and is generally weak. As dimensionality goes to infinity, it is found that asphericity and prolateness for both chains and rings approach slowly yet descendingly values of corresponding asphericity and prolateness factors, with the exception of the chain which shows a minimum value of asphericity when the embedding space has a dimensionality of four.

  14. Macromolecule simulation and CH4 adsorption mechanism of coal vitrinite

    Science.gov (United States)

    Yu, Song; Yan-ming, Zhu; Wu, Li

    2017-02-01

    The microscopic mechanism of interactions between CH4 and coal macromolecules is of significant practical and theoretical importance in CBM development and methane storage. Under periodic boundary conditions, the optimal energy configuration of coal vitrinite, which has a higher torsion degree and tighter arrangement, can be determined by the calculation of molecular mechanics (MM) and molecular dynamics (MD), and annealing kinetics simulation based on ultimate analysis, 13C NMR, FT IR and HRTEM. Macromolecular stabilization is primarily due to the van der Waals energy and covalent bond energy, mainly consisting of bond torsion energy and bond angle energy. Using the optimal configuration as the adsorbent, GCMC simulation of vitrinite adsorption of CH4 is conducted. A saturated state is reached after absorbing 17 CH4s per coal vitrinite molecule. CH4 is preferentially adsorbed on the edge, and inclined to gathering around the branched chains of the inner vitrinite sites. Finally, the adsorption parameters are calculated through first principle DFT. The adsorbability order is as follows: aromatic structure> heteroatom rings > oxygen functional groups. The adsorption energy order is as follows: Top < Bond < Center, Up < Down. The order of average RDF better reflects the adsorption ability and that of [-COOH] is lower than those of [sbnd Cdbnd O] and [Csbnd Osbnd C]. CH4 distributed in the distance of 0.99-16 Å to functional groups in the type of monolayer adsorption and the average distance order manifest as [sbnd Cdbnd O] (1.64 Å) < [Csbnd Osbnd C] (1.89 Å) < [sbnd COOH] (3.78 Å) < [-CH3] (4.11 Å) according to the average RDF curves. CH4 enriches around [sbnd Cdbnd O] and [Csbnd O-C] whereas is rather dispersed about [-COOH] and [CH3]. Simulation and experiment data are both in strong agreement with the Langmuir and D-A isothermal adsorption model and the D-A model fit better than Langmuir model. Preferential adsorption sites and orientations in vitrinite are

  15. Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water.

    Science.gov (United States)

    Mentré, P; Hui Bon Hoa, G

    2001-01-01

    Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.

  16. Improved Measurement of B(sub 22) of Macromolecules in a Flow Cell

    Science.gov (United States)

    Wilson, Wilbur; Fanguy, Joseph; Holman, Steven; Guo, Bin

    2008-01-01

    An improved apparatus has been invented for use in determining the osmotic second virial coefficient of macromolecules in solution. In a typical intended application, the macromolecules would be, more specifically, protein molecules, and the protein solution would be pumped through a flow cell to investigate the physical and chemical conditions that affect crystallization of the protein in question. Some background information is prerequisite to a meaningful description of the novel aspects of this apparatus. A method of determining B22 from simultaneous measurements of the static transmittance (taken as an indication of concentration) and static scattering of light from the same location in a flowing protein solution was published in 2004. The apparatus used to implement the method at that time included a dual-detector flow cell, which had two drawbacks: a) The amount of protein required for analysis of each solution condition was of the order of a milligram - far too large a quantity for a high-throughput analysis system, for which microgram or even nanogram quantities of protein per analysis are desirable. b) The design of flow cell was such that two light sources were used to probe different regions of the flowing solution. Consequently, the apparatus did not afford simultaneous measurements at the same location in the solution and, hence, did not guarantee an accurate determination of B22.

  17. MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines

    Energy Technology Data Exchange (ETDEWEB)

    Zander, Ulrich [European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble (France); Bourenkov, Gleb [European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22607 Hamburg (Germany); Popov, Alexander N.; Sanctis, Daniele de; Svensson, Olof [European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble (France); McCarthy, Andrew A. [European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble (France); Université Grenoble Alpes–EMBL–CNRS, 38042 Grenoble (France); Round, Ekaterina; Gordeliy, Valentin [Université Grenoble Alpes, IBS, 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France); Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich (Germany); Moscow Institute of Physics and Technology, Dolgoprudniy 141700 (Russian Federation); Mueller-Dieckmann, Christoph; Leonard, Gordon A., E-mail: leonard@esrf.fr [European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble (France)

    2015-10-31

    The fully automated collection and merging of partial data sets from a series of cryocooled crystals of biological macromolecules contained on the same support is presented, as are the results of test experiments carried out on various systems. Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.

  18. Detached phenomenon: Its effect on the crystal quality of Ga{sub (1−x)}In{sub x}Sb bulk crystal grown by the VDS technique

    Energy Technology Data Exchange (ETDEWEB)

    Gadkari, Dattatray, E-mail: db.gadkari@gmail.com [Department of Physics, Mithibai College, Mumbai 400056 (India)

    2013-05-15

    Vertical directional solidification (VDS) technique is used on the combined growth principals of the conventional methods since 1994, which leads to the detached growth. For evaluation of the detached growth, five bulk ingots of indium doped gallium–antimonide GaSb:In (In = 0.5, 0.25, 0.15) have been grown – without the seed, without contact to the ampoule wall, without coating and without external pressure. The gap is attributed to compensate the differential thermal dilatation that is grown with the reduced diameter than the diameter of the ampoule. VDS experiments have been proved that the sum of the contact angle and growth angle is large enough to allow detachment without any additional pressure difference under the melt to offset hydrostatic pressure. A meniscus forms at the bottom of the melt, the capillarity effect establishes due to which spontaneous gap could be created by the melt free surface, thus no thermal shear stress and thermo-mechanical stresses at the interface. Detached grown bulk GaSb:In crystals showed superior crystal quality with the highest physical properties and mobility than the crystals grown ever. The axial and radial composition profile of the grown GaSb:In ingots showed variation ≤10%. From the conical region, dislocation density decreases in the growth direction and reaches less than 10{sup 3} cm{sup −2}. - Highlights: ► Detachment: without seed, without ampoule contact, without coating, without external pressure. ► Detached ingot growth samples showed the highest physical properties and the carrier mobility. ► Initial to final transition: in detached growth, dislocations decreases and less than 10{sup 3} cm{sup −2}. ► Detached samples: Raman spectrum shows only TO phonon (110) direction of single orientation. ► Detached ingot: FTIR shows highest transmissions % but decreases on increase doping in samples.

  19. Insulin facilitates transport of macromolecules and nutrients to muscles

    DEFF Research Database (Denmark)

    Christensen, N J; Hilsted, J

    1993-01-01

    , systolic blood pressure and plasma noradrenaline. These changes were absent or attenuated in diabetic patients (without neuropathy) after an oral glucose load. These responses were normalized by insulin infusion. Our results suggest that insulin facilitates the transfer of macromolecules and nutrients from...

  20. DEDUCTION OF EVOLUTIONARY RELATIONSHIPS FROM THE STRUCTURE OF MACROMOLECULES

    NARCIS (Netherlands)

    BEINTEMA, JJ

    1992-01-01

    Macromolecules can be used to derive evolutionary relationships. This discovery has led to the development of a new discipline in biology, molecular evolution. A brief survey of several aspects of this new field of investigation is presented, together with references to historical and more recent li

  1. Crystallogenesis of biological macromolecules. Biological, microgravity and other physicochemical aspects

    NARCIS (Netherlands)

    Giege, R; Drenth, J; Ducruix, A; McPherson, A; Saenger, W

    1995-01-01

    After an historical introduction and justification of the importance of proteins (as well as other macromolecules or macromolecular assemblies of biological origin) in modern biology but also in physics, this review presents the state of the field of macromolecular crystallogenesis. The basic questi

  2. Reduced adipose tissue lymphatic drainage of macromolecules in obese subjects

    DEFF Research Database (Denmark)

    Arngrim, N; Simonsen, L; Holst, Jens Juul

    2012-01-01

    The aim of this study was to investigate subcutaneous adipose tissue lymphatic drainage (ATLD) of macromolecules in lean and obese subjects and, furthermore, to evaluate whether ATLD may change in parallel with adipose tissue blood flow. Lean and obese male subjects were studied before and after ...... online publication, 3 July 2012; doi:10.1038/ijo.2012.98....

  3. Chaperoning roles of macromolecules interacting with proteins in vivo.

    Science.gov (United States)

    Choi, Seong Il; Lim, Keo-Heun; Seong, Baik L

    2011-01-01

    The principles obtained from studies on molecular chaperones have provided explanations for the assisted protein folding in vivo. However, the majority of proteins can fold without the assistance of the known molecular chaperones, and little attention has been paid to the potential chaperoning roles of other macromolecules. During protein biogenesis and folding, newly synthesized polypeptide chains interact with a variety of macromolecules, including ribosomes, RNAs, cytoskeleton, lipid bilayer, proteolytic system, etc. In general, the hydrophobic interactions between molecular chaperones and their substrates have been widely believed to be mainly responsible for the substrate stabilization against aggregation. Emerging evidence now indicates that other features of macromolecules such as their surface charges, probably resulting in electrostatic repulsions, and steric hindrance, could play a key role in the stabilization of their linked proteins against aggregation. Such stabilizing mechanisms are expected to give new insights into our understanding of the chaperoning functions for de novo protein folding. In this review, we will discuss the possible chaperoning roles of these macromolecules in de novo folding, based on their charge and steric features.

  4. Antimicrobial resistance challenged with metal-based antimicrobial macromolecules.

    Science.gov (United States)

    Abd-El-Aziz, Alaa S; Agatemor, Christian; Etkin, Nola

    2017-02-01

    Antimicrobial resistance threatens the achievements of science and medicine, as it deactivates conventional antimicrobial therapeutics. Scientists respond to the threat by developing new antimicrobial platforms to prevent and treat infections from these resistant strains. Metal-based antimicrobial macromolecules are emerging as an alternative to conventional platforms because they combine multiple mechanisms of action into one platform due to the distinctive properties of metals. For example, metals interact with intracellular proteins and enzymes, and catalyse various intracellular processes. The macromolecular architecture offers a means to enhance antimicrobial activity since several antimicrobial moieties can be conjugated to the scaffold. Further, these macromolecules can be fabricated into antimicrobial materials for contact-killing medical implants, fabrics, and devices. As volatilization or leaching out of the antimicrobial moieties from the macromolecular scaffold is reduced, these medical implants, fabrics, and devices can retain their antimicrobial activity over an extended period. Recent advances demonstrate the potential of metal-based antimicrobial macromolecules as effective platforms that prevent and treat infections from resistant strains. In this review these advances are thoroughly discussed within the context of examples of metal-based antimicrobial macromolecules, their mechanisms of action and biocompatibility. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Microfluidic device and method for processing of macromolecules

    DEFF Research Database (Denmark)

    2012-01-01

    to the first set of outlets is guided through the reaction channels, and second inlet and outlet channels for feeding an enzymatic reagent to the reaction chamber essentially without displacing the macromolecule containers trapped in the reaction channels, wherein the second set of inlets and outlets...

  6. Interactions between adsorbed macromolecules : measurements on emulsions and liquid films

    NARCIS (Netherlands)

    Vliet, van T.

    1977-01-01

    The aim of this study was to gain more insight into the factors, determining the inter- and intramolecular interactions between adsorbed macromolecules. To that end several experimental and theoretical approaches were followed, using well-defined systems. It was shown that these interactions could c

  7. Synthesis of main-chain metal carbonyl organometallic macromolecules (MCMCOMs).

    Science.gov (United States)

    Cao, Kai; Murshid, Nimer; Wang, Xiaosong

    2015-04-01

    Synthesis of main-chain metal carbonyl organometallic macromolecules (MCMCOMs) is difficult, mainly due to the instability of metal carbonyl complexes. Despite its challenge a number of MCMCOMs has been prepared by strategically using organometallic, organic, and polymer synthetic chemistry. Main contributions to this research field were reported by the groups of Tyler, Pannell, and Wang and are briefly summarized in this article.

  8. Adsorption of charged macromolecules on a gold electrode

    NARCIS (Netherlands)

    Barten, D.

    2003-01-01

    In this thesis we have examined the role of electrostatic interactions in the adsorption of charged macromolecules from aqueous solution to a solid surface and the possibilitiesfor manipulatingthis process through the electric potential

  9. Bioenergetic aspects of the translocation of macromolecules across bacterial membranes

    NARCIS (Netherlands)

    Palmen, Ronald; Driessen, Arnold J.M.; Hellingwerf, K

    1994-01-01

    Bacteria are extremely versatile in the sense that they have gained the ability to transport all three major classes of biopolymers through their cell envelope: proteins, nucleic acids, and polysaccharides. These macromolecules are translocated across membranes in a large number of cellular processe

  10. Chaperoning Roles of Macromolecules Interacting with Proteins in Vivo

    Directory of Open Access Journals (Sweden)

    Baik L. Seong

    2011-03-01

    Full Text Available The principles obtained from studies on molecular chaperones have provided explanations for the assisted protein folding in vivo. However, the majority of proteins can fold without the assistance of the known molecular chaperones, and little attention has been paid to the potential chaperoning roles of other macromolecules. During protein biogenesis and folding, newly synthesized polypeptide chains interact with a variety of macromolecules, including ribosomes, RNAs, cytoskeleton, lipid bilayer, proteolytic system, etc. In general, the hydrophobic interactions between molecular chaperones and their substrates have been widely believed to be mainly responsible for the substrate stabilization against aggregation. Emerging evidence now indicates that other features of macromolecules such as their surface charges, probably resulting in electrostatic repulsions, and steric hindrance, could play a key role in the stabilization of their linked proteins against aggregation. Such stabilizing mechanisms are expected to give new insights into our understanding of the chaperoning functions for de novo protein folding. In this review, we will discuss the possible chaperoning roles of these macromolecules in de novo folding, based on their charge and steric features.

  11. Roles of Oxygen and Hydrogen in Crystal Orientation Transition of Copper Foils for High-Quality Graphene Growth

    Science.gov (United States)

    Hu, Junxiong; Xu, Jianbao; Zhao, Yanfei; Shi, Lin; Li, Qi; Liu, Fengkui; Ullah, Zaka; Li, Weiwei; Guo, Yufen; Liu, Liwei

    2017-01-01

    The high-quality graphene film can be grown on single-crystal Cu substrate by seamlessly stitching the aligned graphene domains. The roles of O2 and H2 have been intensively studied in the graphene growth kinetics, including lowering the nucleation sites and tailoring the domain structures. However, how the O2 and H2 influence Cu orientations during recrystallization prior to growing graphene, still remains unclear. Here we report that the oxidation of Cu surface tends to stabilize the Cu(001) orientation while impedes the evolution of Cu(111) single domain during annealing process. The crystal orientation-controlled synthesis of aligned graphene seeds is further realized on the long-range ordered Cu(111) substrate. With decreasing the thickness of oxide layer on Cu surface by introducing H2, the Cu(001) orientation changes into Cu(111) orientation. Meanwhile, the average domain size of Cu foils is increased from 50 μm to larger than 1000 μm. The density functional theory calculations reveal that the oxygen increases the energy barrier for Cu(111) surface and makes O/Cu(001) more stable than O/Cu(111) structure. Our work can be helpful for revealing the roles of O2 and H2 in controlling the formation of Cu single-crystal substrate as well as in growing high-quality graphene films. PMID:28367988

  12. Light-Switchable Azobenzene-Containing Macromolecules: From UV to Near Infrared.

    Science.gov (United States)

    Weis, Philipp; Wu, Si

    2017-06-23

    Azobenzene-containing macromolecules (azo-macromolecules) such as azobenzene-containing polymers (azopolymers) and azobenzene-functionalized biomacromolecules are photoswitchable macromolecules. Trans-to-cis photoisomerization in conventional azo-macromolecules is induced by ultraviolet (UV) light. However, UV light cannot penetrate deeply into issue and has a very small fraction in sunlight. Therefore, conventional azo-macromolecules are problematic for biomedical and solar-energy-related applications. In this Feature Article, the strategies for constructing visible and near-infrared (NIR) light-responsive azo-macromolecules are reviewed, and the potential applications of visible- and NIR-light-responsive azo-macromolecules in biomedicine and solar energy conversion are highlighted. The remaining challenges in the field of photoswitchable azo-macromolecules are discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Surface Characteristics and Adhesion Behavior of Escherichia coli O157:H7: Role of Extracellular Macromolecules

    Science.gov (United States)

    Surface macromolecule cleavage experiments were conducted on enterohaemorrhagic Escherichia coli O157:H7 cells to investigate the influence of these macromolecules on cell surface properties. Electrophoretic mobility, hydrophobicity, and titration experiments were carried out on proteinase K treate...

  14. Vesicular uptake of macromolecules by human placental amniotic epithelial cells.

    Science.gov (United States)

    Sharshiner, Rita; Brace, Robert A; Cheung, Cecilia Y

    2017-09-01

    Studies in animal models have shown that unidirectional vesicular transport of amniotic fluid across the amnion plays a primary role in regulating amniotic fluid volume. Our objective was to explore vesicle type, vesicular uptake and intracellular distribution of vesicles in human amnion cells using high- and super-resolution fluorescence microscopy. Placental amnion was obtained at cesarean section and amnion cells were prepared and cultured. At 20%-50% confluence, the cells were incubated with fluorophore conjugated macromolecules for 1-30 min at 22 °C or 37 °C. Fluorophore labeled macromolecules were selected as markers of receptor-mediated caveolar and clathrin-coated vesicular uptake as well as non-specific endocytosis. After fluorophore treatment, the cells were fixed, imaged and vesicles counted using Imaris(®) software. Vesicular uptake displayed first order saturation kinetics with half saturation times averaging 1.3 min at 37 °C compared to 4.9 min at 22 °C, with non-specific endocytotic uptake being more rapid at both temperatures. There was extensive cell-to-cell variability in uptake rate. Under super-resolution microscopy, the pattern of intracellular spatial distribution was distinct for each macromolecule. Co-localization of fluorescently labeled macromolecules was very low at vesicular dimensions. In human placental amnion cells, 1) vesicular uptake of macromolecules is rapid, consistent with the concept that vesicular transcytosis across the amnion plays a role in the regulation of amniotic fluid volume; 2) uptake is temperature dependent and variable among individual cells; 3) the unique intracellular distributions suggest distinct functions for each vesicle type; 4) non-receptor mediated vesicular uptake may be a primary vesicular uptake mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

    Science.gov (United States)

    Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

    2016-02-26

    Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

  16. Structural properties, crystal quality and growth modes of MOCVD-grown AlN with TMAl pretreatment of sapphire substrate

    Science.gov (United States)

    Sun, Haiding; Wu, Feng; tahtamouni, T. M. Al; Alfaraj, Nasir; Li, Kuang-Hui; Detchprohm, Theeradetch; Dupuis, Russell D.; Li, Xiaohang

    2017-10-01

    The growth of high quality AlN epitaxial films relies on precise control of the initial growth stages. In this work, we examined the influence of the trimethylaluminum (TMAl) pretreatment of sapphire substrates on the structural properties, crystal quality and growth modes of heteroepitaxial AlN films on (0 0 0 1) sapphire substrates. Without the pretreatment, the AlN films nucleated on the smooth surface but exhibited mixed crystallographic Al- (N-) polarity, resulting in rough AlN film surfaces. With increasing the pretreatment time from 1 to 5 s, the N-polarity started to be impeded. However, small islands were formed on sapphire surface due to the decompostion of TMAl. As a result, small voids became noticeable at the nucleation layer (NL) because the growth started as quasi three-dimensional (3D) but transformed to 2D mode as the film grew thicker and got coalesced, leading to smoother and Al-polar films. On the other hand, longer pretreatment time of 40 s formed large 3D islands on sapphire, and thus initiated a 3D-growth mode of the AlN film, generating Al-polar AlN nanocolumns with different facets, which resulted into rougher film surfaces. The epitaxial growth modes and their correlation with the AlN film crystal quality under different TMAl pretreatments are also discussed.

  17. Enhanced Crystal Quality of AlxIn1-xAsySb1-y for Terahertz Quantum Cascade Lasers

    Directory of Open Access Journals (Sweden)

    Tobias Zederbauer

    2016-04-01

    Full Text Available This work provides a detailed study on the growth of AlxIn1-xAsySb1-y lattice-matched to InAs by Molecular Beam Epitaxy. In order to find the conditions which lead to high crystal quality deep within the miscibility gap, AlxIn1-xAsySb1-y with x = 0.462 was grown at different growth temperatures as well as As2 and Sb2 beam equivalent pressures. The crystal quality of the grown layers was examined by high-resolution X-ray diffraction and atomic force microscopy. It was found that the incorporation of Sb into Al0.462In0.538AsySb1-y is strongly temperature-dependent and reduced growth temperatures are necessary in order to achieve significant Sb mole fractions in the grown layers. At 480 ∘ C lattice matching to InAs could not be achieved. At 410 ∘ C lattice matching was possible and high quality films of Al0.462In0.538AsySb1-y were obtained.

  18. Structural properties, crystal quality and growth modes of MOCVD-grown AlN with TMAl pretreatment of sapphire substrate

    KAUST Repository

    Sun, Haiding

    2017-08-08

    The growth of high quality AlN epitaxial films relies on precise control of the initial growth stages. In this work, we examined the influence of the trimethylaluminum (TMAl) pretreatment of sapphire substrates on the structural properties, crystal quality and growth modes of heteroepitaxial AlN films on (0001) sapphire substrates. Without the pretreatment, the AlN films nucleated on the smooth surface but exhibited mixed crystallographic Al- (N-) polarity, resulting in rough AlN film surfaces. With increasing the pretreatment time from 1 to 5 s, the N-polarity started to be impeded. However, small islands were formed on sapphire surface due to the decompostion of TMAl. As a result, small voids became noticeable at the nucleation layer (NL) because the growth started as quasi three-dimensional (3D) but transformed to 2D mode as the film grew thicker and got coalesced, leading to smoother and Al-polar films. On the other hand, longer pretreatment time of 40 s formed large 3D islands on sapphire, and thus initiated a 3D-growth mode of the AlN film, generating Al-polar AlN nanocolumns with different facets, which resulted into rougher film surfaces. The epitaxial growth modes and their correlation with the AlN film crystal quality under different TMAl pretreatments are also discussed.

  19. Macromolecule Mediated Transport and Retention of Escherichia coli O157:H7 in Saturated Porous Media

    Science.gov (United States)

    The role of extracellular macromolecules on Escherichia coli O157:H7 transport and retention was investigated in saturated porous media. To compare the relative transport and retention of E. coli cells that are macromolecule rich and deficient, macromolecules were partially cleaved using a proteolyt...

  20. Measuring Equilibrium Binding Affinity of Biological Macromolecules in Solution by Thermophoresis

    Science.gov (United States)

    2015-05-18

    Approved for Public Release; Distribution Unlimited Final Report: Measuring Equilibrium Binding Affinity of Biological Macromolecules in Solution by...Equilibrium Binding Affinity of Biological Macromolecules in Solution by Thermophoresis Report Title The primary research focus of the San Diego State...equilibrium binding affinities of biological macromolecules in solution. This qauntitative information plays a vital role in supporting the static

  1. High Resolution X-Ray Diffraction of Macromolecules with Synchrotron Radiation

    Science.gov (United States)

    Stojanoff, Vivian; Boggon, Titus; Helliwell, John R.; Judge, Russell; Olczak, Alex; Snell, Edward H.; Siddons, D. Peter; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    We recently combined synchrotron-based monochromatic X-ray diffraction topography methods with triple axis diffractometry and rocking curve measurements: high resolution X-ray diffraction imaging techniques, to better understand the quality of protein crystals. We discuss these methods in the light of results obtained on crystals grown under different conditions. These non destructive techniques are powerful tools in the characterization of the protein crystals and ultimately will allow to improve, develop, and understand protein crystal growth. High resolution X-ray diffraction imaging methods will be discussed in detail in light of recent results obtained on Hen Egg White Lysozyme crystals and other proteins.

  2. Terahertz gas sensing based on a simple one-dimensional photonic crystal cavity with high-quality factors

    DEFF Research Database (Denmark)

    Chen, T.; Han, Z. H.; Liu, J. J.

    2014-01-01

    exhibits high-quality factors, facilitating the realization of high sensitivity in the gas refractive index sensing. In our experiment, 6% of the change of hydrogen concentration in air, which corresponds to a refractive index change of 1.4 x 10(-5), can be steadily detected, and different gas samples can......We report in this paper terahertz gas sensing using a simple 1D photonic crystal cavity. The resonant frequencies of the cavity depend linearly on the refractive index of the ambient gas, which can then be measured by monitoring the resonance shift. Although quite easy to manufacture, this cavity...

  3. Electrical and thermal tuning of quality factor and free spectral range of optical resonance of nematic liquid crystal microdroplets

    Science.gov (United States)

    Sofi, Junaid Ahmad; Mohiddon, M. A.; Dutta, N.; Dhara, Surajit

    2017-08-01

    We experimentally study the effect of temperature and electric field on the quality (Q ) factor and free spectral range (FSR) of whispering-gallery-mode optical resonance of dye-doped nematic liquid crystal microdroplets. Both the Q factor and the FSR are highly sensitive to the temperature and electric field and are tunable. The Q factor decreases, whereas the FSR increases substantially, with increasing temperature and electric field. The variation of the Q factor and FSR is understood based on the change in the effective refractive index and the dynamic size of the microdroplets.

  4. Introduction to protein crystallization.

    Science.gov (United States)

    McPherson, Alexander; Gavira, Jose A

    2014-01-01

    Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies.

  5. ProteinShader: illustrative rendering of macromolecules

    Directory of Open Access Journals (Sweden)

    Weber Joseph R

    2009-03-01

    Full Text Available Abstract Background Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings. Results The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline. Conclusion By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images.

  6. Solubility and stability of curcumin in solutions containing alginate and other viscosity modifying macromolecules. Studies of curcumin and curcuminoids. XXX.

    Science.gov (United States)

    Tønnesen, H Hjorth

    2006-08-01

    The solubility, chemical- and photochemical stability of curcumin in aqueous solutions containing alginate, gelatin or other viscosity modifying macromolecules have been investigated in order to obtain an alternative to the use of surfactants or cyclodextrins. The solubility of curcumin in aqueous solution at pH 5 increased by a factor > or = 10(4) in the presence of 0.5% (w/v) alginate (various qualities) or gelatin compared to plain buffer, while propylene glycol alginate ester, cesapectin and sodium carboxymethyl cellulose did not have a similar solubilizing effect. The solubilization was slightly influenced by pH, ionic strength and type and concentration of buffer salts. The macromolecules do, however, not stabilize towards hydrolytic- or photolytic degradation of curcumin.

  7. Effect of nucleation layer morphology on crystal quality, surface morphology and electrical properties of AlGaN/GaN heterostructures

    Institute of Scientific and Technical Information of China (English)

    Duan Huantao; Hao Yue; Zhang Jincheng

    2009-01-01

    Nucleation layer formation is a key factor for high quality gallium nitride (GaN) growth on a sapphire substrate. We found that the growth rate substantially affected the nucleation layer morphology, thereby having a great impact on the crystal quality, surface morphology and electrical properties of AIGaN/GaN heterostructures on sapphire substrates. A nucleation layer with a low growth rate of 2.5 nm/min is larger and has better coalescence than one grown at a high growth rate of 5 nm/min. AIGaN/GaN heterostructures on a nucleation layer with low growth rate have better crystal quality, surface morphology and electrical properties.

  8. Controlled synthesis of high-quality crystals of monolayer MoS2 for nanoelectronic device application

    DEFF Research Database (Denmark)

    Yang, Xiaonian; Li, Qiang; Hu, Guofeng

    2016-01-01

    Two-dimensional layered materials have attracted significant interest for their potential applications in electronic and optoelectronics devices. Among them, transition metal dichalcogenides (TMDs), especially molybdenum disulfide (MoS2), is extensively studied because of its unique properties....... Monolayer MoS2 so far can be obtained by mechanical exfoliation or chemical vapor deposition (CVD). However, controllable synthesis of large area monolayer MoS2 with high quality needs to be improved and their growth mechanism requires more studies. Here we report a systematical study on controlled...... synthesis of high-quality monolayer MoS2 single crystals using low pressure CVD. Large-size monolayer MoS2 triangles with an edge length up to 405 mu m were successfully synthesized. The Raman and photoluminescence spectroscopy studies indicate high homogenous optical characteristic of the synthesized...

  9. Relationships between the surface quality of a single crystal copper ingot and the process parameters of a heated mould continuous casting method

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    The relationships between the surface quality of a single crystal copper ingot and the process parameters of heated mould continuous casting method were studied experimentally using our own design of horizontal heated mould continuous casting apparatus, and the mechanism by which process parameters affect the surface quality of a single crystal copper ingot is analyzed in the present paper. The results show that the process parameters affect the surface quality of a pure copper ingot by affecting the position of the liquid-solid interface in the mould. The position of the liquid-solid interface in the mould must be controlled carefully within an appropriate range, which is determined through a series of experiments,in order to gain a single crystal copper ingot with good surface quality.

  10. A historical perspective on protein crystallization from 1840 to the present day.

    Science.gov (United States)

    Giegé, Richard

    2013-12-01

    Protein crystallization has been known since 1840 and can prove to be straightforward but, in most cases, it constitutes a real bottleneck. This stimulated the birth of the biocrystallogenesis field with both 'practical' and 'basic' science aims. In the early years of biochemistry, crystallization was a tool for the preparation of biological substances. Today, biocrystallogenesis aims to provide efficient methods for crystal fabrication and a means to optimize crystal quality for X-ray crystallography. The historical development of crystallization methods for structural biology occurred first in conjunction with that of biochemical and genetic methods for macromolecule production, then with the development of structure determination methodologies and, recently, with routine access to synchrotron X-ray sources. Previously, the identification of conditions that sustain crystal growth occurred mostly empirically but, in recent decades, this has moved progressively towards more rationality as a result of a deeper understanding of the physical chemistry of protein crystal growth and the use of idea-driven screening and high-throughput procedures. Protein and nucleic acid engineering procedures to facilitate crystallization, as well as crystallization methods in gelled-media or by counter-diffusion, represent recent important achievements, although the underlying concepts are old. The new nanotechnologies have brought a significant improvement in the practice of protein crystallization. Today, the increasing number of crystal structures deposited in the Protein Data Bank could mean that crystallization is no longer a bottleneck. This is not the case, however, because structural biology projects always become more challenging and thereby require adapted methods to enable the growth of the appropriate crystals, notably macromolecular assemblages.

  11. Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity

    Science.gov (United States)

    Duff,, Michael R.; Grubbs, Jordan; Howell, Elizabeth E.

    2011-01-01

    Isothermal titration calorimetry (ITC) is a useful tool for understanding the complete thermodynamic picture of a binding reaction. In biological sciences, macromolecular interactions are essential in understanding the machinery of the cell. Experimental conditions, such as buffer and temperature, can be tailored to the particular binding system being studied. However, careful planning is needed since certain ligand and macromolecule concentration ranges are necessary to obtain useful data. Concentrations of the macromolecule and ligand need to be accurately determined for reliable results. Care also needs to be taken when preparing the samples as impurities can significantly affect the experiment. When ITC experiments, along with controls, are performed properly, useful binding information, such as the stoichiometry, affinity and enthalpy, are obtained. By running additional experiments under different buffer or temperature conditions, more detailed information can be obtained about the system. A protocol for the basic setup of an ITC experiment is given. PMID:21931288

  12. High and low thermal conductivity of amorphous macromolecules

    Science.gov (United States)

    Xie, Xu; Yang, Kexin; Li, Dongyao; Tsai, Tsung-Han; Shin, Jungwoo; Braun, Paul V.; Cahill, David G.

    2017-01-01

    We measure the thermal conductivity, heat capacity and sound velocity of thin films of five polymers, nine polymer salts, and four caged molecules to advance the fundamental understanding of the lower and upper limits to heat conduction in amorphous macromolecules. The thermal conductivities vary by more than one order of magnitude, from 0.06 W m-1K-1 for [6,6]-phenyl-C71-butyric acid methyl ester to 0.67 W m-1K-1 for poly(vinylphosphonic acid calcium salt). Minimum thermal conductivity calculated from the measured sound velocity and effective atomic density is in good agreement with the thermal conductivity of macromolecules with various molecular structures and intermolecular bonding strength.

  13. Plasmodesmata: intercellular tunnels facilitating transport of macromolecules in plants.

    Science.gov (United States)

    Kragler, Friedrich

    2013-04-01

    In plants, intercellular structures named plasmodesmata (PD) form a continuous cytoplasmic network between neighboring cells. PD pores provide channels for intercellular symplasmic (cell-to-cell) transport throughout most tissues of the plant body. Cell-defining proteins, such as transcription factors, and regulatory non-coding sequences, such as short interfering RNA, micro RNA, protein-encoding messenger RNAs, viroids, and viral RNA/DNA genomes move via PD channels to adjacent cells. PD-mediated intercellular transport of macromolecules is a regulated process depending on the tissue, developmental stage, and nature of the transported macromolecule. In this review, PD channels and their similarity to tunneling nanotubes present in animals are highlighted. In addition, homeodomain protein movement and cellular components regulating transport are discussed.

  14. Analysis of an industrial production suspension of Bacillus lentus subtilisin crystals by powder diffraction: a powerful quality-control tool.

    Science.gov (United States)

    Frankaer, Christian G; Moroz, Olga V; Turkenburg, Johan P; Aspmo, Stein I; Thymark, Majbritt; Friis, Esben P; Stahl, Kenny; Nielsen, Jens E; Wilson, Keith S; Harris, Pernille

    2014-04-01

    A microcrystalline suspension of Bacillus lentus subtilisin (Savinase) produced during industrial large-scale production was analysed by X-ray powder diffraction (XRPD) and X-ray single-crystal diffraction (MX). XRPD established that the bulk microcrystal sample representative of the entire production suspension corresponded to space group P212121, with unit-cell parameters a = 47.65, b = 62.43, c = 75.74 Å, equivalent to those for a known orthorhombic crystal form (PDB entry 1ndq). MX using synchrotron beamlines at the Diamond Light Source with beam dimensions of 20 × 20 µm was subsequently used to study the largest crystals present in the suspension, with diffraction data being collected from two single crystals (∼20 × 20 × 60 µm) to resolutions of 1.40 and 1.57 Å, respectively. Both structures also belonged to space group P2(1)2(1)2(1), but were quite distinct from the dominant form identified by XRPD, with unit-cell parameters a = 53.04, b = 57.55, c = 71.37 Å and a = 52.72, b = 57.13, c = 65.86 Å, respectively, and refined to R = 10.8% and Rfree = 15.5% and to R = 14.1% and Rfree = 18.0%, respectively. They are also different from any of the forms previously reported in the PDB. A controlled crystallization experiment with a highly purified Savinase sample allowed the growth of single crystals of the form identified by XRPD; their structure was solved and refined to a resolution of 1.17 Å with an R of 9.2% and an Rfree of 11.8%. Thus, there are at least three polymorphs present in the production suspension, albeit with the 1ndq-like microcrystals predominating. It is shown how the two techniques can provide invaluable and complementary information for such a production suspension and it is proposed that XRPD provides an excellent quality-control tool for such suspensions.

  15. Synthesis, Characterisation and Application of 68Ga-labelled Macromolecules

    OpenAIRE

    Velikyan, Irina

    2005-01-01

    The positron emitting radionuclide 68Ga (T1/2 = 68 min) might become of practical interest for clinical positron emission tomography (PET). The metallic cation, 68Ga(III), is suitable for complexation with chelators, either naked or conjugated with biological macromolecules. Such labelling procedures require pure and concentrated preparations of 68Ga(III), which cannot be sufficiently fulfilled by the presently available 68Ge/68Ga generator eluate. This thesis presents methods to increase the...

  16. SETOR: hardware-lighted three-dimensional solid model representations of macromolecules.

    Science.gov (United States)

    Evans, S V

    1993-06-01

    SETOR is designed to exploit the hardware lighting capabilities of the IRIS-4D series graphics workstations to render high-quality raster images of macromolecules that can undergo rotation and translation interactively. SETOR can render standard all-atom and backbone models of proteins or nucleic acids, but focuses on displaying protein molecules by highlighting elements of secondary structure. The program has a very friendly user interface that minimizes the number of input files by allowing the user to interactively edit parameters, such as colors, lighting coefficients, and descriptions of secondary structure via mouse activated dialogue boxes. The choice of polymer chain representation can be varied from standard vector models and van der Waal models, to a B-spline fit of polymer backbones that yields a smooth ribbon that approximates the polymer chain, to strict Cardinal splines that interpolate the smoothest curve possible that will precisely follow the polymer chain. The program provides a photograph mode, save/restore facilities, and efficient generation of symmetry-related molecules and packing diagrams. Additionally, SETOR is designed to accept commands and model coordinates from the standard input stream, and to control standard output. Ancillary programs provide a method to interactively edit hardcopy plots of all vector and many solid models generated by SETOR, and to produce standard HPGL or PostScript files. Examples of figures rendered by SETOR of a number of macromolecules of various classes are presented.

  17. Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution

    Energy Technology Data Exchange (ETDEWEB)

    Pernot, Petra, E-mail: rejma@esrf.fr [ESRF, 6 Jules Horowitz, F-38043 Grenoble (France); Round, Adam [EMBL, 6 Jules Horowitz, F-38042 Grenoble (France); Barrett, Ray; De Maria Antolinos, Alejandro [ESRF, 6 Jules Horowitz, F-38043 Grenoble (France); Gobbo, Alexandre [EMBL, 6 Jules Horowitz, F-38042 Grenoble (France); Gordon, Elspeth [ESRF, 6 Jules Horowitz, F-38043 Grenoble (France); Huet, Julien [EMBL, 6 Jules Horowitz, F-38042 Grenoble (France); Kieffer, Jerôme; Lentini, Mario; Mattenet, Muriel; Morawe, Christian; Mueller-Dieckmann, Christoph; Ohlsson, Staffan; Schmid, Werner; Surr, John; Theveneau, Pascal; Zerrad, Louiza; McSweeney, Sean [ESRF, 6 Jules Horowitz, F-38043 Grenoble (France)

    2013-07-01

    A description of the new ESRF BioSAXS beamline is given. The beamline presented is dedicated to small-angle X-ray scattering of macromolecules in solution operating with a high-throughput sample-changer robot and automated data analysis for quality control and feedback. Small-angle X-ray scattering (SAXS) measurements of proteins in solution are becoming increasingly popular with biochemists and structural biologists owing to the presence of dedicated high-throughput beamlines at synchrotron sources. As part of the ESRF Upgrade program a dedicated instrument for performing SAXS from biological macromolecules in solution (BioSAXS) has been installed at the renovated BM29 location. The optics hutch has been equipped with new optical components of which the two principal elements are a fixed-exit double multilayer monochromator and a 1.1 m-long toroidal mirror. These new dedicated optics give improved beam characteristics (compared with the previous set-up on ID14-3) regarding the energy tunability, flux and focusing at the detector plane leading to reduced parasitic scattering and an extended s-range. User experiments on the beamline have been successfully carried out since June 2012. A description of the new BioSAXS beamline and the set-up characteristics are presented together with examples of obtained data.

  18. Self-organization of amphiphilic macromolecules with local helix structure in concentrated solutions.

    Science.gov (United States)

    Glagolev, M K; Vasilevskaya, V V; Khokhlov, A R

    2012-08-28

    Concentrated solutions of amphiphilic macromolecules with local helical structure were studied by means of molecular dynamic simulations. It is shown that in poor solvent the macromolecules are assembled into wire-like aggregates having complex core-shell structure. The core consists of a hydrophobic backbone of the chains which intertwine around each other. It is protected by the shell of hydrophilic side groups. In racemic mixture of right-hand and left-hand helix macromolecules the wire-like complex is a chain of braid bundles of macromolecules with the same chirality stacking at their ends. The average number of macromolecules in the wire cross-section is close to that of separate bundles observed in dilute solutions of such macromolecules. The effects described here could serve as a simple model of self-organization in solutions of macromolecules with local helical structure.

  19. High quality single crystal Ge nano-membranes for opto-electronic integrated circuitry

    Energy Technology Data Exchange (ETDEWEB)

    Shah, V. A., E-mail: vishal.shah@warwick.ac.uk; Gammon, P. M. [Department of Engineering, The University of Warwick, Coventry CV4 7AL (United Kingdom); Department of Physics, The University of Warwick, Coventry CV4 7AL (United Kingdom); Rhead, S. D.; Halpin, J. E.; Trushkevych, O.; Wilson, N. R.; Myronov, M.; Edwards, R. S.; Patchett, D. H.; Allred, P. S.; Prest, M. J.; Whall, T. E.; Parker, E. H. C.; Leadley, D. R. [Department of Physics, The University of Warwick, Coventry CV4 7AL (United Kingdom); Chávez-Ángel, E. [ICN2-Institut Catala de Nanociencia i Nanotecnologia, Campus UAB, 08193 Bellaterra (Barcelona) (Spain); Department of Physics, UAB, 08193 Bellaterra (Barcelona) (Spain); Shchepetov, A.; Prunnila, M. [VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo (Finland); Kachkanov, V.; Dolbnya, I. P. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Reparaz, J. S. [ICN2-Institut Catala de Nanociencia i Nanotecnologia, Campus UAB, 08193 Bellaterra (Barcelona) (Spain); and others

    2014-04-14

    A thin, flat, and single crystal germanium membrane would be an ideal platform on which to mount sensors or integrate photonic and electronic devices, using standard silicon processing technology. We present a fabrication technique compatible with integrated-circuit wafer scale processing to produce membranes of thickness between 60 nm and 800 nm, with large areas of up to 3.5 mm{sup 2}. We show how the optical properties change with thickness, including appearance of Fabry-Pérot type interference in thin membranes. The membranes have low Q-factors, which allow the platforms to counteract distortion during agitation and movement. Finally, we report on the physical characteristics showing sub-nm roughness and a homogenous strain profile throughout the freestanding layer, making the single crystal Ge membrane an excellent platform for further epitaxial growth or deposition of materials.

  20. Crystal growth of CVD diamond and some of its peculiarities

    CERN Document Server

    Piekarczyk, W

    1999-01-01

    Experiments demonstrate that CVD diamond can form in gas environments that are carbon undersaturated with respect to diamond. This fact is, among others, the most serious violation of principles of chemical thermodynamics. In this $9 paper it is shown that none of the principles is broken when CVD diamond formation is considered not a physical process consisting in growth of crystals but a chemical process consisting in accretion of macro-molecules of polycyclic $9 saturated hydrocarbons belonging to the family of organic compounds the smallest representatives of which are adamantane, diamantane, triamantane and so forth. Since the polymantane macro-molecules are in every respect identical with $9 diamond single crystals with hydrogen-terminated surfaces, the accretion of polymantane macro- molecules is a process completely equivalent to the growth of diamond crystals. However, the accretion of macro-molecules must be $9 described in a way different from that used to describe the growth of crystals because so...

  1. A concave photonic crystal waveguide with a corrugated surface for high-quality focusing

    Institute of Scientific and Technical Information of China (English)

    Hong Wu; Liyong Jiang; Haipeng Li; Wei Jia; Gaige Zheng; Haixia Qiang; Xiangyin Li

    2011-01-01

    @@ A concave two-dimensional (2D) photonic crystal waveguide (PCW) with corrugated surface is theoretically used as a focusing structure. To design this structure, a genetic algorithm is combined with the finite-difference time-domain method. For PCWs with different degrees of concaveness, the power reaches about 80% at different focusing points when the morphology of the concave surface is optimized. More importantly, the focusing location is easily controlled by changing the location of the detector placed in the output field.%A concave two-dimensional (2D) photonic crystal waveguide (PCW) with corrugated surface is theoretically used as a focusing structure. To design this structure, a genetic algorithm is combined with the finite-difference time-domain method. For PCWs with different degrees of concaveness, the power reaches about 80% at different focusing points when the morphology of the concave surface is optimized. More importantly, the focusing location is easily controlled by changing the location of the detector placed in the output field.

  2. Effects of AIN nucleation layer thickness on crystal quality of AIN grown by plasma-assisted molecular beam epitaxy

    Institute of Scientific and Technical Information of China (English)

    Ren Fan; Hao Zhi-Biao; Hu Jian-Nan; Zhang Chen; Luo Yi

    2010-01-01

    In this paper,the effects of thickness of AIN nucleation layer grown at high temperature on AIN epi-layer crystalline quality are investigated.Crack-free AIN samples with various nucleation thicknesses are grown on sapphire substrates by plasma-assisted molecular beam epitaxy.The AIN crystalline quality is analysed by transmission electron microscope and x-ray diffraction(XRD)rocking curves in both(002)and(102)planes.The surface profiles of nucleation layer with different thicknesses after in-situ annealing are also analysed by atomic force microscope.A critical nucleation thickness for realising high quality AIN films is found.When the nucleation thickness is above a certain value,the(102)XRD full width at half maximum(FWHM)of AIN bulk increases with nucleation thickness increasing,whereas the(002)XRD FWHM shows an opposite trend.These phenomena can be attributed to the characteristics of nucleation islands and the evolution of crystal grains during AIN main layer growth.

  3. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  4. High quality 2D crystals made by anodic bonding: a general technique for layered materials.

    Science.gov (United States)

    Gacem, Karim; Boukhicha, Mohamed; Chen, Zhesheng; Shukla, Abhay

    2012-12-21

    Anodic bonding of nanolayers is an easy technique based on a simple apparatus, which has already proven successful in application in the fabrication of high quality graphene. Here we demonstrate its extension to the fabrication of high quality nanolayers from several layered materials. The strengths of this technique are its high throughput rate and ease of application. All fabrication parameters are controllable and need to be determined carefully. We report optimal parameters found for nine layered materials. In general, using optimal parameters results in high quality 2D layers, in most cases much larger than those obtained by 'Scotch tape' microcleavage, with higher yields and which are easily transferable to other substrates. Moreover the samples obtained are clean and the good optical contrast of these layers on the glass substrate makes their identification very easy. This is thus the technique of choice for making nanolayers in the laboratory from any layered material.

  5. High quality 2D crystals made by anodic bonding: a general technique for layered materials

    Science.gov (United States)

    Gacem, Karim; Boukhicha, Mohamed; Chen, Zhesheng; Shukla, Abhay

    2012-12-01

    Anodic bonding of nanolayers is an easy technique based on a simple apparatus, which has already proven successful in application in the fabrication of high quality graphene. Here we demonstrate its extension to the fabrication of high quality nanolayers from several layered materials. The strengths of this technique are its high throughput rate and ease of application. All fabrication parameters are controllable and need to be determined carefully. We report optimal parameters found for nine layered materials. In general, using optimal parameters results in high quality 2D layers, in most cases much larger than those obtained by ‘Scotch tape’ microcleavage, with higher yields and which are easily transferable to other substrates. Moreover the samples obtained are clean and the good optical contrast of these layers on the glass substrate makes their identification very easy. This is thus the technique of choice for making nanolayers in the laboratory from any layered material.

  6. Planar ring-shaped phononic crystal anchoring boundaries for enhancing the quality factor of Lamb mode resonators

    Science.gov (United States)

    Binci, L.; Tu, C.; Zhu, H.; Lee, J. E.-Y.

    2016-11-01

    We report the use of planar ring-shaped phononic crystals (PnCs) as anchor boundaries of very-high-frequency band piezoelectric-on-silicon Lamb mode resonators for the purpose of enhancing their quality factor (Q). Here, we exploit the acoustic bandgap associated with the PnC anchoring boundaries to reduce acoustic energy leakage out of the micromechanical resonator. The proposed approach provides greater mechanical robustness (by merit of interlocking the cells in a matrix) and the possibility of electrical routing through the PnC cells. We experimentally show enhancements in Q by a factor of three using the proposed approach of hybridizing planar ring-shaped PnCs with micromechanical resonators. The effect of these PnCs on resonator Q is further corroborated by their effects in suppressing transmission when incorporated into a delay line.

  7. Strong optomechanical coupling in a slotted photonic crystal nanobeam cavity with an ultrahigh quality factor-to-mode volume ratio

    CERN Document Server

    Schneider, Katharina

    2016-01-01

    We describe the design, fabrication, and characterization of a one-dimensional silicon photonic crystal cavity in which a central slot is used to enhance the overlap between highly localized optical and mechanical modes. The optical mode has an extremely small mode volume of 0.017 $(\\lambda_{vac}/n)^3$, and an optomechanical vacuum coupling rate of 310 kHz is measured. With optical quality factors up to $1.2 \\cdot 10^5$, fabricated devices are in the resolved-sideband regime. The electric field has its maximum at the slot wall and couples to the in-plane breathing motion of the slot. The optomechanical coupling is thus dominated by the moving-boundary effect, which we simulate to be six times greater than the photoelastic effect, in contrast to most structures, where the photoelastic effect is often the primary coupling mechanism.

  8. High quality factor and high sensitivity chalcogenide 1D photonic crystal microbridge cavity for mid-infrared sensing

    Science.gov (United States)

    Xu, Peipeng; Yu, Zenghui; Shen, Xiang; Dai, Shixun

    2017-01-01

    We present and theoretically investigate a mid-infrared (mid-IR) optical sensor based on a Ge11.5As24Se64.5 one-dimensional photonic crystal microbridge cavity (PhC-MC). Optimizing the structure of the PhC-MC strongly confines the resonant mode field to the air region, thereby greatly enhancing the overlap and interaction of the light field and target analytes. A high calculated sensitivity (2280 nm per refractive index unit) is achieved with a resonant wavelength of 4132 nm. The figure of merit of the device for sensing is extremely high (929,750) because of the high quality factor and sensitivity of the cavity. The sensing part of the cavity is also small (50×3 μm2). The proposed PhC-MC can be an ideal platform for on-chip integrated mid-IR optical sensing.

  9. Heuristic modeling of macromolecule release from PLGA microspheres

    Directory of Open Access Journals (Sweden)

    Szlęk J

    2013-12-01

    Full Text Available Jakub Szlęk,1 Adam Pacławski,1 Raymond Lau,2 Renata Jachowicz,1 Aleksander Mendyk11Department of Pharmaceutical Technology and Biopharmaceutics, Jagiellonian University Medical College, Krakow, Poland; 2School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU, SingaporeAbstract: Dissolution of protein macromolecules from poly(lactic-co-glycolic acid (PLGA particles is a complex process and still not fully understood. As such, there are difficulties in obtaining a predictive model that could be of fundamental significance in design, development, and optimization for medical applications and toxicity evaluation of PLGA-based multiparticulate dosage form. In the present study, two models with comparable goodness of fit were proposed for the prediction of the macromolecule dissolution profile from PLGA micro- and nanoparticles. In both cases, heuristic techniques, such as artificial neural networks (ANNs, feature selection, and genetic programming were employed. Feature selection provided by fscaret package and sensitivity analysis performed by ANNs reduced the original input vector from a total of 300 input variables to 21, 17, 16, and eleven; to achieve a better insight into generalization error, two cut-off points for every method was proposed. The best ANNs model results were obtained by monotone multi-layer perceptron neural network (MON-MLP networks with a root-mean-square error (RMSE of 15.4, and the input vector consisted of eleven inputs. The complicated classical equation derived from a database consisting of 17 inputs was able to yield a better generalization error (RMSE of 14.3. The equation was characterized by four parameters, thus feasible (applicable to standard nonlinear regression techniques. Heuristic modeling led to the ANN model describing macromolecules release profiles from PLGA microspheres with good predictive efficiency. Moreover genetic programming technique resulted in classical equation with

  10. Bending dynamics of semi-flexible macromolecules in isotropic turbulence

    CERN Document Server

    Ali, Aamir; Vincenzi, Dario

    2014-01-01

    We study the Lagrangian dynamics of semi-flexible macromolecules in laminar as well as in homogeneous and isotropic turbulent flows by means of analytically solvable stochastic models and direct numerical simulations. The statistics of the bending angle is qualitatively different in laminar and turbulent flows and exhibits a strong dependence on the topology of the velocity field. In particular, in two-dimensional turbulence, particles are either found in a fully extended or in a fully folded configuration; in three dimensions, the predominant configuration is the fully extended one.

  11. Floating-zone growth and property characterizations of high-quality La2-xSrxCuO4 superconductor crystals

    Institute of Scientific and Technical Information of China (English)

    Shen Xiao-Li; Li Zheng-Cai; Shen Cai-Xia; Lu Wei; Dong Xiao-Li; Zhou Fang; Zhao Zhong-Xian

    2009-01-01

    We have grown underdoped (x = 0.11, 0.12) and optimally doped (x = 0.16) La2-xSrxCuO4 single crystals by the traveling-solvent floating-zone technique. In order to prepare good quality cuprate crystals, we have made much effort to optimize the preparation procedures. For example, we haveadopted the sol-gel route to prepare a highly fine and homogeneous La2-xSrxCuO4 precursor powder for fabricating a very dense ceramic feed rod used for the floating-zone growth, and we have also used quite a slow growth rate. The high quality of the grown crystals has been verified by double-crystal x-ray rocking curves, with the full-width-at-half-maximum being only 113-150 arcseconds, which are the best data reported so far for La2-xSrxCuO4 crystals. The superconducting critical temperatures of the grown crystals are 30, 31 and 38.5 K for x = 0.11, 0.12 and 0.16 samples, respectively, according to magnetic measurements.

  12. Arrangement of a nanostructure array to control equilibrium and nonequilibrium transports of macromolecules.

    Science.gov (United States)

    Yasui, Takao; Kaji, Noritada; Ogawa, Ryo; Hashioka, Shingi; Tokeshi, Manabu; Horiike, Yasuhiro; Baba, Yoshinobu

    2015-05-13

    Exploiting the nonequilibrium transport of macromolecules makes it possible to increase the separation speed without any loss of separation resolution. Here we report the arrangement of a nanostructure array in microchannels to control equilibrium and nonequilibrium transports of macromolecules. The direct observation and separation of macromolecules in the nanopillar array reported here are the first to reveal the nonequilibrium transport, which has a potential to overcome the intrinsic trade-off between the separation speed and resolution.

  13. Dual Use of Amphiphilic Macromolecules As Cholesterol Efflux Triggers and Inhibitors of Macrophage Athero-inflammation

    Science.gov (United States)

    Iverson, Nicole; Plourde, Nicole M.; Sparks, Sarah M.; Wang, Jinzhong; Patel, Ekta; Shah, Pratik; Lewis, Daniel R.; Zablocki, Kyle; Nackman, Gary B.; Uhrich, Kathryn E.; Moghe, Prabhas V.

    2011-01-01

    Activated vascular wall macrophages can rapidly internalize modified lipoproteins and escalate the growth of atherosclerotic plaques. This article proposes a biomaterials-based therapeutic intervention for depletion of non-regulated cholesterol accumulation and inhibition of inflammation of macrophages. Macromolecules with high scavenger receptor (SR)-binding activity were investigated for SR-mediated delivery of agonists to cholesterol-trafficking nuclear liver-X receptors. From a diverse feature space of a family of amphiphilic macromolecules of linear and aromatic mucic acid backbones modified with varied aliphatic chains and conjugated with differentially branched poly(ethylene glycol), a key molecule (carboxyl-terminated, C12-derivatized, linear mucic acid backbone) was selected for its ability to preferentially bind scavenger receptor A (SR-A) as the key target. At a basal level, this macromolecule suppressed the pro-inflammatory signaling of activated THP-1 macrophages while competitively lowering oxLDL uptake in vitro through scavenger receptor SRA-1 targeting. To further deplete intracellular cholesterol, the core macromolecule structure was exploited to solubilize a hydrophobic small molecule agonist for nuclear Liver-X Receptors, which regulate the efflux of intracellular cholesterol. The macromolecule-encapsulated agonist system was found to reduce oxLDL accumulation by 88% in vitro in comparison to controls. In vivo studies were designed to release the macromolecules (with or without encapsulated agonist) to injured carotid arteries within Sprague Dawley rats fed a high fat diet, conditions that yield enhanced cholesterol accumulation and macrophage recruitment. The macromolecules lowered intimal levels of accumulated cholesterol (50% for macromolecule alone; 70% for macromolecule-encapsulated agonist) and inhibited macrophage retention (92% for macromolecule; 96% for macromolecule-encapsulated agonist; 4 days) relative to non-treated controls. Thus

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lazzerini, Giovanni Mattia; Yacoot, Andrew [National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Paternò, Giuseppe Maria; Tregnago, Giulia; Cacialli, Franco [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom); Treat, Neil; Stingelin, Natalie [Department of Materials Science, Imperial College London, London SW7 2AZ (United Kingdom)

    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.

  16. Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

    Energy Technology Data Exchange (ETDEWEB)

    Chaikuad, Apirat, E-mail: apirat.chaikuad@sgc.ox.ac.uk [University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ (United Kingdom); Knapp, Stefan [University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ (United Kingdom); Johann Wolfgang Goethe-University, Building N240 Room 3.03, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany); Delft, Frank von, E-mail: apirat.chaikuad@sgc.ox.ac.uk [University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ (United Kingdom)

    2015-07-28

    An alternative strategy for PEG sampling is suggested through the use of four newly defined PEG smears to enhance chemical space in reduced screens with a benefit towards protein crystallization. The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.

  17. Selective extraction of proteins and other macromolecules from biological samples using molecular imprinted polymers.

    Science.gov (United States)

    Stevenson, Derek; El-Sharif, Hazim F; Reddy, Subrayal M

    2016-11-01

    The accurate determination of intact macromolecules in biological samples, such as blood, plasma, serum, urine, tissue and feces is a challenging problem. The increased interest in macromolecules both as candidate drugs and as biomarkers for diagnostic purposes means that new method development approaches are needed. This review charts developments in the use of molecularly imprinted polymers first for small-molecular-mass compounds then for proteins and other macromolecules. Examples of the development of molecularly imprinted polymers for macromolecules are highlighted. The two main application areas to date are sensors and separation science, particularly SPE. Examples include peptides and polypeptides, lysozyme, hemoglobin, ovalbumin, bovine serum albumin and viruses.

  18. Genetically targeted fluorogenic macromolecules for subcellular imaging and cellular perturbation.

    Science.gov (United States)

    Magenau, Andrew J D; Saurabh, Saumya; Andreko, Susan K; Telmer, Cheryl A; Schmidt, Brigitte F; Waggoner, Alan S; Bruchez, Marcel P

    2015-10-01

    The alteration of cellular functions by anchoring macromolecules to specified organelles may reveal a new area of therapeutic potential and clinical treatment. In this work, a unique phenotype was evoked by influencing cellular behavior through the modification of subcellular structures with genetically targetable macromolecules. These fluorogen-functionalized polymers, prepared via controlled radical polymerization, were capable of exclusively decorating actin, cytoplasmic, or nuclear compartments of living cells expressing localized fluorgen-activating proteins. The macromolecular fluorogens were optimized by establishing critical polymer architecture-biophysical property relationships which impacted binding rates, binding affinities, and the level of internalization. Specific labeling of subcellular structures was realized at nanomolar concentrations of polymer, in the absence of membrane permeabilization or transduction domains, and fluorogen-modified polymers were found to bind to protein intact after delivery to the cytosol. Cellular motility was found to be dependent on binding of macromolecular fluorogens to actin structures causing rapid cellular ruffling without migration. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Terahertz spectroscopy of dry, hydrated, and thermally denatured biological macromolecules

    Science.gov (United States)

    Lipscomb, Dawn; Echchgadda, Ibtissam; Ibey, Bennett L.; Beier, Hope; Thomas, Robert J.; Peralta, Xomalin; Wilmink, Gerald J.

    2012-03-01

    Terahertz time-domain spectroscopy (THz-TDS) is an effective technique to probe the intermolecular and collective vibrational modes of biological macromolecules at THz frequencies. To date, the vast majority of spectroscopic studies have been performed on dehydrated biomolecular samples. Given the fact that all biochemical processes occur in aqueous environments and water is required for proper protein folding and function, we hypothesize that valuable information can be gained from spectroscopic studies performed on hydrated biomolecules in their native conformation. In this study, we used a THz-TDS system that exploits photoconductive techniques for THz pulse generation and freespace electro-optical sampling approaches for detection. We used the THz spectrometer to measure the time-dependent electric field of THz waves upon interaction with water, phosphate buffered saline (PBS), and collagen gels. By comparing these waveforms with references, we simultaneously determined each sample's index of refraction (n) and absorption coefficients (μa) as a function of frequency. Our data show that the properties we measure for the water, PBS and collagen are comparable to those reported in the literature. In the future, we plan to examine the effect that both temperature and pH have on the optical properties of other biological macromolecules. Studies will also be performed to compare our results to those generated using molecular dynamics simulations.

  20. A Few Good Crystals Please

    Science.gov (United States)

    Judge, Russell A.; Snell, Edward H.

    1999-01-01

    Part of the challenge of macromolecular crystal growth for structure determination is obtaining an appropriate number of crystals with a crystal volume suitable for X-ray analysis. In this respect an understanding of the effect of solution conditions on macromolecule nucleation rates is advantageous. This study investigated the effects of solution conditions on the nucleation rate and final crystal size of two crystal systems; tetragonal lysozyme and glucose isomerase. Batch crystallization plates were prepared at given solution concentration and incubated at set temperatures over one week. The number of crystals per well with their size and axial ratios were recorded and correlated with solution conditions. Duplicate experiments indicate the reproducibility of the technique. Results for each system showing the effect of supersaturation, incubation temperature and solution pH on nucleation rates will be presented and discussed. In the case of lysozyme, having optimized solution conditions to produce an appropriate number of crystals of a suitable size, a batch of crystals were prepared under exactly the same conditions. Fifty of these crystals were analyzed by x-ray techniques. The results indicate that even under the same crystallization conditions, a marked variation in crystal properties exists.

  1. Origin and use of crystallization phase diagrams.

    Science.gov (United States)

    Rupp, Bernhard

    2015-03-01

    Crystallization phase diagrams are frequently used to conceptualize the phase relations and also the processes taking place during the crystallization of macromolecules. While a great deal of freedom is given in crystallization phase diagrams owing to a lack of specific knowledge about the actual phase boundaries and phase equilibria, crucial fundamental features of phase diagrams can be derived from thermodynamic first principles. Consequently, there are limits to what can be reasonably displayed in a phase diagram, and imagination may start to conflict with thermodynamic realities. Here, the commonly used `crystallization phase diagrams' are derived from thermodynamic excess properties and their limitations and appropriate use is discussed.

  2. Decades of Data: Extracting Trends from Microgravity Crystallization History

    Science.gov (United States)

    Judge, R. A.; Snell, E. H.; Kephart, R.; vanderWoerd, M.

    2004-01-01

    The reduced acceleration environment of an orbiting spacecraft has been proposed as an ideal environment for biological crystal growth as the first sounding rocket flight in 1981 many crystallization experiments have flown with some showing improvement and others not. To further explore macromolecule crystal improvement in microgravity we have accumulated data from published reports and reports submitted by 63 missions including the Space Shuttle program, unmanned satellites, the Russian Space Station MIR and sounding rocket experiments. While it is not at this point in time a comprehensive record of all flight crystallization experimental results, there is however sufficient information for emerging trends to be identified. In this study the effects of the acceleration environment, the techniques of crystallization, sample molecular weight and the response of individual macromolecules to microgravity crystallization will be investigated.

  3. CZT sensors for Computed Tomography: from crystal growth to image quality

    Science.gov (United States)

    Iniewski, K.

    2016-12-01

    Recent advances in Traveling Heater Method (THM) growth and device fabrication that require additional processing steps have enabled to dramatically improve hole transport properties and reduce polarization effects in Cadmium Zinc Telluride (CZT) material. As a result high flux operation of CZT sensors at rates in excess of 200 Mcps/mm2 is now possible and has enabled multiple medical imaging companies to start building prototype Computed Tomography (CT) scanners. CZT sensors are also finding new commercial applications in non-destructive testing (NDT) and baggage scanning. In order to prepare for high volume commercial production we are moving from individual tile processing to whole wafer processing using silicon methodologies, such as waxless processing, cassette based/touchless wafer handling. We have been developing parametric level screening at the wafer stage to ensure high wafer quality before detector fabrication in order to maximize production yields. These process improvements enable us, and other CZT manufacturers who pursue similar developments, to provide high volume production for photon counting applications in an economically feasible manner. CZT sensors are capable of delivering both high count rates and high-resolution spectroscopic performance, although it is challenging to achieve both of these attributes simultaneously. The paper discusses material challenges, detector design trade-offs and ASIC architectures required to build cost-effective CZT based detection systems. Photon counting ASICs are essential part of the integrated module platforms as charge-sensitive electronics needs to deal with charge-sharing and pile-up effects.

  4. Recent Advances in Non-Invasive Delivery of Macromolecules using Nanoparticulate Carriers System.

    Science.gov (United States)

    Shadab, Md; Haque, Shadabul; Sheshala, Ravi; Meng, Lim Wei; Meka, Venkata Srikanth; Ali, Javed

    2017-01-01

    The drug delivery of macromolecules such as proteins and peptides has become an important area of research and represents the fastest expanding share of the market for human medicines. The most common method for delivering macromolecules is parenterally. However parenteral administration of some therapeutic macromolecules has not been effective because of their rapid clearance from the body. As a result, most macromolecules are only therapeutically useful after multiple injections, which causes poor compliance and systemic side effects. Therefore, there is a need to improve delivery of therapeutic macromolecules to enable non-invasive delivery routes, less frequent dosing through controlled-release drug delivery, and improved drug targeting to increase efficacy and reduce side effects. Non-invasive administration routes such as intranasal, pulmonary, transdermal, ocular and oral delivery have been attempted intensively by formulating macromolecules into nanoparticulate carriers system such as polymeric and lipidic nanoparticles. This review discusses barriers to drug delivery and current formulation technologies to overcome the unfavorable properties of macromolecules via non-invasive delivery (mainly intranasal, pulmonary, transdermal oral and ocular) with a focus on nanoparticulate carrier systems. This review also provided a summary and discussion of recent data on non-invasive delivery of macromolecules using nanoparticulate formulations. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. The Origin and the Future of Macromolecule Ionization by Laser Irradiation

    Institute of Scientific and Technical Information of China (English)

    KoichiTanaka

    2004-01-01

    Starting in 1984,a Shimadzu Corporation Central Research Laboratory development team set about the challenge of developinng an instrument for analyzing macromolecules such as proteins. At the time, the conventional consensus among chemists was that, “laser ionization of macromolecules exceeding a molecular weight of 10,000 is imposible”. However, not being a chemist, I was unaware of this widelyheld belief.

  6. Organometallic macromolecules with piano stool coordination repeating units: chain configuration and stimulated solution behaviour.

    Science.gov (United States)

    Cao, Kai; Ward, Jonathan; Amos, Ryan C; Jeong, Moon Gon; Kim, Kyoung Taek; Gauthier, Mario; Foucher, Daniel; Wang, Xiaosong

    2014-09-11

    Theoretical calculations illustrate that organometallic macromolecules with piano stool coordination repeating units (Fe-acyl complex) adopt linear chain configuration with a P-Fe-C backbone surrounded by aromatic groups. The macromolecules show molecular weight-dependent and temperature stimulated solution behaviour in DMSO.

  7. The flavonoid herbacetin diglucoside as a constituent of the lignan macromolecule from flaxseed hulls

    NARCIS (Netherlands)

    Struijs, K.; Vincken, J.P.; Verhoef, R.P.; Oostveen, van W.H.M.; Voragen, A.G.J.; Gruppen, H.

    2007-01-01

    Lignans in flaxseed are known to be part of a macromolecule in which they are connected through the linker-molecule hydroxy-methyl-glutaric acid (HMGA). In this study, the lignan macromolecule was extracted from flaxseed hulls and degraded to its monomeric constituents by complete saponification. Be

  8. Covalent binding of foreign chemicals to tissue macromolecules. [Acetaminophen

    Energy Technology Data Exchange (ETDEWEB)

    Thorgeirsson, S.S.; Wirth, P.J.

    1977-03-01

    In vivo and in vitro covalent binding of foreign chemicals to tissue macromolecules via metabolic activation is described, using the analgesic acetaminophen as an example. Acetaminophen is metabolized through a variety of pathways. The arylating metabolite is formed by a cytochrome P-450 dependent N-hydroxylation process. The resulting hydroxamic acid is then conjugated with glutathione, and the resulting conjugate is subsequently excreted as the mercapturic acid in the urine. It is not until the glutathione concentration is reduced to about 20% of the initial concentration that covalent binding of acetaminophen to amino acids of proteins occurs and subsequent liver necrosis is seen. The extent of in vitro binding correlates with treatments that alter hepatic necrosis and in vivo binding, indicating that in vitro binding is a valid index of acetaminophen hepatotoxicity. A simple bacterial test system for detecting chemical carcinogens as mutagens is described.

  9. Novel macromolecules derived from coumarin: synthesis and antioxidant activity

    Science.gov (United States)

    Al-Amiery, Ahmed A.; Al-Majedy, Yasameen K.; Kadhum, Abdul Amir H.; Mohamad, Abu Bakar

    2015-07-01

    The rational design of 4-hydroxycoumarins with tailor-made antioxidant activities is required nowadays due to the wide variety of pharmacologically significant, structurally interesting of coumarins and researcher orientation toward green chemistry and natural products. A simple and unique coumarins have been achieved by reaction of 4-hydroxycoumarin with aromatic aldehyde accompanied with the creation of a macromolecules have 2-aminothiazolidin-4-one. The molecular structures of the compounds were characterized by the Fourier transformation infrared and Nuclear magnetic resonance spectroscopies, in addition to CHN analysis. The scavenging abilities of new compounds against stable DPPH radical (DPPH•) and hydrogen peroxide were done and the results show that the compounds exhibited high antioxidant activates.

  10. Surface induced self-organization of comb-like macromolecules

    Science.gov (United States)

    Popov, Konstantin I; Palyulin, Vladimir V; Möller, Martin; Khokhlov, Alexei R

    2011-01-01

    Summary We present a review of the theoretical and experimental evidence for the peculiar properties of comb copolymers, demonstrating the uniqueness of these materials among other polymer architectures. These special properties include an increase in stiffness upon increasing side-chain length, the spontaneous curvature of adsorbed combs, rod–globule transition, and specific intramolecular self-assembly. We also propose a theory of chemically heterogeneous surface nanopattern formation in ultrathin films of comblike macromolecules containing two different types (A and B) of incompatible side chains (so-called binary combs). Side chains of the binary combs are strongly adsorbed on a surface and segregated with respect to the backbone. The thickness of surface domains formed by the B side chains is controlled by the interaction with the substrate. We predict the stability of direct and inverse disc-, torus- and stripelike nanostructures. Phase diagrams of the film are constructed. PMID:22003463

  11. Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules.

    Science.gov (United States)

    Ottiger, M; Bax, A

    1998-10-01

    Weak alignment of solute molecules with the magnetic field can be achieved in a dilute liquid crystalline medium, consisting of an aqueous mixture of dimyristoyl-phosphatidylcholine (DMPC) and dihexanoyl-phosphatidylcholine (DHPC). For a certain range of molar ratios, DMPC and DHPC can form large, disc-shaped particles, commonly referred to as bicelles (Sanders and Schwonek, 1992), which cooperatively align in the magnetic field and induce a small degree of alignment on asymmetrically shaped solute molecules. As a result, dipolar couplings between pairs of 1H, 13C or 15N nuclei are no longer averaged to zero by rotational diffusion and they can be readily measured, providing valuable structural information. The stability of these liquid crystals and the degree of alignment of the solute molecules depend strongly on experimental variables such as the DMPC:DHPC ratio and concentration, the preparation protocol of the DMPC/DHPC mixtures, as well as salt, temperature, and pH. The lower temperature limit for which the liquid crystalline phase is stable can be reduced to 20 degrees C by using a ternary mixture of DHPC, DMPC, and 1-myristoyl-2-myristoleoyl-sn-glycero-3-phosphocholine, or a binary mixture of DHPC and ditridecanoyl-phosphatidylcholine. These issues are discussed, with an emphasis on the use of the medium for obtaining weak alignment of biological macromolecules.

  12. Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Ottiger, Marcel; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    1998-10-15

    Weak alignment of solute molecules with the magnetic field can be achieved in a dilute liquid crystalline medium, consisting of an aqueous mixture of dimyristoyl-phosphatidylcholine (DMPC) and dihexanoyl-phosphatidylcholine (DHPC). For a certain range of molar ratios, DMPC and DHPC can form large, disc-shaped particles, commonly referred to as bicelles (Sanders and Schwonek, 1992), which cooperatively align in the magnetic field and induce a small degree of alignment on asymmetrically shaped solute molecules. As a result, dipolar couplings between pairs of {sup 1}H, {sup 13}C or {sup 15}N nuclei are no longer averaged to zero by rotational diffusion and they can be readily measured, providing valuable structural information. The stability of these liquid crystals and the degree of alignment of the solute molecules depend strongly on experimental variables such as the DMPC:DHPC ratio and concentration, the preparation protocol of the DMPC/DHPC mixtures, as well as salt, temperature, and pH. The lower temperature limit for which the liquid crystalline phase is stable can be reduced to 20 deg. C by using a ternary mixture of DHPC, DMPC, and 1-myristoyl-2-myristoleoyl-sn-glycero-3-phosphocholine, or a binary mixture of DHPC and ditridecanoyl-phosphatidylcholine. These issues are discussed, with an emphasis on the use of the medium for obtaining weak alignment of biological macromolecules.

  13. Electron Microscopy and Image Processing: Essential Tools for Structural Analysis of Macromolecules.

    Science.gov (United States)

    Belnap, David M

    2015-11-02

    Macromolecular electron microscopy typically depicts the structures of macromolecular complexes ranging from ∼200 kDa to hundreds of MDa. The amount of specimen required, a few micrograms, is typically 100 to 1000 times less than needed for X-ray crystallography or nuclear magnetic resonance spectroscopy. Micrographs of frozen-hydrated (cryogenic) specimens portray native structures, but the original images are noisy. Computational averaging reduces noise, and three-dimensional reconstructions are calculated by combining different views of free-standing particles ("single-particle analysis"). Electron crystallography is used to characterize two-dimensional arrays of membrane proteins and very small three-dimensional crystals. Under favorable circumstances, near-atomic resolutions are achieved. For structures at somewhat lower resolution, pseudo-atomic models are obtained by fitting high-resolution components into the density. Time-resolved experiments describe dynamic processes. Electron tomography allows reconstruction of pleiomorphic complexes and subcellular structures and modeling of macromolecules in their cellular context. Significant information is also obtained from metal-coated and dehydrated specimens. Copyright © 2015 John Wiley & Sons, Inc.

  14. Role of macromolecules in the safety of use of body wash cosmetics.

    Science.gov (United States)

    Bujak, Tomasz; Wasilewski, Tomasz; Nizioł-Łukaszewska, Zofia

    2015-11-01

    One of the most challenging problems related to the use of surfactants in body wash cosmetics is their potential to cause skin irritations. Surfactants can bind with proteins, remove lipids from the epidermal surface, contribute to the disorganization of liquid crystal structures in the intercellular lipids, and interact with living skin cells. These processes can lead to skin irritations and allergic reactions, and impair the epidermal barrier function. The present study is an attempt to assess the effect of polymers and hydrolysed proteins present in the formulations of model body wash cosmetics on product properties. Special attention was given to the safety of use of this product type. The study examined three macromolecules: polyvinylpyrrolidone (PVP), hydrolysed wheat protein (HWP) and polyvinylpyrrolidone/hydrolysed wheat protein crosspolymer (PVP/HWP). The addition of the substances under study was found to improve the foaming properties of body wash cosmetics, increase their stability during storage, and contribute significantly to an improvement in the safety of product use by reducing the irritant potential. The strongest ability to reduce the skin irritation potential was determined for the formula enriched with the PVP/HWP crosspolymer.

  15. Supramolecular Chemistry and Mechanochemistry of Macromolecules: Recent Advances by Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Cheng, Bo; Cui, Shuxun

    2015-01-01

    Atomic force spectroscopy (AFM)-based single-molecule force spectroscopy (SMFS) was invented in the 1990s. Since then, SMFS has been developed into a powerful tool to study the inter- and intra-molecular interactions of macromolecules. Using SMFS, a number of problems in the field of supramolecular chemistry and mechanochemistry have been studied at the single-molecule level, which are not accessible by traditional ensemble characterization methods. In this review, the principles of SMFS are introduced, followed by the discussion of several problems of contemporary interest at the interface of supramolecular chemistry and mechanochemistry of macromolecules, including single-chain elasticity of macromolecules, interactions between water and macromolecules, interactions between macromolecules and solid surface, and the interactions in supramolecular polymers.

  16. Growth and characterization of large, high quality single crystal diamond substrates via microwave plasma assisted chemical vapor deposition

    Science.gov (United States)

    Nad, Shreya

    Single crystal diamond (SCD) substrates can be utilized in a wide range of applications. Important issues in the chemical vapor deposition (CVD) of such substrates include: shrinking of the SCD substrate area, stress and cracking, high defect density and hence low electronic quality and low optical quality due to high nitrogen impurities. The primary objective of this thesis is to begin to address these issues and to find possible solutions for enhancing the substrate dimensions and simultaneously improving the quality of the grown substrates. The deposition of SCD substrates is carried out in a microwave cavity plasma reactor via the microwave plasma assisted chemical vapor deposition technique. The operation of the reactor was first optimized to determine the safe and efficient operating regime. By adjusting the matching of the reactor cavity with the help of four internal tuning length variables, the system was further matched to operate at a maximum overall microwave coupling efficiency of ˜ 98%. Even with adjustments in the substrate holder position, the reactor remains well matched with a coupling efficiency of ˜ 95% indicating good experimental performance over a wide range of operating conditions. SCD substrates were synthesized at a high pressure of 240 Torr and with a high absorbed power density of 500 W/cm3. To counter the issue of shrinking substrate size during growth, the effect of different substrate holder designs was studied. An increase in the substrate dimensions (1.23 -- 2.5 times) after growth was achieved when the sides of the seeds were shielded from the intense microwave electromagnetic fields in a pocket holder design. Using such pocket holders, high growth rates of 16 -- 32 mum/hr were obtained for growth times of 8 -- 72 hours. The polycrystalline diamond rim deposition was minimized/eliminated from these growth runs, hence successfully enlarging the substrate size. Several synthesized CVD SCD substrates were laser cut and separated

  17. Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA

    Institute of Scientific and Technical Information of China (English)

    SALON; Jozef

    2010-01-01

    The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids.Selenium can serve as an excellent anomalous scattering center to solve the phase problem,which is one of the two major bottlenecks in macromolecule X-ray crystallography.The other major bottleneck is crystallization.It has been demonstrated that the incorporated selenium functionality at the 2′-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation.Furthermore,it was observed that the 2′-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality.Herein,we describe a convenient synthesis of the 2′-Se-adenosine phosphoramidite,and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2′-Se-A derivatization.The 3D structure of 2′-Se-A-DNA decamer 5′-GTACGCGT(2′-Se-A)C-3′2 was determined at 1.75 ? resolution,the 2′-Se-functionality points to the minor groove,and the Se-modified and native structures are virtually identical.Moreover,we have observed that the 2′-Se-A modification can greatly facilitate the crystal growth with high diffraction quality.In conjunction with the crystallization facilitation by the 2′-Se-U and 2′-Se-T,this novel observation on the 2′-Se-A functionality suggests that the 2′-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.

  18. Fabrication of high-quality colloidal photonic crystals with sharp band edges for ultrafast all-optical switching

    Institute of Scientific and Technical Information of China (English)

    Feng Tian-Hua; Dai Qiao-Feng; Wu Li-Jun; Guo Qi; Hu Wei; Lan Sheng

    2008-01-01

    Application of the pressure controlled isothermal heating vertical deposition method to the fabrication of colloidal photonic crystals is systematically investigated in this paper. The fabricated samples are characterized by scanning electron microscope and transmission spectrum. High-quality samples with large transmissions in the pass bands and the sharp band edges are obtained and the optimum growth condition is determined. For the best sample, the transmission in the pass bands approaches 0.9 while that in the band gap reaches 0.1. More importantly, the maximum differential transmission as high as 0.1/nm is achieved. In addition, it is found that the number of stacking layers does not increase linearly with concentration of PS spheres in a solution, and a gradual saturation occurs when the concentration of PS spheres exceeds 1.5 wt.%. The uniformity of the fabricated samples is examined by transmission measurements on areas with different sizes. Finally, the tolerance of the fabricated samples to baking was studied.

  19. Optical study on intrinsic exciton states in high-quality CH3NH3PbBr3 single crystals

    Science.gov (United States)

    Thu Ha Do, T.; Granados del Águila, A.; Cui, Chao; Xing, Jun; Ning, Zhijun; Xiong, Qihua

    2017-08-01

    Organolead halide perovskites have emerged as potential building blocks for photovoltaic and optoelectronic devices. Yet the underlying fundamental physics is not well understood. There is lack of agreement on the electronic band structures and binding energies of coupled electron-hole pairs (excitons), which drive the photophysical processes. In this work, we conducted temperature-dependent reflectance and photoluminescence experiments on high-quality CH3NH3PbBr3 single crystals. Two direct optical transitions corresponding to intrinsic free-excitons are clearly resolved, showing excellent consistence between the low-temperature (T =10 K) reflectance and photoluminescence spectra. Remarkably, the excitons have different binding energies and behave oppositely with temperature, suggesting distinctive origins. Moreover, the asymmetric photoluminescence profile is counterintuitively dominated by the high-energy exciton that is explained by a long relaxation time between levels and by the favorable generation rate of electron-hole pairs at the high-energy band. Our study opens access to the intrinsic properties of CH3NH3PbBr3 and sheds light to reconcile the large range of binding energies reported on these emergent direct band-gap semiconductors.

  20. [Role of rapid movement of spin labels in interpreting EPR spectra for spin-labelled macromolecules].

    Science.gov (United States)

    Nikol'skiĭ, D O; Timofeev, V P

    2003-01-01

    The method of spin labeling was used to monitor quick movements of side residues in protein monocrystals. The EPR spectra of monocrystals of spin-labeled lysozyme at different orientations of the tetrahonal crystal relative to the direction of the magnetic field were interpreted using the molecular dynamics method. A simple model was proposed, which enables one to calculate the trajectory of movements of the spin label by the molecular dynamic method over a relatively short period of time. The entire "frozen" protein molecule and a "defrozen" spin-labeled amino acid residue were considered in the framework of the model. To calculate the trajectories in vacuum, a model of spin-labeled lysozyme was constructed, and the parameters of force potentials for the atoms of the protein molecule and the spin label were specified. It follows from the calculations that the protein environment sterically hinders the range of eventual angular reorientations of the reporter NO-group of nitroxyl incorporated into the spin label, thereby affecting the shape of the EPR spectrum. However, the scatter in the positions of the reporter group in the angular space turned out to correspond to the Gauss distribution. Using the atomic coordinates of the spin label, obtained in a chosen time interval by the method of molecular dynamics, and taking into account the distribution of the states of the spin label in the ensemble of spin-labeled macromolecules in the crystal, we simulated the EPR spectra of monocrystals of spin-labeled lysozyme. The theoretical EPR spectra coincide well with the experimental.

  1. Rappertk: a versatile engine for discrete restraint-based conformational sampling of macromolecules

    Directory of Open Access Journals (Sweden)

    Karmali Anjum M

    2007-03-01

    Full Text Available Abstract Background Macromolecular structures are modeled by conformational optimization within experimental and knowledge-based restraints. Discrete restraint-based sampling generates high-quality structures within these restraints and facilitates further refinement in a continuous all-atom energy landscape. This approach has been used successfully for protein loop modeling, comparative modeling and electron density fitting in X-ray crystallography. Results Here we present a software toolkit (Rappertk which generalizes discrete restraint-based sampling for use in structural biology. Modular design and multi-layered architecture enables Rappertk to sample conformations of any macromolecule at many levels of detail and within a variety of experimental restraints. Performance against a Cα-tracing benchmark shows that the efficiency has not suffered despite the overhead required by this flexibility. We demonstrate the toolkit's capabilities by building high-quality β-sheets and by introducing restraint-driven sampling. RNA sampling is demonstrated by rebuilding a protein-RNA interface. Ability to construct arbitrary ligands is used in sampling protein-ligand interfaces within electron density. Finally, secondary structure and shape information derived from EM are combined to generate multiple conformations of a protein consistent with the observed density. Conclusion Through its modular design and ease of use, Rappertk enables exploration of a wide variety of interesting avenues in structural biology. This toolkit, with illustrative examples, is freely available to academic users from http://www-cryst.bioc.cam.ac.uk/~swanand/mysite/rtk/index.html.

  2. Synthesis of biocontrol macromolecules by derivative of chitosan with surfactin and antifungal evaluation.

    Science.gov (United States)

    Yuan, Bo; Xu, Pei-Yuan; Zhang, Yue-Ji; Wang, Pei-Pei; Yu, Hong; Jiang, Ji-Hong

    2014-05-01

    A derivative of chitosan was prepared with chitosan and β-cyclodextrins, which was synthesized by the immobilization reaction, as a carrier to adsorb surfactin produced from Bacillus amyloliquefaciens and got biological macromolecules. The antifungal activity against three sapstain fungi by a combination of macromolecules was tested. The results showed that the macromolecules inhibited the mycelium growth of sapstain fungi Lasiodiplodia rubropurpurea, L. crassispora, and L. theobromae by about 73.22%, 76.72%, and 70.22%, respectively. The macromolecules were relatively thermally stable with more than 50% of the antifungal activity even after being held at 121°C for 30 min. Meanwhile, the activity of the macromolecules remained more than 55% at a pH value ranging from 4 to 12. The macromolecules were resistant to hydrolysis by most protein-denaturing detergents and other enzymes. The results indicated the macromolecules might provide an alternative bioresource for the bio-control of sapstain. Copyright © 2014. Published by Elsevier B.V.

  3. Transpapillary (Nipple) Delivery of Macromolecules to the Breast: Proof of Concept Study.

    Science.gov (United States)

    Dave, Kaushalkumar; Alsharif, Fahd M; Perumal, Omathanu

    2016-11-07

    Localized drug delivery to the breast can maximize drug concentration at the target site and minimize systemic drug distribution. To this end, the study explored the feasibility of delivering macromolecules to the breast through mammary papilla (nipple). The in vitro penetration of model macromolecules (inulin, dextran, ovalbumin, and bovine serum albumin) varying in molecular weight from 5 to 67 kDa was studied using excised porcine and human mammary papilla. The penetration of macromolecules decreased with increase in molecular weight. The penetration of the macromolecules was significantly higher through the mammary papilla in comparison to breast skin. In vitro penetration of the macromolecules was similar in human and porcine mammary papilla. Iontophoresis was used to enhance the transport of bovine serum albumin (BSA) through the mammary papilla. The flux and cumulative amount permeated was increased by 2- to 4-fold by iontophoresis. The macromolecules were transported through the ducts and the surrounding connective tissue in the mammary papilla. Overall, the results from this study for the first time demonstrate the feasibility of delivering macromolecules through the mammary papilla. These findings have implications for developing safe and effective localized therapeutic approaches for breast cancer.

  4. Control of Process Operations and Monitoring of Product Qualities through Generic Model-based Framework in Crystallization Processes

    DEFF Research Database (Denmark)

    Abdul Samad, Noor Asma Fazli Bin

    A generic and systematic model-based framework for the design of a process monitoring and control system to achieve the desired crystal size distribution (CSD) and crystal shape for a wide range of crystallization processes has been developed. This framework combines a generic multi......-dimensional to a twodimensional description; b) the systematic framework is used in a case study to design a monitoring and control (PAT) system for a potassium dichromate and KDP crystallization processes to achieve the desired target CSD respectively; and c) Based on the PAT system design in b), the application of uncertainty......-dimensional modelling framework, tools for design of set point profiles, for design of PAT (Process Analytical Technology) systems as well as option to perform the uncertainty and sensitivity analysis of the PAT system design. Through this framework, it is possible for a wide range of crystallization processes...

  5. Physical Delivery of Macromolecules using High-Aspect Ratio Nanostructured Materials.

    Science.gov (United States)

    Lee, Kunwoo; Lingampalli, Nithya; Pisano, Albert P; Murthy, Niren; So, Hongyun

    2015-10-28

    There is great need for the development of an efficient delivery method of macromolecules, including nucleic acids, proteins, and peptides, to cell cytoplasm without eliciting toxicity or changing cell behavior. High-aspect ratio nanomaterials have addressed many challenges present in conventional methods, such as cell membrane passage and endosomal degradation, and have shown the feasibility of efficient high-throughput macromolecule delivery with minimal perturbation of cells. This review describes the recent advances of in vitro and in vivo physical macromolecule delivery with high-aspect ratio nanostructured materials and summarizes the synthesis methods, material properties, relevant applications, and various potential directions.

  6. Channel-Forming Bacterial Toxins in Biosensing and Macromolecule Delivery

    Directory of Open Access Journals (Sweden)

    Philip A. Gurnev

    2014-08-01

    Full Text Available To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on “Intracellular Traffic and Transport of Bacterial Protein Toxins”, reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their “second life” in a variety of developing medical and technological applications.

  7. Channel-forming bacterial toxins in biosensing and macromolecule delivery.

    Science.gov (United States)

    Gurnev, Philip A; Nestorovich, Ekaterina M

    2014-08-21

    To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.

  8. Graphical Methods for Quantifying Macromolecules through Bright Field Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Hang; DeFilippis, Rosa Anna; Tlsty, Thea D.; Parvin, Bahram

    2008-08-14

    Bright ?eld imaging of biological samples stained with antibodies and/or special stains provides a rapid protocol for visualizing various macromolecules. However, this method of sample staining and imaging is rarely employed for direct quantitative analysis due to variations in sample fixations, ambiguities introduced by color composition, and the limited dynamic range of imaging instruments. We demonstrate that, through the decomposition of color signals, staining can be scored on a cell-by-cell basis. We have applied our method to Flbroblasts grown from histologically normal breast tissue biopsies obtained from two distinct populations. Initially, nuclear regions are segmented through conversion of color images into gray scale, and detection of dark elliptic features. Subsequently, the strength of staining is quanti?ed by a color decomposition model that is optimized by a graph cut algorithm. In rare cases where nuclear signal is significantly altered as a result of samplepreparation, nuclear segmentation can be validated and corrected. Finally, segmented stained patterns are associated with each nuclear region following region-based tessellation. Compared to classical non-negative matrix factorization, proposed method (i) improves color decomposition, (ii) has a better noise immunity, (iii) is more invariant to initial conditions, and (iv) has a superior computing performance

  9. Quantification of the Molecular Topology for Hierarchical Macromolecules

    Science.gov (United States)

    Beaucage, Gregory

    2009-03-01

    Hierarchical structures are often produced from ramified macromolecules such as comb, star, hyperbranched and dendritic polymers. We have recently derived a method for the description of complex molecular and nanostructural topologies based on a statistical analysis [1,2]. The method has been applied to a wide range of hierarchical materials from long chain branched polyolefins, hyperbranched polymers [3], star polymers, H-branched polymers to cyclics, biopolymers [4], and branched nanostructured aggregates. This method, when applied to neutron scattering data, yields the mole fraction of a structure involved in branching, the number of branch sites, the average branch length, and the number if inner chain segments. Further, quantitative measures of the convolution or tortuosity of the structure and the connectivity of the branching network can be made, opening a new window for our understanding of complex molecular topologies. This understanding has recently been applied to biological chain molecules to understand protein and RNA folding [4] for example as well as to aggregated, nanostructured, carbon soot. [0pt] [1] Beaucage, G, Phys. Rev. E 2004, 70, 031401. [2] Kulkarni, AS & Beaucage, G, J. Polym. Sci. Part B: Polym. Phys. 2006, 44, 1395. [3] Kulkarni, AS & Beaucage, G, Macromol. Rapid Comm. 2007, 28, 1312.?4) Beaucage, G, Biophysical J. 2008, 95, 503.

  10. The Circle of Dust: From Nanoparticles to Macromolecules and Beyond

    Science.gov (United States)

    Micelotta, E.; Jones, A.; Bocchio, M.; Cami, J.; Peeters, E.; Bernard-Salas, J.

    There is increasing observational evidence that a non-negligible fraction of the cosmic carbon is locked up into macromolecules and nanoparticles. Carbonaceous nanoparticles and Hydrogenated Amorphous Carbon (HAC) nanoparticles represent one of the main components of interstellar dust. HAC nanoparticles have been proposed as a viable carrier for the Unidentified InfraRed (UIR) bands, which dominate the mid-infrared spectrum of almost any astronomical object. Fullerene molecules C60 and C70 have been detected in various circumstellar and interstellar environments. We present some of our recent results about the evolution of such carbonaceous structures and the possible connections between each other. We show how photo-processing of HAC nanoparticles can lead to the formation of C60 and C70 in space. There the low density of the gas precludes the formation of fullerene materials following known vaporization or combustion synthesis routes, even on astronomical timescales. We then discuss the processing of small hydrocarbon dust by energetic ions and electrons under extreme conditions, e.g., in shocked regions. Finally, we derive the astrophysical implications of such processing in terms of the observed emission.

  11. Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

    Science.gov (United States)

    Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

    2002-01-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately

  12. Intramolecular Charge Transfer of Conjugated Liquid Crystal Ferrocene Macromolecules - Synthesis and Characterization

    Science.gov (United States)

    2016-04-12

    MX 8.  PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) AFOSR/SOARD U.S. Embassy Santiago Av. Andres... precipitate formation is observed. Then, the solution is filtered, washed with toluene and H2O and the precipitated is used without more purification...a precipitate that was filtered off and washed with toluene H2O to obtain a pale orange powder in 82 % yield. mp 210-220°C. 1H NMR (300 MHz, CDCl3

  13. COMPUTATIONAL METHODS FOR STUDYING THE INTERACTION BETWEEN POLYCYCLIC AROMATIC HYDROCARBONS AND BIOLOGICAL MACROMOLECULES

    Science.gov (United States)

    Computational Methods for Studying the Interaction between Polycyclic Aromatic Hydrocarbons and Biological Macromolecules .The mechanisms for the processes that result in significant biological activity of PAHs depend on the interaction of these molecules or their metabol...

  14. Electric Birefringence: A Simple Apparatus for Determining Physical Parameters of Macromolecules and Colloids.

    Science.gov (United States)

    Trimm, Harold H.; And Others

    1984-01-01

    Describes a birefringence apparatus that can be assembled for less than $100 and can be used to measure both the dimensions and dipole moments of many macromolecules. Details are given of the construction and manipulation of the apparatus. (JN)

  15. Development of modified release gliclazide biological macromolecules using natural biodegradable polymers.

    Science.gov (United States)

    Prajapati, Vipulkumar D; Mashru, Krupa H; Solanki, Himanshu K; Jani, Girish K

    2013-04-01

    Modified release biological macromolecules (beads) of gliclazide using sodium alginate combined with either gellan gum or pectin in different ratios were prepared by Ionotropic gelation method. Biological macromolecules were evaluated for different physico-chemical parameters. Increase in polymers proportion showed difficulty in production of biological macromolecules due to high viscosity of dispersion. As the polymer concentration increases, the swelling and entrapment efficiency of drug increased. Compared to all other batches and commercial modified release gliclazide tablet, formulated biological macromolecules of sodium alginate with pectin (2:1 ratio) and with gellan gum (6:0.75 ratio) exhibited spherical shape, biphasic in vitro release profile and initial high drug release followed by moderate release up to 12 h as matrix diffusion kinetics and Higuchi model as well as Korsmeyer model. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Effect of impurities and growth parameters on the quality of Tl3AsSe3 optical crystal

    Science.gov (United States)

    Singh, N. B.; Su, Ching-Hua; Arnold, Bradley; Choa, Fow-Sen; Nagaradona, Teja

    2016-10-01

    Thallium arsenic selenide (Tl3AsSe3) stoichiometric source materials suitable for crystal growth was synthesized in a horizontal furnace using purified parent components Tl, As and Se. Single crystal was grown using a two zone vertical Bridgman furnace using capillary for nucleation. A thermal gradient 18-20 K/cm and growth speed of 1 cm/day was used in vertical Bridgman furnace during crystal growth. Crystals were free from micro cracks and precipitates and demonstrated good fabricability. Results indicated that lower gradient and low growth rate are key to reduce thermal stresses in this ternary Tl-As-Se material system. Measured dielectric values in the range of 10 Hz to 100 KHz were almost constant indicating its suitability for applications in a range of frequency where constant dielectric is required.

  17. Calculations and surface quality measurements of high-asymmetry angle x-ray crystal monochromators for advanced x-ray imaging and metrological applications

    Science.gov (United States)

    Zápražný, Zdenko; Korytár, Dušan; Jergel, Matej; Šiffalovič, Peter; Dobročka, Edmund; Vagovič, Patrik; Ferrari, Claudio; Mikulík, Petr; Demydenko, Maksym; Mikloška, Marek

    2015-03-01

    We present the numerical optimization and the technological development progress of x-ray optics based on asymmetric germanium crystals. We show the results of several basic calculations of diffraction properties of germanium x-ray crystal monochromators and of an analyzer-based imaging method for various asymmetry factors using an x-ray energy range from 8 to 20 keV. The important parameter of highly asymmetric monochromators as image magnifiers or compressors is the crystal surface quality. We have applied several crystal surface finishing methods, including advanced nanomachining using single-point diamond turning (SPDT), conventional mechanical lapping, chemical polishing, and chemomechanical polishing, and we have evaluated these methods by means of atomic force microscopy, diffractometry, reciprocal space mapping, and others. Our goal is to exclude the chemical etching methods as the final processing technique because it causes surface undulations. The aim is to implement very precise deterministic methods with a control of surface roughness down to 0.1 nm. The smallest roughness (˜0.3 nm), best planarity, and absence of the subsurface damage were observed for the sample which was machined using an SPDT with a feed rate of 1 mm/min and was consequently polished using a fine polishing 15-min process with a solution containing SiO2 nanoparticles (20 nm).

  18. Insights and Lessons from a Scientific Conference on Non-Invasive Delivery of Macromolecules.

    Science.gov (United States)

    Savla, Ronak; Mrsny, Randall J; Park, Kinam; Aubert, Isabelle; Stamoran, Cornell

    2017-06-01

    A growing share of the pharmaceutical development pipeline is occupied by macromolecule drugs, which are primarily administered by injection. Despite decades of attempts, non-invasive delivery of macromolecules has seen only a few success stories. Potential benefits of non-invasive administration include better patient acceptance and adherence and potentially better efficacy and safety. Greater inter-disciplinary dialogue and collaboration are integral to realizing these benefits.

  19. A simple model for electrical charge in globular macromolecules and linear polyelectrolytes in solution

    Science.gov (United States)

    Krishnan, M.

    2017-05-01

    We present a model for calculating the net and effective electrical charge of globular macromolecules and linear polyelectrolytes such as proteins and DNA, given the concentration of monovalent salt and pH in solution. The calculation is based on a numerical solution of the non-linear Poisson-Boltzmann equation using a finite element discretized continuum approach. The model simultaneously addresses the phenomena of charge regulation and renormalization, both of which underpin the electrostatics of biomolecules in solution. We show that while charge regulation addresses the true electrical charge of a molecule arising from the acid-base equilibria of its ionizable groups, charge renormalization finds relevance in the context of a molecule's interaction with another charged entity. Writing this electrostatic interaction free energy in terms of a local electrical potential, we obtain an "interaction charge" for the molecule which we demonstrate agrees closely with the "effective charge" discussed in charge renormalization and counterion-condensation theories. The predictions of this model agree well with direct high-precision measurements of effective electrical charge of polyelectrolytes such as nucleic acids and disordered proteins in solution, without tunable parameters. Including the effective interior dielectric constant for compactly folded molecules as a tunable parameter, the model captures measurements of effective charge as well as published trends of pKa shifts in globular proteins. Our results suggest a straightforward general framework to model electrostatics in biomolecules in solution. In offering a platform that directly links theory and experiment, these calculations could foster a systematic understanding of the interrelationship between molecular 3D structure and conformation, electrical charge and electrostatic interactions in solution. The model could find particular relevance in situations where molecular crystal structures are not available or

  20. Surrogate Seeds For Growth Of Crystals

    Science.gov (United States)

    Shlichta, Paul J.

    1989-01-01

    Larger crystals of higher quality grown. Alternative method for starting growth of crystal involves use of seed crystal of different material instead of same material as solution. Intended for growing single-crystal proteins for experiments but applicable in general to growth of crystals from solutions and to growth of semiconductor or other crystals from melts.

  1. Sub-terahertz resonance spectroscopy of biological macromolecules and cells

    Science.gov (United States)

    Globus, Tatiana; Moyer, Aaron; Gelmont, Boris; Khromova, Tatyana; Sizov, Igor; Ferrance, Jerome

    2013-05-01

    Recently we introduced a Sub-THz spectroscopic system for characterizing vibrational resonance features from biological materials. This new, continuous-wave, frequency-domain spectroscopic sensor operates at room temperature between 315 and 480 GHz with spectral resolution of at least 1 GHz and utilizes the source and detector components from Virginia Diode, Inc. In this work we present experimental results and interpretation of spectroscopic signatures from bacterial cells and their biological macromolecule structural components. Transmission and absorption spectra of the bacterial protein thioredoxin, DNA and lyophilized cells of Escherichia coli (E. coli), as well as spores of Bacillus subtillis and B. atrophaeus have been characterized. Experimental results for biomolecules are compared with absorption spectra calculated using molecular dynamics simulation, and confirm the underlying physics for resonance spectroscopy based on interactions between THz radiation and vibrational modes or groups of modes of atomic motions. Such interactions result in multiple intense and narrow specific resonances in transmission/absorption spectra from nano-gram samples with spectral line widths as small as 3 GHz. The results of this study indicate diverse relaxation dynamic mechanisms relevant to sub-THz vibrational spectroscopy, including long-lasting processes. We demonstrate that high sensitivity in resolved specific absorption fingerprints provides conditions for reliable detection, identification and discrimination capability, to the level of strains of the same bacteria, and for monitoring interactions between biomaterials and reagents in near real-time. Additionally, it creates the basis for the development of new types of advanced biological sensors through integrating the developed system with a microfluidic platform for biomaterial samples.

  2. The flavonoid herbacetin diglucoside as a constituent of the lignan macromolecule from flaxseed hulls.

    Science.gov (United States)

    Struijs, Karin; Vincken, Jean-Paul; Verhoef, René; van Oostveen-van Casteren, Willemiek H M; Voragen, Alphons G J; Gruppen, Harry

    2007-04-01

    Lignans in flaxseed are known to be part of a macromolecule in which they are connected through the linker-molecule hydroxy-methyl-glutaric acid (HMGA). In this study, the lignan macromolecule was extracted from flaxseed hulls and degraded to its monomeric constituents by complete saponification. Besides secoisolariciresinol diglucoside (SDG), the phenolic compounds p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) were isolated, which was expected based on indications from the literature. Also the flavonoid herbacetin diglucoside (HDG) was found. The presence of HDG was confirmed by NMR following preparative RP-HPLC purification. Also the presence of the three other constituents (CouAG, FeAG and SDG) was confirmed by NMR. To prove that HDG is a substructure of the lignan macromolecule, the macromolecule was fragmented by partial saponification. A fragment consisting of HDG and HMGA was indicated. This fragment was isolated by preparative RP-HPLC and its identity was confirmed by NMR. It is concluded that the flavonoid HDG is a substructure of the lignan macromolecule from flaxseed hulls and that it is incorporated in the macromolecule via the same linker-molecule as SDG.

  3. PlaMoM: a comprehensive database compiles plant mobile macromolecules

    Science.gov (United States)

    Guan, Daogang; Yan, Bin; Thieme, Christoph; Hua, Jingmin; Zhu, Hailong; Boheler, Kenneth R.; Zhao, Zhongying; Kragler, Friedrich; Xia, Yiji; Zhang, Shoudong

    2017-01-01

    In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein–protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/. PMID:27924044

  4. High-quality β-Ga2O3 single crystals grown by edge-defined film-fed growth

    Science.gov (United States)

    Kuramata, Akito; Koshi, Kimiyoshi; Watanabe, Shinya; Yamaoka, Yu; Masui, Takekazu; Yamakoshi, Shigenobu

    2016-12-01

    β-Ga2O3 bulk crystals were grown by the edge-defined film-fed growth (EFG) process and the floating zone process. Semiconductor substrates containing no twin boundaries with sizes up to 4 in. in diameter were fabricated. It was found that Si was the main residual impurity in the EFG-grown crystals and that the effective donor concentration (N d - N a) of unintentionally doped crystals was governed by the Si concentration. Intentional n-type doping was shown to be possible. An etch pit observation revealed that the dislocation density was on the order of 103 cm-3. N d - N a for the samples annealed in nitrogen ambient was almost the same as the Si concentration, while for the samples annealed in oxygen ambient, it was around 1 × 1017 cm-3 and independent of the Si concentration.

  5. A closure relation to molecular theory of solvation for macromolecules

    Science.gov (United States)

    Kobryn, Alexander E.; Gusarov, Sergey; Kovalenko, Andriy

    2016-10-01

    We propose a closure to the integral equations of molecular theory of solvation, particularly suitable for polar and charged macromolecules in electrolyte solution. This includes such systems as oligomeric polyelectrolytes at a finite concentration in aqueous and various non-aqueous solutions, as well as drug-like compounds in solution. The new closure by Kobryn, Gusarov, and Kovalenko (KGK closure) imposes the mean spherical approximation (MSA) almost everywhere in the solvation shell but levels out the density distribution function to zero (with the continuity at joint boundaries) inside the repulsive core and in the spatial regions of strong density depletion emerging due to molecular associative interactions. Similarly to MSA, the KGK closure reduces the problem to a linear equation for the direct correlation function which is predefined analytically on most of the solvation shells and has to be determined numerically on a relatively small (three-dimensional) domain of strong depletion, typically within the repulsive core. The KGK closure leads to the solvation free energy in the form of the Gaussian fluctuation (GF) functional. We first test the performance of the KGK closure coupled to the reference interaction site model (RISM) integral equations on the examples of Lennard-Jones liquids, polar and nonpolar molecular solvents, including water, and aqueous solutions of simple ions. The solvation structure, solvation chemical potential, and compressibility obtained from RISM with the KGK closure favorably compare to the results of the hypernetted chain (HNC) and Kovalenko-Hirata (KH) closures, including their combination with the GF solvation free energy. We then use the KGK closure coupled to RISM to obtain the solvation structure and thermodynamics of oligomeric polyelectrolytes and drug-like compounds at a finite concentration in electrolyte solution, for which no convergence is obtained with other closures. For comparison, we calculate their solvation

  6. Regulation of synaptic vesicle docking by different classes of macromolecules in active zone material.

    Science.gov (United States)

    Szule, Joseph A; Harlow, Mark L; Jung, Jae Hoon; De-Miguel, Francisco F; Marshall, Robert M; McMahan, Uel J

    2012-01-01

    The docking of synaptic vesicles at active zones on the presynaptic plasma membrane of axon terminals is essential for their fusion with the membrane and exocytosis of their neurotransmitter to mediate synaptic impulse transmission. Dense networks of macromolecules, called active zone material, (AZM) are attached to the presynaptic membrane next to docked vesicles. Electron tomography has shown that some AZM macromolecules are connected to docked vesicles, leading to the suggestion that AZM is somehow involved in the docking process. We used electron tomography on the simply arranged active zones at frog neuromuscular junctions to characterize the connections of AZM to docked synaptic vesicles and to search for the establishment of such connections during vesicle docking. We show that each docked vesicle is connected to 10-15 AZM macromolecules, which fall into four classes based on several criteria including their position relative to the presynaptic membrane. In activated axon terminals fixed during replacement of docked vesicles by previously undocked vesicles, undocked vesicles near vacated docking sites on the presynaptic membrane have connections to the same classes of AZM macromolecules that are connected to docked vesicles in resting terminals. The number of classes and the total number of macromolecules to which the undocked vesicles are connected are inversely proportional to the vesicles' distance from the presynaptic membrane. We conclude that vesicle movement toward and maintenance at docking sites on the presynaptic membrane are directed by an orderly succession of stable interactions between the vesicles and distinct classes of AZM macromolecules positioned at different distances from the membrane. Establishing the number, arrangement and sequence of association of AZM macromolecules involved in vesicle docking provides an anatomical basis for testing and extending concepts of docking mechanisms provided by biochemistry.

  7. Surface characteristics and adhesion behavior of Escherichia coli O157:H7: role of extracellular macromolecules.

    Science.gov (United States)

    Kim, Hyunjung N; Hong, Yongsuk; Lee, Ilkeun; Bradford, Scott A; Walker, Sharon L

    2009-09-14

    Experiments were conducted using enterohemorrhagic Escherichia coli O157:H7 cells to investigate the influence of extracellular macromolecules on cell surface properties and adhesion behavior to quartz sand. Partial removal of the extracellular macromolecules on cells by a proteolytic enzyme (proteinase K) was confirmed using Fourier transform infrared spectroscopy analyses. The proteinase K treated cells exhibited more negative electrophoretic mobility (EPM) at an ionic strength (IS) macromolecules resulted in polymeric layers outside the cell surface that were less electrophoretically soft. The more negative mobility for the treated cells was likely due to the combined effects of a change in the distribution of functional groups and an increase in the charges per unit volume after enzyme treatment and not just removal of extracellular macromolecules. The proteolytic digestion of extracellular macromolecules led to a significant difference in the cell adhesion to quartz sand. The adhesion behavior for treated cells was consistent with DLVO theory and increased with IS due to less negativity in the EPM. In contrast, the adhesion behavior of untreated cells was much more complex and exhibited a maximum at IS = 1 mM. The treated cells exhibited less adhesion than the untreated cells when the IS or = 10 mM, a sudden decrease in the removal efficiency was observed only for the untreated cells even through EPM values were similar for both treated and untreated cells. This result suggested that an additional non-DLVO type interaction, electrosteric repulsion, occurred at higher IS (> or =10 mM in this study) for the untreated cells due to the presence of extracellular macromolecules that hindered cell adhesion to the quartz surface. This finding provides important insight into the role of macromolecule-induced E. coli O157:H7 interactions in aquatic environments.

  8. Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form

    Directory of Open Access Journals (Sweden)

    Boguslaw Stec

    2007-10-01

    Full Text Available We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCOfrom the red algae Galdieria Sulphuraria. The protein crystallized in two different crystalforms, the I422 crystal form being obtained from high salt and the P21 crystal form beingobtained from lower concentration of salt and PEG. We report here the crystallization,preliminary stages of structure determination and the detection of the structural phasetransition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzymebelongs to the hexadecameric class (L8S8 with an approximate molecular weight 0.6MDa.The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a singlehexadecamer per asymmetric unit. The preservation of diffraction power in a phasetransition for such a large macromolecule is rare.

  9. Colloidal properties of biomacromolecular solutions: Towards urate oxidase crystal design

    Science.gov (United States)

    Bonneté, Françoise

    2013-02-01

    Crystallization of biological macromolecules is governed by weak interaction forces, attractive and repulsive. Knowledge of solution properties, via second virial coefficient measurements, makes it possible to select physico-chemical parameters that govern and control phase diagrams and thus to grow crystals for specific applications (bio-crystallography or pharmaceutical processes). We highlight here with urate oxidase a salting-in effect that increases its solubility and the depletion effect of amphiphilic polymer, at a polymer concentration above its cmc, in order to grow diffracting crystals of urate oxidase. These two effects were used to grow crystals for high pressure crystallography and in a purification process.

  10. Analysis of an industrial production suspension of Bacillus lentus subtilisin crystals by powder diffraction: a powerful quality-control tool

    DEFF Research Database (Denmark)

    Frankær, Christian Grundahl; Moroz, Olga V.; Turkenburg, Johan P.

    2014-01-01

    A microcrystalline suspension of Bacillus lentus subtilisin (Savinase) produced during industrial large-scale production was analysed by X-ray powder diffraction (XRPD) and X-ray single-crystal diffraction (MX). XRPD established that the bulk microcrystal sample representative of the entire...

  11. Imaging Macromolecules with X-ray laser pulses

    CERN Document Server

    CERN. Geneva

    2017-01-01

    The short wavelength of X-rays allows us to resolve atoms, but in practise for biological materials the achievable resolution is limited by the destruction of the sample by the radiation that forms the image.  For over 100 years, the workaround to this problem of radiation damage has been to average signals from repeating copies of the object arranged in a large crystal.  It is now possible to overcome damage limits by using intense X-ray pulses that vaporise the sample, but which are short enough in duration to freeze any motion of the sample on the atomic scale.  With the advent of X-ray FELs we have been able to confirm this principle, and are now applying it to overcoming a major bottleneck for protein crystallography, which is the need for large well-diffracting crystals.  The intense pulses also open up opportunities to help solve the crystallographic phase problem.  In particular we have found that commonly-occurring disordered crystals that are usually not ...

  12. Comprehensive approach to intrinsic charge carrier mobility in conjugated organic molecules, macromolecules, and supramolecular architectures.

    Science.gov (United States)

    Saeki, Akinori; Koizumi, Yoshiko; Aida, Takuzo; Seki, Shu

    2012-08-21

    Si-based inorganic electronics have long dominated the semiconductor industry. However, in recent years conjugated polymers have attracted increasing attention because such systems are flexible and offer the potential for low-cost, large-area production via roll-to-roll processing. The state-of-the-art organic conjugated molecular crystals can exhibit charge carrier mobilities (μ) that nearly match or even exceed that of amorphous silicon (1-10 cm(2) V(-1) s(-1)). The mean free path of the charge carriers estimated from these mobilities corresponds to the typical intersite (intermolecular) hopping distances in conjugated organic materials, which strongly suggests that the conduction model for the electronic band structure only applies to μ > 1 cm(2) V(-1) s(-1) for the translational motion of the charge carriers. However, to analyze the transport mechanism in organic electronics, researchers conventionally use a disorder formalism, where μ is usually less than 1 cm(2) V(-1) s(-1) and dominated by impurities, disorders, or defects that disturb the long-range translational motion. In this Account, we discuss the relationship between the alternating-current and direct-current mobilities of charge carriers, using time-resolved microwave conductivity (TRMC) and other techniques including field-effect transistor, time-of-flight, and space-charge limited current. TRMC measures the nanometer-scale mobility of charge carriers under an oscillating microwave electric field with no contact between the semiconductors and the metals. This separation allows us to evaluate the intrinsic charge carrier mobility with minimal trapping effects. We review a wide variety of organic electronics in terms of their charge carrier mobilities, and we describe recent studies of macromolecules, molecular crystals, and supramolecular architecture. For example, a rigid poly(phenylene-co-ethynylene) included in permethylated cyclodextrin shows a high intramolecular hole mobility of 0.5 cm(2) V

  13. Solution-Based High-Density Arrays of Dielectric Microsphere Structures for Improved Crystal Quality of III-Nitride Layers on Si Substrates

    Directory of Open Access Journals (Sweden)

    Ho-Jun Lee

    2015-01-01

    Full Text Available The recent development of dielectric microsphere lithography has been able to open up new means of performing simple and easy patterning on the semiconductor surfaces. Here, we report uniform and high-density arrays of microspheres using a solution-based spin-coating method. The arrays of microspheres were used for etching mask to form the arrays of III-nitride microrods. By regrowing GaN layer on the microrod structures, high-quality GaN layer was achieved in terms of surface morphology as well as XRD characterization. To apply the advantages such as improved crystal quality and light extraction enhancement, light-emitting diodes (LEDs were grown and then fabricated. The regrown LEDs with microspheres showed much improved optical output power and forward voltage characteristics in the same current injection. Therefore, we believe that this approach is quite useful for the development of high efficiency LEDs for future lighting.

  14. Assessing the quality of x-ray optic surfaces of Si crystals cut by diamond-wire and rotating-blade sawing techniques.

    Energy Technology Data Exchange (ETDEWEB)

    Wieczorek, M.; Huang, X.; Maj, J.; Conley, R.; Qian, J.; Macrander, A.; Christensen, C.; Hodsden, J.; Khachatryan, R. (X-Ray Science Division); (Diamondwire Technology)

    2008-01-01

    The next generation of X-ray diffraction optics will benefit from crystal surfaces with very high quality (extremely flat and strain-free), but knowledge on how to achieve such surfaces and how surface imperfections affect the diffraction properties is sparse in the literature. As a first step to initialize a systematic study on this topic, we evaluate in this paper the surface quality of two Si (111) wafers cut by a diamond-wire saw and a rotating blade saw, respectively. We concentrate on revealing lattice strains induced by the two cutting methods and on strain evolution during three rounds of chemical etching (without polishing). The measurements also provide some important clues as to how surface roughness affects rocking curve widths and other diffraction properties.

  15. Assessment of permeability barriers to macromolecules in the rodent endometrium at the onset of implantation.

    Science.gov (United States)

    Bany, Brent M; Hamilton, G Scot

    2011-01-01

    In rodents, embryo implantation is an invasive process, which begins with its attachment to the uterine wall and culminates in the formation of the definitive placenta several days later. It is critical that the endometrium provide a supportive environment for the implanting embryo during this process, as the placenta is not yet established. The concept of changing permeability barriers to macromolecules between different extracellular compartments in the rodent uterus at the onset of implantation has been established. This chapter provides protocols that can be used to assess this changing permeability barrier and the associated redistribution of macromolecules during the early phases of implantation in rodents. An increased permeability of the endometrial vasculature to plasma proteins occurs in areas adjacent to the implanting blastocyst. In addition, alterations in the extracellular matrix enhance the accumulation of fluid and extravasated macromolecules. We describe several protocols proven to be effective in studying and quantifying early vascular and extravascular responses to natural and artificial "implantation stimuli." The first three protocols represent qualitative and quantitative methods to assess the early endometrial "vascular permeability" response. On the contrary, the fourth protocol addresses the onset of decidualization and the arising permeability barrier, which restricts the movement of macromolecules through the extracellular space. This barrier is believed to provide transient protection for the implanting embryo against potentially harmful maternal serum proteins. This protocol describes assessment of resistance of the primary decidual zone to the movement of macromolecules across the compartments of the extracellular space.

  16. Nanoscale amphiphilic macromolecules as lipoprotein inhibitors: the role of charge and architecture

    Science.gov (United States)

    Wang, Jinzhong; Plourde, Nicole M; Iverson, Nicole; Moghe, Prabhas V; Uhrich, Kathryn E

    2007-01-01

    A series of novel amphiphilic macromolecules composed of alkyl chains as the hydrophobic block and poly(ethylene glycol) as the hydrophilic block were designed to inhibit highly oxidized low density lipoprotein (hoxLDL) uptake by synthesizing macromolecules with negatively charged moieties (ie, carboxylic acids) located in the two different blocks. The macromolecules have molecular weights around 5,500 g/mol, form micelles in aqueous solution with an average size of 20–35 nm, and display critical micelle concentration values as low as 10−7 M. Their charge densities and hydrodynamic size in physiological buffer solutions correlated with the hydrophobic/hydrophilic block location and quantity of the carboxylate groups. Generally, carboxylate groups located in the hydrophobic block destabilize micelle formation more than carboxylate groups in the hydrophilic block. Although all amphiphilic macromolecules inhibited unregulated uptake of hoxLDL by macrophages, inhibition efficiency was influenced by the quantity and location of the negatively charged-carboxylate on the macromolecules. Notably, negative charge is not the sole factor in reducing hoxLDL uptake. The combination of smaller size, micellar stability and charge density is critical for inhibiting hoxLDL uptake by macrophages. PMID:18203436

  17. Active macromolecules of honey form colloidal particles essential for honey antibacterial activity and hydrogen peroxide production.

    Science.gov (United States)

    Brudzynski, Katrina; Miotto, Danielle; Kim, Linda; Sjaarda, Calvin; Maldonado-Alvarez, Liset; Fukś, Henryk

    2017-08-09

    Little is known about the global structure of honey and the arrangement of its main macromolecules. We hypothesized that the conditions in ripened honeys resemble macromolecular crowding in the cell and affect the concentration, reactivity, and conformation of honey macromolecules. Combined results from UV spectroscopy, DLS and SEM showed that the concentration of macromolecules was a determining factor in honey structure. The UV spectral scans in 200-400 nm visualized and allowed quantification of UV-absorbing compounds in the following order: dark > medium > light honeys (p macromolecules promoted their self-assembly to micron-size superstructures, visible in SEM as two-phase system consisting of dense globules distributed in sugar solution. These particles showed increased conformational stability upon dilution. At the threshold concentration, the system underwent phase transition with concomitant fragmentation of large micron-size particles to nanoparticles in hierarchical order. Honey two-phase conformation was an essential requirement for antibacterial activity and hydrogen peroxide production. These activities disappeared beyond the phase transition point. The realization that active macromolecules of honey are arranged into compact, stable multicomponent assemblies with colloidal properties reframes our view on global structure of honey and emerges as a key property to be considered in investigating its biological activity.

  18. Receptor-mediated endocytosis of macromolecules and strategy to enhance their transport in alveolar epithelial cells.

    Science.gov (United States)

    Takano, Mikihisa; Kawami, Masashi; Aoki, Ayako; Yumoto, Ryoko

    2015-05-01

    Pulmonary delivery is an attractive administration route for therapeutic proteins and peptides. In this context, endocytosis/transcytosis at the distal lung epithelial barrier is an important process in the pulmonary absorption of therapeutic macromolecules. The alveolar epithelium is comprised of type I and type II cells. Understanding the transport mechanisms in these cells is essential for the development of efficient pulmonary delivery systems of therapeutic macromolecules. Endocytic pathways for albumin and insulin in alveolar epithelial cells and possible receptors for the endocytosis are discussed. Strategies to enhance the endocytosis and pulmonary absorption of macromolecules are also discussed, by focusing on the effects of cationic poly(amino acid)s. Although the surface area occupied by type II cells in alveoli is much smaller than that covered by type I cells, type II cells may significantly contribute to the endocytosis/transcytosis of macromolecules such as albumin. Identification of the receptors involved in the cellular uptake of each macromolecule is prerequisite for the understanding and regulation of its transport into and across alveolar epithelial cells. Establishment of novel in-vitro culture cell models of type I and type II cells would be a great help for the future advance of this research field.

  19. Cathepsin B degradable star-shaped peptidic macromolecules for delivery of 2-methoxyestradiol.

    Science.gov (United States)

    Shankar, Ravi; Samykutty, Abhilash; Riggin, Corinne; Kannan, Sneha; Wenzel, Ursula; Kolhatkar, Rohit

    2013-10-07

    2-Methoxyestradiol (2ME), a natural metabolite of estradiol, has antiproliferative and antiangiogenic activity. However, its clinical success is limited due to poor water solubility and poor pharmacokinetic parameters suggesting the need for a delivery vehicle. In this study we evaluated cathepsin B degradable star-shaped peptidic macromolecules (SPMs) that can potentially be used to create higher generation and high molecular weight peptidic polymer as delivery vehicle of 2ME. Two peptidic macromolecules having positively charged amine (ASPM) or negatively charged carboxyl surface groups (CSPM) were synthesized and evaluated for their degradation in the presence of cathepsin B and stability in the presence of neutral or acidic buffer and serum. Both ASPM and CSPM degraded rapidly in the presence of cathepsin B. Both were stable in neutral and acidic buffer whereas only CSPM exhibited substantial stability in the presence of serum. Both macromolecules were nontoxic toward breast cancer cells whereas 2ME-containing macromolecules exhibited antiproliferative activity in the micromolar range. Overall, results from the current study indicate that tetrapeptide GFLG can be used to create star-shaped macromolecules that are degraded in the presence of cathepsin B and have the potential to be developed as delivery vehicles of 2ME.

  20. Locust bean gum in the development of sustained release mucoadhesive macromolecules of aceclofenac.

    Science.gov (United States)

    Prajapati, Vipul D; Jani, Girish K; Moradiya, Naresh G; Randeria, Narayan P; Maheriya, Pankaj M; Nagar, Bhanu J

    2014-11-26

    The study shows the development and optimization of locust bean gum (LBG)-alginate mucoadhesive macromolecules containing aceclofenac through ionotropic-gelation using 3(2) factorial design. The effect of amount of LBG and sodium alginate on drug entrapment efficiency (%DEE), % mucoadhesion at 8h (M8) and % in vitro drug release at 10h (%Q10h) were optimized. The percentage yield, average size and DEE of macromolecules were found within the range of 93.19 to 96.65%, 1.328 ± 0.11 to 1.428 ± 0.13 μm, and 56.37 to 68.54%, respectively. The macromolecules were also characterized by SEM, FTIR and DSC. The in vitro drug release from these macromolecules (84.95 ± 2.02 to 95.33 ± 1.56% at 10h) exhibited sustained release (first-order) pattern with super case-II transport mechanism. The swelling and mucoadhesivity of these macromolecules were affected by pH of the medium. The design established the role of derived polynomial equations and plots in predicting the values of dependent variables for the preparation and optimization. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Mechanoporation of living cells for delivery of macromolecules using nanoneedle array.

    Science.gov (United States)

    Matsumoto, Daisuke; Yamagishi, Ayana; Saito, Megumi; Sathuluri, Ramachandra Rao; Silberberg, Yaron R; Iwata, Futoshi; Kobayashi, Takeshi; Nakamura, Chikashi

    2016-12-01

    Efficient and rapid delivery of macromolecule probes, such as quenchbodies and other large biomarkers that cannot readily pass through the plasma membrane, is necessary for live-cell imaging and other intracellular analyses. We present here an alternative, simple method for delivery of macromolecules into live cells. In this method, which we term here mechanoporation, a nanoneedle array is used for making transient pores in the plasma membrane to allow access of desired macromolecules into thousands of live cells, simultaneously. This rapid, 3-step method facilitates an efficient delivery by adding macromolecules into the medium, inserting nanoneedles into the cells and oscillating the nanoneedle array, a process that takes no more than 5 min in total. In addition, we demonstrate here how this method can repeatedly and reproducibly deliver molecules into specifically-selected locations on a given cell culture dish. The results presented here show how this unique mechanoporation method enables rapid and high-throughput bio-macromolecule delivery and live-cell imaging. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  2. New design of nozzle structures and its effect on the surface and crystal qualities of thick GaN using a horizontal HVPE reactor

    Energy Technology Data Exchange (ETDEWEB)

    Wu Jiejun [Research Center for Wide-gap Semiconductors, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871 (China)], E-mail: wujiejun@opt.elec.mie-u.ac.jp; Zhao Lubing; Wen Dongyuan; Xu Ke; Yang Zhijian; Zhang Guoyi [Research Center for Wide-gap Semiconductors, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871 (China); Li Hui; Zuo Ran [School of Energy and Power Engineering, Jiangsu University, Zhenjiang 212013 (China)

    2009-03-15

    High-quality thick GaN films without cracks were achieved by using a new nozzle structure in the reactor grown by the hydride vapor phase epitaxy on sapphire substrates. Optical contrast microscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray double diffraction (XRD) and cathodoluminescence (CL) were carried out to reveal the surface, crystal and optical properties of the GaN epilayer. It was found that the nozzle structure in the reactor has a large effect on the growth rate, surface flat, crystal quality, and the uniformity of the growth. Compared with the old one, the new nozzle structure (denoted as multi-layers nozzle) can improve dramatically the properties of thick GaN. Mirror, colorless and flat GaN thick film was obtained and its (0 0 0 2) FWHM results were reduced from 1000 to 300 arcsec when the new nozzle was used. AFM result revealed a step flow growth mode for GaN layer with the new nozzle. Room-temperature CL spectra on the GaN films showed a strong near-band-edge peak for the new nozzle, but there is only weak emitting peak for the old nozzle. New nozzle structure can improve the uniform of flow field near the surface of substrates compared with the old one, which leads to the improvement of properties of GaN thick film by hydride vapor phase epitaxy (HVPE)

  3. The effect of composition on diffusion of macromolecules in a crowded environment.

    Science.gov (United States)

    Kondrat, Svyatoslav; Zimmermann, Olav; Wiechert, Wolfgang; von Lieres, Eric

    2015-05-28

    We study diffusion of macromolecules in a crowded cytoplasm-like environment, focusing on its dependence on composition and its crossover to the anomalous subdiffusion. The crossover and the diffusion itself depend on both the volume fraction and the relative concentration of macromolecules. In accordance with previous theoretical and experimental studies, diffusion slows down when the volume fraction increases. Contrary to expectations, however, the diffusion is also strongly dependent on the molecular composition. The crossover time decreases and diffusion slows down when the smaller macromolecules start to dominate. Interestingly, diffusion is faster in a cytoplasm-like (more polydisperse) system than it is in a two-component system, at comparable packing fractions, or even when the cytoplasm packing fraction is larger.

  4. Anisotropic diffusion of macromolecules in the contiguous nucleocytoplasmic fluid during eukaryotic cell division.

    Science.gov (United States)

    Pawar, Nisha; Donth, Claudia; Weiss, Matthias

    2014-08-18

    Character and rapidity of protein diffusion in intracellular fluids are key determinants of the dynamics and steady state of a plethora of biochemical reactions. So far, an anomalous diffusion in cytoplasmic fluids with viscoelastic and even glassy characteristics has been reported in a variety of organisms on several length scales and timescales. Here, we show that the contiguous fluid of former cytoplasm and nucleoplasm features an anisotropically varying diffusion of macromolecules during eukaryotic cell division. In metaphase, diffusion in the contiguous nucleocytoplasmic fluid appears less anomalous along the spindle axis as compared to perpendicular directions. As a consequence, the long-time diffusion of macromolecules preferentially points along the spindle axis, leading to prolonged residence of macromolecules in the spindle region. Based on our experimental data, we suggest that anisotropic diffusion facilitates the encounter and interaction of spindle-associated proteins, e.g., during the formation of a dynamic spindle matrix. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature.

    Science.gov (United States)

    Aggarwal, Ankush; May, Eric R; Brooks, Charles L; Klug, William S

    2016-01-01

    Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic thermal fluctuations obtained from molecular dynamics simulation at any coarse-grained scale using a potential of the mean-force approach. We present the results for a mutant of Sesbania mosaic virus capsid, where we calculate the elastic moduli at different scales and observe an apparent problem with the chosen reference configuration in some cases. We present a possible explanation using an elastic network model, where inducing random prestrain results in a similar behavior. This phenomenon provides a novel insight into the continuum nature of macromolecules and defines the limits on details that the elasticity theory can capture. Further investigation into prestrains could elucidate important aspects of conformational dynamics of macromolecules.

  6. Scalable synthesis of sequence-defined, unimolecular macromolecules by Flow-IEG.

    Science.gov (United States)

    Leibfarth, Frank A; Johnson, Jeremiah A; Jamison, Timothy F

    2015-08-25

    We report a semiautomated synthesis of sequence and architecturally defined, unimolecular macromolecules through a marriage of multistep flow synthesis and iterative exponential growth (Flow-IEG). The Flow-IEG system performs three reactions and an in-line purification in a total residence time of under 10 min, effectively doubling the molecular weight of an oligomeric species in an uninterrupted reaction sequence. Further iterations using the Flow-IEG system enable an exponential increase in molecular weight. Incorporating a variety of monomer structures and branching units provides control over polymer sequence and architecture. The synthesis of a uniform macromolecule with a molecular weight of 4,023 g/mol is demonstrated. The user-friendly nature, scalability, and modularity of Flow-IEG provide a general strategy for the automated synthesis of sequence-defined, unimolecular macromolecules. Flow-IEG is thus an enabling tool for theory validation, structure-property studies, and advanced applications in biotechnology and materials science.

  7. Improved microchip design and application for in situ transmission electron microscopy of macromolecules.

    Science.gov (United States)

    Dukes, Madeline J; Thomas, Rebecca; Damiano, John; Klein, Kate L; Balasubramaniam, Sharavanan; Kayandan, Sanem; Riffle, Judy S; Davis, Richey M; McDonald, Sarah M; Kelly, Deborah F

    2014-04-01

    Understanding the fundamental properties of macromolecules has enhanced the development of emerging technologies used to improve biomedical research. Currently, there is a critical need for innovative platforms that can illuminate the function of biomedical reagents in a native environment. To address this need, we have developed an in situ approach to visualize the dynamic behavior of biomedically relevant macromolecules at the nanoscale. Newly designed silicon nitride devices containing integrated "microwells" were used to enclose active macromolecular specimens in liquid for transmission electron microscopy imaging purposes.We were able to successfully examine novel magnetic resonance imaging contrast reagents, micelle suspensions, liposome carrier vehicles, and transcribing viral assemblies. With each specimen tested, the integrated microwells adequately maintained macromolecules in discrete local environments while enabling thin liquid layers to be produced.

  8. Equilibrium partitioning of macromolecules in confining geometries: Improved universality with a new molecular size parameter

    DEFF Research Database (Denmark)

    Wang, Yanwei; Peters, Günther H.J.; Hansen, Flemming Yssing

    2008-01-01

    We present a new framework for the description of macromolecules subject to confining geometries. The two main ingredients are a new computational method and the definition of a new molecular size parameter. The computational method, hereafter referred to the confinement analysis from bulk...... structures (CABS), allows the computation of equilibrium partition coefficients as a function of confinement size solely based on a single sampling of the configuration space of a macromolecule in bulk. Superior in computational speed to previous computational methods, CABS is capable of handling slits...... parameter for characterization of spatial confinement effects on macromolecules. Results for the equilibrium partition coefficient in the weak confinement regime depend only on the ratio ofR-s to the confinement size regardless of molecular details....

  9. Extracellular matrix macromolecules: potential tools and targets in cancer gene therapy.

    Science.gov (United States)

    Sainio, Annele; Järveläinen, Hannu

    2014-01-01

    Tumour cells create their own microenvironment where they closely interact with a variety of soluble and non-soluble molecules, different cells and numerous other components within the extracellular matrix (ECM). Interaction between tumour cells and the ECM is bidirectional leading to either progression or inhibition of tumourigenesis. Therefore, development of novel therapies targeted primarily to tumour microenvironment (TME) is highly rational. Here, we give a short overview of different macromolecules of the ECM and introduce mechanisms whereby they contribute to tumourigenesis within the TME. Furthermore, we present examples of individual ECM macromolecules as regulators of cell behaviour during tumourigenesis. Finally, we focus on novel strategies of using ECM macromolecules as tools or targets in cancer gene therapy in the future.

  10. Intracellular uptake of macromolecules by brain lymphatic endothelial cells during zebrafish embryonic development.

    Science.gov (United States)

    van Lessen, Max; Shibata-Germanos, Shannon; van Impel, Andreas; Hawkins, Thomas A; Rihel, Jason; Schulte-Merker, Stefan

    2017-05-12

    The lymphatic system controls fluid homeostasis and the clearance of macromolecules from interstitial compartments. In mammals brain lymphatics were only recently discovered, with significant implications for physiology and disease. We examined zebrafish for the presence of brain lymphatics and found loosely connected endothelial cells with lymphatic molecular signature covering parts of the brain without forming endothelial tubular structures. These brain lymphatic endothelial cells (BLECs) derive from venous endothelium, are distinct from macrophages, and are sensitive to loss of Vegfc. BLECs endocytose macromolecules in a selective manner, which can be blocked by injection of mannose receptor ligands. This first report on brain lymphatic endothelial cells in a vertebrate embryo identifies cells with unique features, including the uptake of macromolecules at a single cell level. Future studies will address whether this represents an uptake mechanism that is conserved in mammals and how these cells affect functions of the embryonic and adult brain.

  11. Silicification and biosilicification: The role of macromolecules in bioinspired silica synthesis

    Science.gov (United States)

    Patwardhan, Siddharth Vijay

    Diatoms, sponges and grasses are all known to produce ornate biogenic silica structures under ambient conditions. Some aspects of the molecular mechanism controlling biosilicification have recently been elucidated. The entrapment of the catalyzing/templating/scaffolding biomacromolecules enables them to be recovered by selective dissolution of biosilica. The proteins extracted from the diatom Cylindrotheca fusiformis (silaffins) and the sponge Tethya aurantia (silicateins) have been shown to precipitate silica from silica precursors in vitro. The identification of synthetic macromolecules that can act as catalysts/templates/scaffolds for silica formation gives exciting possibilities for bioinspired silica synthesis. Herein, the role of various synthetic (bio)macromolecules in silicification is studied. Attempts have also been made to understand the mechanism(s) governing (bio)macromolecule mediated (bio)silicification. Furthermore, the results and the understanding gained from various synthetic systems are used to demonstrate the potential of such bioinspired routes to develop new materials.

  12. Global analysis of fluorescence decays to probe the internal dynamics of fluorescently labeled macromolecules.

    Science.gov (United States)

    Duhamel, Jean

    2014-03-11

    The aim of this review is to introduce the reader first to the mathematical complexity associated with the analysis of fluorescence decays acquired with solutions of macromolecules labeled with a fluorophore and its quencher that are capable of interacting with each other via photophysical processes within the macromolecular volume, second to the experimental and mathematical approaches that have been proposed over the years to handle this mathematical complexity, and third to the information that one can expect to retrieve with respect to the internal dynamics of such fluorescently labeled macromolecules. In my view, the ideal fluorophore-quencher pair to use in studying the internal dynamics of fluorescently labeled macromolecules would involve a long-lived fluorophore, a fluorophore and a quencher that do not undergo energy migration, and a photophysical process that results in a change in fluorophore emission upon contact between the excited fluorophore and quencher. Pyrene, with its ability to form an excimer on contact between excited-state and ground-state species, happens to possess all of these properties. Although the concepts described in this review apply to any fluorophore and quencher pair sharing pyrene's exceptional photophysical properties, this review focuses on the study of pyrene-labeled macromolecules that have been characterized in great detail over the past 40 years and presents the main models that are being used today to analyze the fluorescence decays of pyrene-labeled macromolecules reliably. These models are based on Birks' scheme, the DMD model, the fluorescence blob model, and the model free analysis. The review also provides a step-by-step protocol that should enable the noneducated user to achieve a successful decay analysis exempt of artifacts. Finally, some examples of studies of pyrene-labeled macromolecules are also presented to illustrate the different types of information that can be retrieved from these fluorescence decay

  13. PlaMoM: a comprehensive database compiles plant mobile macromolecules.

    Science.gov (United States)

    Guan, Daogang; Yan, Bin; Thieme, Christoph; Hua, Jingmin; Zhu, Hailong; Boheler, Kenneth R; Zhao, Zhongying; Kragler, Friedrich; Xia, Yiji; Zhang, Shoudong

    2017-01-04

    In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein-protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Hydrodynamic Forces on Macromolecules Protruding from Lipid Bilayers Due to External Liquid Flows.

    Science.gov (United States)

    Jönsson, Peter; Jönsson, Bengt

    2015-11-24

    It has previously been observed that an externally applied hydrodynamic shear flow above a fluid lipid bilayer can change the local concentration of macromolecules that are associated with the lipid bilayer. The external liquid flow results in a hydrodynamic force on molecules protruding from the lipid bilayer, causing them to move in the direction of the flow. However, there has been no quantitative study about the magnitude of these forces. We here use finite element simulations to investigate how the magnitude of the external hydrodynamic forces varies with the size and shape of the studied macromolecule. The simulations show that the hydrodynamic force is proportional to the effective hydrodynamic area of the studied molecule, Ahydro, multiplied by the mean hydrodynamic shear stress acting on the membrane surface, σhydro. The parameter Ahydro depends on the size and shape of the studied macromolecule above the lipid bilayer and scales with the cross-sectional area of the molecule. We also investigate how hydrodynamic shielding from other surrounding macromolecules decreases Ahydro when the surface coverage of the shielding macromolecules increases. Experiments where the protein streptavidin is anchored to a supported lipid bilayer on the floor of a microfluidic channel were finally performed at three different surface concentrations, Φ = 1%, 6%, and 10%, where the protein is being moved relative to the lipid bilayer by a liquid flow through the channel. From photobleaching measurements of fluorescently labeled streptavidin we found the experimental drift data to be within good accuracy of the simulated results, less than 12% difference, indicating the validity of the results obtained from the simulations. In addition to giving a deeper insight into how a liquid flow can affect membrane-associated molecules in a lipid bilayer, we also see an interesting potential of using hydrodynamic flow experiments together with the obtained results to study the size and

  15. Synthesis and Characterization of a Chondroitin Sulfate Based Hybrid Bio/Synthetic Biomimetic Aggrecan Macromolecule

    Science.gov (United States)

    Sarkar, Sumona

    Lower back pain resulting from intervertebral disc degeneration is one of the leading musculoskeletal disorders confronting our health system. In order to mechanically stabilize the disc early in the degenerative cascade and prevent the need for spinal fusion surgeries, we have proposed the development of a hybrid-bio/synthetic biomimetic proteoglycan macromolecule for injection into the disc in the early stages of degeneration. The goal of this thesis was to incorporate natural chondroitin sulfate (CS) chains into bottle brush polymer synthesis strategies for the fabrication of CS-macromolecules which mimic the proteoglycan structure and function while resisting enzymatic degradation. Both the "grafting-to" and "grafting-through" techniques of bottle brush synthesis were explored. CS was immobilized via a terminal primary amine onto a model polymeric backbone (polyacrylic acid) for investigation of the "grafting-to" strategy and an epoxy-amine step-growth polymerization technique was utilized for the "grafting-through" synthesis of CS-macromolecules with polyethylene glycol backbone segments. Incorporation of a synthetic polymeric backbone at the terminal amine of CS was confirmed via biochemical assays, 1H-NMR and FTIR spectroscopy, and CS-macromolecule size was demonstrated to be higher than that of natural CS via gel permeation chromatography, transmission electron microscopy and viscosity measurements. Further analysis of CS-macromolecule functionality indicated maintenance of natural CS properties such as high fixed charge density, high osmotic potential and low cytotoxicity with nucleus pulposus cells. These studies are the first attempt at the incorporation of natural CS into biomimetic bottle brush structures. CS-macromolecules synthesized via the methods developed in these studies may be utilized in the treatment and prevention of debilitating back pain as well as act as mimetics for other proteoglycans implicated in cartilage, heart valve, and nervous

  16. Crystallization Growth of Single Crystal Cu by ContinuousCasting

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Crystallization growth of single-crystal Cu by continuous casting has been investigated using selfdesigned horizontal continuous casting equipment and XRD. Experimental results showed that the crystallization plane of (311), (220) and (111) were eliminated sequentially in evolutionary process. The final growth plane of crystal was (200), the direction of crystallization was [100],the growth direction of both sides of the rod inclined to axis, and the degree of deviation of direction [100] from the crystal axis was less than 10. In order to produce high quality single crystal, the solid-liquid interface morphology must be smooth, even be planar.

  17. "Bio"-macromolecules: polymer-protein conjugates as emerging scaffolds for therapeutics.

    Science.gov (United States)

    Borchmann, Dorothee E; Carberry, Tom P; Weck, Marcus

    2014-01-01

    Polymer-protein conjugates are biohybrid macromolecules derived from covalently connecting synthetic polymers with polypeptides. The resulting materials combine the properties of both worlds: chemists can engineer polymers to stabilize proteins, to add functionality, or to enhance activity; whereas biochemists can exploit the specificity and complexity that Nature has bestowed upon its macromolecules. This has led to a wealth of applications, particularly within the realm of biomedicine. Polymer-protein conjugation has expanded to include scaffolds for drug delivery, tissue engineering, and microbial inhibitors. This feature article reflects upon recent developments in the field and discusses the applications of these hybrids from a biomaterials standpoint.

  18. Single molecule optical measurements of orientation and rotations of biological macromolecules

    Science.gov (United States)

    Shroder, Deborah Y.; Lippert, Lisa G.; Goldman, Yale E.

    2016-12-01

    Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

  19. Method for selective immobilization of macromolecules on self assembled monolayer surfaces

    Science.gov (United States)

    Laskin, Julia [Richland, WA; Wang, Peng [Billerica, MA

    2011-11-29

    Disclosed is a method for selective chemical binding and immobilization of macromolecules on solid supports in conjunction with self-assembled monolayer (SAM) surfaces. Immobilization involves selective binding of peptides and other macromolecules to SAM surfaces using reactive landing (RL) of mass-selected, gas phase ions. SAM surfaces provide a simple and convenient platform for tailoring chemical properties of a variety of substrates. The invention finds applications in biochemistry ranging from characterization of molecular recognition events at the amino acid level and identification of biologically active motifs in proteins, to development of novel biosensors and substrates for stimulated protein and cell adhesion.

  20. Click chemistry approach to functionalize two-dimensional macromolecules of graphene oxide nanosheets

    Institute of Scientific and Technical Information of China (English)

    Liang Kou; Hongkun He; Chao Gao

    2010-01-01

    A facile “click chemistry” approach to functionalize 2D macromolecules of graphene oxide nanosheets with poly (ethylene glycol) of different molecular weights, polystyrene, palmitic acid and various amino acids was presented. FTIR, TGA, Raman spectroscopy, XPS, XRD, TEM, AFM and SEM were utilized to characterize the products. High degree of functionalization was achieved on the flat surfaces of graphene oxide, affording polymer-grafted 2D brushes and amino acids-immobilized nanosheets, which show improved solubility in organic solvents. The click chemistry strategy reported herein provides a facile and general method for functionalization of graphene oxide with macromolecules and desired biomolecules.

  1. A new bead-spring model for simulation of semi-flexible macromolecules

    Science.gov (United States)

    Saadat, Amir; Khomami, Bamin

    2016-11-01

    A bead-spring model for semi-flexible macromolecules is developed to overcome the deficiencies of the current coarse-grained bead-spring models. Specifically, model improvements are achieved through incorporation of a bending potential. The new model is designed to accurately describe the correlation along the backbone of the chain, segmental length, and force-extension behavior of the macromolecule even at the limit of 1 Kuhn step per spring. The relaxation time of different Rouse modes is used to demonstrate the capabilities of the new model in predicting chain dynamics.

  2. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    CERN Document Server

    Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai

    2010-01-01

    Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further spee...

  3. Induced liquid-crystalline ordering in solutions of stiff and flexible amphiphilic macromolecules: Effect of mixture composition.

    Science.gov (United States)

    Glagolev, Mikhail K; Vasilevskaya, Valentina V; Khokhlov, Alexei R

    2016-07-28

    Impact of mixture composition on self-organization in concentrated solutions of stiff helical and flexible macromolecules was studied by means of molecular dynamics simulation. The macromolecules were composed of identical amphiphilic monomer units but a fraction f of macromolecules had stiff helical backbones and the remaining chains were flexible. In poor solvents the compacted flexible macromolecules coexist with bundles or filament clusters from few intertwined stiff helical macromolecules. The increase of relative content f of helical macromolecules leads to increase of the length of helical clusters, to alignment of clusters with each other, and then to liquid-crystalline-like ordering along a single direction. The formation of filament clusters causes segregation of helical and flexible macromolecules and the alignment of the filaments induces effective liquid-like ordering of flexible macromolecules. A visual analysis and calculation of order parameter relaying the anisotropy of diffraction allow concluding that transition from disordered to liquid-crystalline state proceeds sharply at relatively low content of stiff components.

  4. Carbohydrate-Derived Amphiphilic Macromolecules: A Biophysical Structural Characterization and Analysis of Binding Behaviors to Model Membranes

    Science.gov (United States)

    Martin, Adriana A. T.; Tomasini, Michael; Kholodovych, Vladyslav; Gu, Li; Sommerfeld, Sven Daniel; Uhrich, Kathryn E.; Murthy, N. Sanjeeva; Welsh, William J.; Moghe, Prabhas V.

    2015-01-01

    The design and synthesis of enhanced membrane-intercalating biomaterials for drug delivery or vascular membrane targeting is currently challenged by the lack of screening and prediction tools. The present work demonstrates the generation of a Quantitative Structural Activity Relationship model (QSAR) to make a priori predictions. Amphiphilic macromolecules (AMs) “stealth lipids” built on aldaric and uronic acids frameworks attached to poly(ethylene glycol) (PEG) polymer tails were developed to form self-assembling micelles. In the present study, a defined set of novel AM structures were investigated in terms of their binding to lipid membrane bilayers using Quartz Crystal Microbalance with Dissipation (QCM-D) experiments coupled with computational coarse-grained molecular dynamics (CG MD) and all-atom MD (AA MD) simulations. The CG MD simulations capture the insertion dynamics of the AM lipophilic backbones into the lipid bilayer with the PEGylated tail directed into bulk water. QCM-D measurements with Voigt viscoelastic model analysis enabled the quantitation of the mass gain and rate of interaction between the AM and the lipid bilayer surface. Thus, this study yielded insights about variations in the functional activity of AM materials with minute compositional or stereochemical differences based on membrane binding, which has translational potential for transplanting these materials in vivo. More broadly, it demonstrates an integrated computational-experimental approach, which can offer a promising strategy for the in silico design and screening of therapeutic candidate materials. PMID:25855953

  5. Experimental and numerical study on growth of high-quality ZnO single-crystal microtubes by optical vapor supersaturated precipitation method

    Science.gov (United States)

    Wang, Qiang; Yan, Yinzhou; Zeng, Yong; Jiang, Yijian

    2017-06-01

    In this work, high-quality free-standing ZnO single-crystal microtubes with hexagonal cross-section were fabricated by an optical image furnace. Optical vapor supersaturated precipitation (OVSP) and axial photo-thermal-decomposition were proposed to interpret the microrods growth and microtubes formation, respectively. The maximum dimensions of the grown microtube were 5 mm in length, 100 μm in diameter and 1 μm in facet wall thickness. In our previous work, a new room-temperature photoluminescence (PL) peak ( 392 nm) of ZnO microtubes was attributed to VZn-related donor-acceptor-pairs (DAP) transition. This work further confirmed the VZn-related acceptors widely existing during ZnO microrods/ microtubes growth by OVSP. The effects of major growth parameters (e.g. lamp power, filament geometry and growth platform shape) on temperature field at the growth platform of precursor rod were studied by a finite element model as well. The lamp power of 65% (1500 W), thick single-filament and appropriate conical growth platform were optimized for a uniform temperature field to achieve consistent finish quality of microtubes and prevent twin-microtubes formation. This work would be beneficial for batch growth of the novel ZnO microtubes/microrods with high quality for a variety of applications.

  6. Effects of Several Natural Macromolecules on the Stability and Controlled Release Properties of Water-in-Oil-in-Water Emulsions.

    Science.gov (United States)

    Li, Jinlong; Shi, Yiheng; Zhu, Yunping; Teng, Chao; Li, Xiuting

    2016-05-18

    Water-in-oil-in-water (W/O/W) emulsions are effective vehicles for embedding application of active compounds but limited by their thermodynamic instability and rapid release properties. The present study added bovine serum albumin, whey protein isolate, whey protein hydrolysate, sodium caseinate, carboxymethylcellulose sodium, fish gelatin, apple pectin, gum arabic, ι-carrageenan, and hydroxypropyl chitosan separately to the internal or external aqueous phase to investigate their effects on the physical stabilities and controlled release properties of W/O/W emulsions. The effects of the natural macromolecules in the internal and external aqueous phases were different and depended upon the macromolecule structure and its mass fraction. The addition of the natural macromolecule strengthened the interfaces of emulsions, which improved the physical stability. The natural macromolecules that improved the stability often did not improve controlled release. Therefore, the balance between these properties needs to be considered when adding natural macromolecules to a W/O/W emulsion.

  7. Growth of High Quality Al-Doped CsLiB6O10 Crystals Using Cs2O-Li2O-MoO3 Fluxes

    Directory of Open Access Journals (Sweden)

    Xianchao Zhu

    2017-03-01

    Full Text Available Abstract: High quality and large size Al-doped CsLiB6O10 (CLBO single crystals have been successfully grown by top-seeded solution growth (TSSG technique using Cs2O–Li2O–MoO3 fluxes. The advantages of this newly developed flux system were investigated by viscosity measurements and growth experiments. Al-doped CLBO presents a very high transmittance in the visible region and the weak absorption values at 1064 nm along a and c axes are only 140 and 50 ppm/cm, respectively. The measured LIDT of Al-doped CLBO at λ = 1064 nm and τ = 5.0 ns is 5.10 GW/cm2. Moreover, Al-doped CLBO exhibits an apparent enhancement of the hygroscopic nature in contrast with the undoped crystal as determined by the humidity experiments. Finally, a high fourth harmonic generation (FHG conversion efficiency of 63% utilizing Al-doped CLBO has been achieved by a picosecond mode-locked Nd:YAG laser, the results also reveal that Al doping has no obvious impact on the FHG conversion efficiency.

  8. Synthesis and Characterization of Tailored Macromolecules via Stable Free Radical Polymerization Methodologies

    OpenAIRE

    2003-01-01

    The stable free radical polymerization methodology for production of controlled macromolecules was investigated using a novel monomer, 2-vinylnaphthalene. Initial polymerizations resulted in molecular weight distributions typical of conventional free radical polymerization techniques (>2.0). Manipulation of the initiator concentration and the molar ratio of initiator to nitroxide demonstrated no significant control over the resulting polymer products. Analysis of the polymerization kinetics...

  9. A novel method for imaging sites of paracellular passage of macromolecules in epithelial sheets.

    Science.gov (United States)

    Richter, Jan F; Schmauder, Ralf; Krug, Susanne M; Gebert, Andreas; Schumann, Michael

    2016-05-10

    Understanding the dynamics of intestinal barrier function is key to elucidating oral delivery routes of therapeutics as well as to understanding various diseases that involve the mucosal immune system. Passage of macromolecules across barrier-forming epithelia is classically analyzed by means of various tracer flux measurements. This approach averages over contributions from many cells and lacks labeling of passage-sites. Thus, abundance and nature of involved cells have remained unidentified. We present a novel method that allowed for optical analysis of passage of various macromolecules on large-scale and single-cell level. To achieve tracking of passage loci in epithelia at submicrometer resolution we used biotinylated and fluorescent macromolecules that bind to basolateral membranes pre-labeled with cell-adherent avidin. We applied this method to epithelial cell lines and isolated mucosae in order to 3-dimensionally determine barrier leak properties over time. Tracer passage was found in all epithelia examined. However, it was infrequent, strikingly inhomogeneous, depended on culture duration and tightness of the monolayer. Stimulating passage with barrier-perturbing agents increased the number of leaks exposition time-dependently in cell lines and explanted mucosae. After stepwise opening of the paracellular passage pathway, integrated tracer-signal measured by our assay strictly correlated to simultaneously performed standard fluxes. Thus, our assay allows for the study of transepithelial macromolecule passage in various physiological and pathological conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. New strategy to create ultra-thin surface layer of grafted amphiphilic macromolecules.

    Science.gov (United States)

    Lazutin, A A; Govorun, E N; Vasilevskaya, V V; Khokhlov, A R

    2015-05-14

    It was found first that macromolecules made of amphiphilic monomer units could form spontaneously an ultra-thin layer on the surface which the macromolecules are grafted to. The width of such layer is about double size of monomer unit consisting of hydrophilic A (repulsive) and hydrophobic (attractive) B beads. The hydrophilic A beads are connected in a polymer chain while hydrophobic B beads are attached to A beads of the backbone as side groups. Three characteristic regimes are distinguished. At low grafting density, the macromolecules form ultra-thin micelles of the shape changing with decrease of distance d between grafting points as following: circular micelles-prolonged micelles-inverse micelles-homogeneous bilayer. Those micelles have approximately constant height and specific top-down A-BB-A structure. At higher grafting density, the micelles start to appear above the single bilayer of amphiphilic macromolecules. The thickness of grafted layer in these cases is different in different regions of grafting surface. Only at rather high density of grafting, the height of macromolecular layer becomes uniform over the whole grafting surface. The study was performed by computer modeling experiments and confirmed in framework of analytical theory.

  11. Prospective frequency correction for macromolecule-suppressed GABA editing at 3T

    DEFF Research Database (Denmark)

    Edden, Richard A E; Oeltzschner, Georg; Harris, Ashley D

    2016-01-01

    PURPOSE: To investigate the effects of B0 field offsets and drift on macromolecule (MM)-suppressed GABA-editing experiments, and to implement and test a prospective correction scheme. "Symmetric" editing schemes are proposed to suppress unwanted coedited MM signals in GABA editing. MATERIALS...

  12. Stress growth and relaxation of dendritically branched macromolecules in shear and uniaxial extension

    DEFF Research Database (Denmark)

    Huang, Qian; Costanzo, S.; Das, C.

    2017-01-01

    of the remarkable properties of these highly branched macromolecules. In particular, we address three questions pertinent to the specific molecular structure: (i) is steady state attainable during uniaxial extension? (ii) what is the respective transient response in simple shear? and (iii) how does stress relax...

  13. A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components.

    Science.gov (United States)

    Barabash, Yu M; Lyamets, A K

    2016-12-01

    The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions [Formula: see text] is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

  14. Intermediate scattering function for macromolecules in solutions probed by neutron spin echo.

    Science.gov (United States)

    Liu, Yun

    2017-02-01

    The neutron-spin-echo method (NSE) is a powerful technique for studying internal dynamics of macromolecules in solutions because it can simultaneously probe length and time scales comparable to intramolecular density fluctuations of macromolecules. Recently, there has been increased, strong interest in studying protein internal motions using NSE. The coherent intermediate scattering function (ISF) measured by NSE depends on internal, rotational, and translational motions of macromolecules in solutions. It is thus critical, but highly nontrivial, to separate the internal motion from other motions in order to properly understand protein internal dynamics. Even though many experiments are performed at relatively high concentrations, current theories of calculating the ISF of concentrated protein solutions are either inaccurate or flawed by incorrect assumptions for realistic protein systems with anisotropic shapes. Here, a theoretical framework is developed to establish the quantitative relationship of different motions included in the ISF. This theory based on the dynamic decoupling approximation is applicable to a wide range of protein concentrations, including dilute cases. It is also, in general, useful for studying many other types of macromolecule systems studied by NSE.

  15. The spectral properties of DNA and RNA macromolecules at low temperatures: fundamental and applied aspects.

    Science.gov (United States)

    Yashchuk, Valeriy M; Kudrya, Vladislav Yu

    2017-01-18

    This paper summarizes the results of studies of the spectral properties-optical absorption, fluorescence and phosphorescence-of DNA and RNA macromolecules and synthetic poly-, oligo- and mono-nucleotides, which have been carried out in our laboratory. The system of first excited singlet and triplet energy levels for DNA and RNA is evaluated using low-temperature (4.2 K-77 K) luminescent measurements. The traps of the singlet and triplet electronic excitations in these compounds are identified. An important self-protection mechanism against photo-damage of DNA and RNA by UV photons or penetrative radiation based on the capture of triplet electronic-energy excitations by the most photostable centers-in DNA, the complex formed by neighboring adenosine (A) and thymidine (T) links; in RNA, the adenosine links-is described. It is confirmed that despite similarities in the chemical and partly energy structures DNA is more stable than RNA. The spectral manifestation of the telomeres (the important functional system) in DNA macromolecules is examined. The results obtained on telomere fragments provide the possibility of finding the configuration peculiarities of the triplet excitations traps in DNA macromolecules. The resulting spreading length of the migrating singlet (l s) and triplet (l t) excitations for DNA and RNA macromolecules are evaluated.

  16. Theory of Brushes Formed by Ψ-Shaped Macromolecules at Solid-Liquid Interfaces.

    Science.gov (United States)

    Zhulina, Ekaterina B; Leermakers, Frans A M; Borisov, Oleg V

    2015-06-16

    We present a theoretical analysis targeted to describe the structural properties of brushes formed by Ψ-shaped macromolecules tethered by terminal segment of stem to planar surface while exposing multiple free branches to the surrounding solution. We use an analytical self-consistent field approach based on the strong stretching approximation, and the assumption of Gaussian elasticity for linear chain fragments of the tethered macromolecules. The effect of weak and strong polydispersity of branches is analyzed. In the case of weakly polydisperse macromolecules, variations in length of branches lead to a more uniform polymer density distribution with slight increase in the brush thickness compared to the case of monodisperse chains with the same degree of polymerization. We demonstrate that in contrast to linear chains, strong polydispersity of Ψ-shaped macromolecules does not necessarily lead to strong perturbations in polymer density distribution. In particular, mixed brushes of the so-called "mirror" dendrons (in which number of stem monomers in one component coincides with number of monomers in a branch of the other component, and vice versa) give rise to a unified polymer density distribution with shape independent of the brush composition. The predictions of analytical theory are systematically compared to the results of numerical self-consistent field modeling based on the Scheutjens-Fleer approach.

  17. Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization

    Science.gov (United States)

    Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

    2008-01-01

    We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

  18. Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes.

    Science.gov (United States)

    Holm, Christian; Gompper, Gerhard; Dill, Ken A

    2015-12-28

    This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

  19. Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Holm, Christian [Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart (Germany); Gompper, Gerhard [Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich (Germany); Dill, Ken A. [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 (United States)

    2015-12-28

    This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

  20. A screening-corrected additivity rule for the calculation of electron scattering from macro-molecules

    Energy Technology Data Exchange (ETDEWEB)

    Blanco, F [Departamento de Fisica Atomica Molecular y Nuclear, Facultad de Ciencias Fisicas. Universidad Complutense, Avda. Complutense s/n, E-28040 Madrid (Spain); Garcia, G [Instituto de Matematicas y Fisica Fundamental, Consejo Superior de Investigaciones CientIficas, Serrano 121, 28006 Madrid (Spain)], E-mail: pacobr@fis.ucm.es

    2009-07-28

    A simplified form of the well-known screening-corrected additivity rule procedure for the calculation of electron-molecule cross sections is proposed for the treatment of some very large macro-molecules. While the comparison of the standard and simplified treatments for a DNA dodecamer reveals very similar results, the new treatment presents some important advantages for large molecules.

  1. Distribution of various forms of organic nitrogen in a lignite macromolecule

    Energy Technology Data Exchange (ETDEWEB)

    Platonov, V.V.; Proskuryakov, V.A.; Polovetskaya, O.S.; Shavyrina, O.A.; Ryl' tsova, S.V. [Lev Tolstoi State Pedalogical University, Tula (Russian Federation)

    2001-07-01

    The chemical composition of organic bases from tars of stepwise semicoking of lignite was studied. The features of distribution of organic nitrogen in a coal macromolecule and the most probable pathways of thermal degradation of the nitrogen-containing fragments were examined.

  2. Intermediate scattering function for macromolecules in solutions probed by neutron spin echo

    Science.gov (United States)

    Liu, Yun

    2017-02-01

    The neutron-spin-echo method (NSE) is a powerful technique for studying internal dynamics of macromolecules in solutions because it can simultaneously probe length and time scales comparable to intramolecular density fluctuations of macromolecules. Recently, there has been increased, strong interest in studying protein internal motions using NSE. The coherent intermediate scattering function (ISF) measured by NSE depends on internal, rotational, and translational motions of macromolecules in solutions. It is thus critical, but highly nontrivial, to separate the internal motion from other motions in order to properly understand protein internal dynamics. Even though many experiments are performed at relatively high concentrations, current theories of calculating the ISF of concentrated protein solutions are either inaccurate or flawed by incorrect assumptions for realistic protein systems with anisotropic shapes. Here, a theoretical framework is developed to establish the quantitative relationship of different motions included in the ISF. This theory based on the dynamic decoupling approximation is applicable to a wide range of protein concentrations, including dilute cases. It is also, in general, useful for studying many other types of macromolecule systems studied by NSE.

  3. The spectral properties of DNA and RNA macromolecules at low temperatures: fundamental and applied aspects

    Science.gov (United States)

    Yashchuk, Valeriy M.; Kudrya, Vladislav Yu

    2017-03-01

    This paper summarizes the results of studies of the spectral properties—optical absorption, fluorescence and phosphorescence—of DNA and RNA macromolecules and synthetic poly-, oligo- and mono-nucleotides, which have been carried out in our laboratory. The system of first excited singlet and triplet energy levels for DNA and RNA is evaluated using low-temperature (4.2 K-77 K) luminescent measurements. The traps of the singlet and triplet electronic excitations in these compounds are identified. An important self-protection mechanism against photo-damage of DNA and RNA by UV photons or penetrative radiation based on the capture of triplet electronic-energy excitations by the most photostable centers—in DNA, the complex formed by neighboring adenosine (A) and thymidine (T) links; in RNA, the adenosine links—is described. It is confirmed that despite similarities in the chemical and partly energy structures DNA is more stable than RNA. The spectral manifestation of the telomeres (the important functional system) in DNA macromolecules is examined. The results obtained on telomere fragments provide the possibility of finding the configuration peculiarities of the triplet excitations traps in DNA macromolecules. The resulting spreading length of the migrating singlet (l s) and triplet (l t) excitations for DNA and RNA macromolecules are evaluated.

  4. Classification of the ejection mechanisms of charged macromolecules from liquid droplets

    Science.gov (United States)

    Consta, Styliani; Malevanets, Anatoly

    2013-01-01

    The relation between the charge state of a macromolecule and its ejection mechanism from droplets is one of the important questions in electrospray ionization methods. In this article, effects of solvent-solute interaction on the manifestation of the charge induced instability in a droplet are examined. We studied the instabilities in a prototype system of a droplet comprised of charged poly(ethylene glycol) and methanol, acetonitrile, and water solvents. We observed instances of three, previously only conjectured, [S. Consta, J. Phys. Chem. B 114, 5263 (2010), 10.1021/jp912119v] mechanisms of macroion ejection. The mechanism of ejection of charged macroion in methanol is reminiscent of "pearl" model in polymer physics. In acetonitrile droplets, the instability manifests through formation of solvent spines around the solvated macroion. In water, we find that the macroion is ejected from the droplet through contiguous extrusion of a part of the chain. The difference in the morphology of the instabilities is attributed to the interplay between forces arising from the macroion solvation energy and the surface energy of the droplet interface. For the contiguous extrusion of a charged macromolecule from a droplet, we demonstrate that the proposed mechanism leads to ejection of the macromolecule from droplets with sizes well below the Rayleigh limit. The ejected macromolecule may hold charge significantly higher than that suggested by prevailing theories. The simulations reveal new mechanisms of macroion evaporation that differ from conventional charge residue model and ion evaporation mechanisms.

  5. A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

    Science.gov (United States)

    Barabash, Yu. M.; Lyamets, A. K.

    2016-12-01

    The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions (A(t)={sum}_{i=1}^n{a}_i{e}^{-{k}_it}) is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

  6. A chip sustem for size separation of macromolecules and particles by hydrodynamic chromatography

    NARCIS (Netherlands)

    Chmela, Emil; Tijssen, Robert; Blom, M.T.; Gardeniers, Johannes G.E.; van den Berg, Albert

    2002-01-01

    For the first time, a miniaturized hydrodynamic chromatography chip system has been developed and tested on separation of fluorescent nanospheres and macromolecules. The device can be applied to size characterization of synthetic polymers, biopolymers, and particles, as an attractive alternative to

  7. Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

    Directory of Open Access Journals (Sweden)

    Diana Fusco

    Full Text Available X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

  8. Hollow fiber membrane modification with functional zwitterionic macromolecules for improved thromboresistance in artificial lungs.

    Science.gov (United States)

    Ye, Sang-Ho; Arazawa, David T; Zhu, Yang; Shankarraman, Venkat; Malkin, Alexander D; Kimmel, Jeremy D; Gamble, Lara J; Ishihara, Kazuhiko; Federspiel, William J; Wagner, William R

    2015-03-03

    Respiratory assist devices seek optimized performance in terms of gas transfer efficiency and thromboresistance to minimize device size and reduce complications associated with inadequate blood biocompatibility. The exchange of gas with blood occurs at the surface of the hollow fiber membranes (HFMs) used in these devices. In this study, three zwitterionic macromolecules were attached to HFM surfaces to putatively improve thromboresistance: (1) carboxyl-functionalized zwitterionic phosphorylcholine (PC) and (2) sulfobetaine (SB) macromolecules (mPC or mSB-COOH) prepared by a simple thiol-ene radical polymerization and (3) a low-molecular weight sulfobetaine (SB)-co-methacrylic acid (MA) block copolymer (SBMAb-COOH) prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization. Each macromolecule type was covalently immobilized on an aminated commercial HFM (Celg-A) by a condensation reaction, and HFM surface composition changes were analyzed by X-ray photoelectron spectroscopy. Thrombotic deposition on the HFMs was investigated after contact with ovine blood in vitro. The removal of CO2 by the HFMs was also evaluated using a model respiratory assistance device. The HFMs conjugated with zwitterionic macromolecules (Celg-mPC, Celg-mSB, and Celg-SBMAb) showed expected increases in phosphorus or sulfur surface content. Celg-mPC and Celg-SBMAb experienced rates of platelet deposition significantly lower than those of unmodified (Celg-A, >95% reduction) and heparin-coated (>88% reduction) control HFMs. Smaller reductions were seen with Celg-mSB. The CO2 removal rate for Celg-SBMAb HFMs remained comparable to that of Celg-A. In contrast, the rate of removal of CO2 for heparin-coated HFMs was significantly reduced. The results demonstrate a promising approach to modifying HFMs using zwitterionic macromolecules for artificial lung devices with improved thromboresistance without degradation of gas transfer.

  9. Inhalation therapy of macromolecules%大分子的吸入治疗

    Institute of Scientific and Technical Information of China (English)

    周煜

    2001-01-01

    随着重组DNA技术和分子生物学的发展,以蛋白质和多肽为主的大分子成为一类新型药物,并越来越受到重视,新兴的基因治疗技术使得核酸大分子也有可能成为药物。目前,绝大部分大分子药物都是通过注射途径给药, 病人在医院注射费用昂贵且不方便,因而许多注射替代给药途径成为研究热门,通过肺部吸入给药就是一种很有吸引力的非侵入性给药途径。本文介绍了肺吸收大分子的可能机制和大分子吸入治疗的临床与基础研究以及面临的问题。%Advances in molecular biology and recombinant DNA technology have led to the development of macromolecule as therapeutic agents for a variety of diseases including proteins, peptides and even nucleic acids. At present most of macromolecules are delivered by injection. Other routes of drug administration are being actively investigated. The inhalation therapy of macromolecule is an attractive noninvasive drug delivery method. In this review we describe the possible mechanisms of macromolecule absorption by the lung, then discuss the clinical and basic research of macromolecular inhalation therapy and analyze the problems of macromolecule inhalation delivery.

  10. Nucleation and Crystallization in nucleated Polymers

    Science.gov (United States)

    Schick, Christoph; Zhuravlev, Evgeny; Wurm, Andreas

    2012-02-01

    Crystallization is commonly considered as nucleation followed by a growth process. Here we apply the recently developed technique, differential fast scanning calorimetry (DFSC), for a unique, new look at the crystal growth of poly(epsilon-caprolactone) (PCL) and PCL carbon nanotube composites from 185 K, below the glass transition temperature, to 330 K, close to the equilibrium melting temperature. The DFSC allows temperature control of the sample and determination of its heat capacity during temperature treatments by employing cooling and heating rates from 50 to 50,000 K/s. First, the crystal nucleation and overall crystallization half times were determined simultaneously in the range of temperatures where crystallization of PCL occurs. After attempting to analyze the experiments with the classical nucleation and growth model a new methodology is described, which addresses the specific problems of crystallization of flexible linear macromolecules. The structures seem to range from having practically unmeasurable latent heats of ordering (nuclei) to being clearly-recognizable, ordered species with rather sharp disordering endotherms at temperatures from the glass transition to equilibrium melting (increasingly perfect and larger crystals). The mechanisms and kinetics of growth (if any) involve a detailed understanding of the interaction with the surrounding rigid amorphous fraction (RAF) in dependence of crystal size and perfection. E. Zhuravlev, J.W.P. Schmelzer, B. Wunderlich and C. Schick, Kinetics of nucleation and crystallization in poly(epsilon-caprolactone) (PCL), Polymer 52 (2011) 1983-1997.

  11. Photonic Crystal Microchip Laser

    Science.gov (United States)

    Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

    2016-09-01

    The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the “photonic crystal microchip laser”, a very compact and efficient light source emitting high spatial quality high brightness radiation.

  12. Permselectivity of the liver blood-lymph (ascitic fluid) barrier to macromolecules in decompensated cirrhosis: relation to calculated pore-size

    DEFF Research Database (Denmark)

    Henriksen, Jens Henrik Sahl

    1983-01-01

    ) exchange of endogeneous macromolecules. A significant 'sieving' is present in this barrier to the largest macromolecule (IgM). Calculations of pore-size equivalent to the observed permselectivity of macromolecules suggest microvascular gaps (or channels) with an average radius about 300 A, i...

  13. Crystal sedimentation and stone formation.

    Science.gov (United States)

    Baumann, Johannes Markus; Affolter, Beat; Meyer, Rolf

    2010-02-01

    Mechanisms of crystal collision being the first step of aggregation (AGN) were analyzed for calcium oxalate monohydrate (COM) directly produced in urine. COM was produced by oxalate titration in urine of seven healthy men, in solutions of urinary macromolecules and in buffered distilled water (control). Crystal formation and sedimentation were followed by a spectrophotometer and analyzed by scanning electron microscopy. Viscosity of urine was measured at 37 degrees C. From results, sedimentation rate (v (S)), particle diffusion (D) and incidences of collision of particles in suspension by sedimentation (I (S)) and by diffusion (I (D)) were calculated. Calculations were related to average volume and urinary transit time of renal collecting ducts (CD) and of renal pelvis. v (S) was in urine 0.026 +/- 0.012, in UMS 0.022 +/- 0.01 and in control 0.091 +/- 0.02 cm min(-1) (mean +/- SD). For urine, a D of 9.53 +/- 0.97 mum within 1 min can be calculated. At maximal crystal concentration, I (S) was only 0.12 and I (D) was 0.48 min(-1) cm(-3) which, even at an unrealistic permanent and maximal crystalluria, would only correspond to less than one crystal collision/week/CD, whereas to the same tubular wall being in horizontal position 1.3 crystals/min and to a renal stone 624 crystals/cm(2) min could drop by sedimentation. Sedimentation to renal tubular or pelvic wall, where crystals can accumulate and meet with a tissue calcification or a stone, is probably essential for stone formation. Since v (S) mainly depends on particle size, reducing urinary supersaturation and crystal growth by dietary oxalate restriction seems to be an important measure to prevent aggregation.

  14. [Evaluation of image quality using the normalized-rank approach for primary class liquid-crystal display (LCD) monitors with different colors and resolution].

    Science.gov (United States)

    Kuroki, Hidefumi; Katayama, Reiji; Sakaguchi, Taro; Maeda, Takashi; Morishita, Junji; Hayabuchi, Naofumi

    2010-11-20

    The purposes of this study were to evaluate the image quality of five types of liquid-crystal display (LCD) monitors by utilizing the normalized-rank approach and to investigate the effect of LCD monitor specifications, such as display colors, luminance, and resolution, on the evaluators' ranking. The LCD monitors used in this study were 2, 3 and 5 mega-pixel monochrome LCD monitors, and 2 and 3 mega-pixel color LCD monitors (Eizo Nanao Corporation). All LCD monitors were calibrated to the grayscale standard display function (GSDF) with different maximum luminance (recommended luminance) settings. Also, four kinds of radiographs were used for observer study based on the normalized-rank approach: three adult chest radiographs, three pediatric chest radiographs, three ankle joint radiographs, and four double-contrasted upper gastrointestinal radiographs. Ten radiological technologists participated in the observer study. Monochrome LCD monitors exhibited superior ranking with statistically significant differences (pLCD monitors in all kinds of radiographs. The major difference between monochrome and color monitors was luminance. Therefore, it is considered that the luminance of LCD monitors affects observers' evaluations based on image quality. Moreover, in the case of radiographs that include high frequency image components, the monitor resolution also affects the evaluation. In clinical practice, it is necessary to optimize the luminance and choose appropriate LCD monitors for diagnostic images.

  15. High-throughput crystallization screening.

    Science.gov (United States)

    Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

    2014-01-01

    Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

  16. Crystals in crystals

    DEFF Research Database (Denmark)

    Christensen, Claus H.; Schmidt, I.; Carlsson, A.;

    2005-01-01

    A major factor governing the performance of catalytically active particles supported on a zeolite carrier is the degree of dispersion. It is shown that the introduction of noncrystallographic mesopores into zeolite single crystals (silicalite-1, ZSM-5) may increase the degree of particle dispersion...... of the zeolite particles, particularly after thermal treatment. When using mesoporous zeolites, the particles were evenly distributed throughout the mesopore system of the zeolitic support, even after calcination, leading to nanocrystals within mesoporous zeolite single crystals....

  17. Hydroxycinnamic acids are ester-linked directly to glucosyl moieties within the lignan macromolecule from flaxseed hulls.

    Science.gov (United States)

    Struijs, Karin; Vincken, Jean-Paul; Verhoef, René; Voragen, Alphons G J; Gruppen, Harry

    2008-03-01

    In flaxseed hulls, lignans are present in an oligomeric structure. Secoisolariciresinol diglucoside (SDG), ester-linked to hydroxy-methyl-glutaric acid (HMGA), forms the backbone of this lignan macromolecule. The hydroxycinnamic acids p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) are also part of the lignan macromolecule. However, their position and type of linkage are still unknown. The aim of this study was to investigate how CouAG and FeAG are linked within the lignan macromolecule from flaxseed hulls. Fragments of the lignan macromolecule were obtained by partial saponification. After isolation of the fragments by preparative RP-HPLC, several key structures were identified by MS and NMR. Within the lignan macromolecule, CouAG is attached to the C-6 position of a glucosyl moiety of SDG. FeA is linked to the C-2 position of a glucosyl moiety of SDG. FeAG is ester-linked within the lignan macromolecule with its carboxyl group, but it remains unclear whether FeAG links to the C-2 or C-6 position of SDG. Attachment of HMGA to the glucosyl moiety of CouAG or FeAG was not observed. The results clearly show that within the lignan macromolecule, the hydroxycinnamic acids are linked directly via an ester bond to the glucosyl moiety of SDG.

  18. Large-volume protein crystal growth for neutron macromolecular crystallography.

    Science.gov (United States)

    Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

    2015-04-01

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  19. The paradoxical role of urinary macromolecules in the aggregation of calcium oxalate: a further plea to increase diuresis in stone metaphylaxis.

    Science.gov (United States)

    Baumann, J M; Affolter, B

    2016-08-01

    This study was designed to get information on aggregation (AGN) of urinary calcium oxalate crystals (CaOx) which seems to occur in stone formation despite a protecting coat of urinary macromolecules (UMs). CaOx crystallization was directly produced in urine, control and albumin solution by Ox titration and was spectrophotometrically followed. A rapid decrease of optical density indicating AGN was absent in 14 of 15 freshly voided urines of 5 healthy controls. However, in the presence of UM-coated hydroxyapatite all urines with relative high sodium concentration, being an indicator of concentrated urine, showed a pronounced AGN which was abolished when these urines were diluted. Albumin relatively found to be an inhibitor of AGN showed after temporary adsorption on Ca Phosphate (CaP) massive self-AGN and changed to a promoter of CaOx AGN. Self-AGN after adsorption on surfaces especially of CaP, being an important compound of Randall's plaques, can thus explain this paradoxical behavior of UMs. Aggregated UMs probably bridge zones of electrostatic repulsion between UM-coated crystals with identical electrical surface charge. These zones extend by urine dilution which decreases ionic strength. Diminution of urinary concentration by increasing diuresis seems, therefore, to be important in stone metaphylaxis.

  20. Self-Organized Crystallization Patterns from Evaporating Droplets of Common Wheat Grain Leakages as a Potential Tool for Quality Analysis

    Directory of Open Access Journals (Sweden)

    Maria Olga Kokornaczyk

    2011-01-01

    Full Text Available We studied the evaporation-induced pattern formation in droplets of common wheat kernel leakages prepared out of ancient and modern wheat cultivars as a possible tool for wheat quality analysis. The experiments showed that the substances which passed into the water during the soaking of the kernels created crystalline structures with different degrees of complexity while the droplets were evaporating. The forms ranged from spots and simple structures with single ramifications, through dendrites, up to highly organized hexagonal shapes and fractal-like structures. The patterns were observed and photographed using dark field microscopy in small magnifications. The evaluation of the patterns was performed both visually and by means of the fractal dimension analysis. From the results, it can be inferred that the wheat cultivars differed in their pattern-forming capacities. Two of the analyzed wheat cultivars showed poor pattern formation, whereas another two created well-formed and complex patterns. Additionally, the wheat cultivars were analyzed for their vigor by means of the germination test and measurement of the electrical conductivity of the grain leakages. The results showed that the more vigorous cultivars also created more complex patterns, whereas the weaker cultivars created predominantly poor forms. This observation suggests a correlation between the wheat seed quality and droplet evaporation patterns.

  1. Improvement of crystal quality of GaN grown on AlN template by MOCVD using HT-AlN interlayer

    Energy Technology Data Exchange (ETDEWEB)

    Yuebin, Tao; Zhizhong, Chen; Zhijian, Yang; Liwen, Sang; Zhitao, Chen; Ding, Li; Hao, Fang; Guoyi, Zhang [State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing (China); Yaobo, Pan; Jianfeng, Yan; Guangmin, Zhu; Cheng, Chen; Shitao, Li; Maosheng, Hao [Epilight Technology Co., Ltd., Shanghai (China)

    2009-06-15

    Two GaN samples, with and without high temperature (HT)-AlN interlayer (labelled as sample A and B, respectively) grown by MOCVD on AlN template, were investigated by double-crystal X-ray diffraction (DC-XRD), photoluminescence (PL), and atomic force microscope (AFM) measurements. It was found that the crystal quality of GaN could be greatly improved by the HT-AlN interlayer. The full width at half maximum (FWHM) of (102) reflection in XRD rocking curve was narrower for sample A than that for sample B. However, the FWHMs of (002) reflections were almost the same for the two samples. In addition, the tilt degree which reflected screw dislocation density was almost the same, while the twist degree which reflected edge dislocation density changed from 0.214 to 0.152 when the HT-AlN interlayer was used. Both the intensities of (102) reflection in XRD and band edge emission in PL for sample A were stronger too. In the AFM images, the atomic growth steps of sample A were clearer than those of sample B. According to the results of the in situ optical reflectivity spectra and the atomic force microscope (AFM) images, the above results were attributed to the three-dimensional (3D) growth mode of the HT-AlN interlayer. The HT-AlN interlayer may work as a kind of ''micro-area'' seed for epitaxial lateral overgrowth (ELOG) resulting in bending some dislocations. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

    Directory of Open Access Journals (Sweden)

    Pawlowski Marcin

    2012-11-01

    Full Text Available Abstract Background Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR, a common method to solve the phase problem faced by macromolecular crystallography. The success of MR depends on the accuracy of a search model. Unfortunately, this parameter remains unknown until the final structure of the target protein is determined. During the last few years, several Model Quality Assessment Programs (MQAPs that predict the local accuracy of theoretical models have been developed. In this article, we analyze whether the application of MQAPs improves the utility of theoretical models in MR. Results For our dataset of 615 search models, the real local accuracy of a model increases the MR success ratio by 101% compared to corresponding polyalanine templates. On the contrary, when local model quality is not utilized in MR, the computational models solved only 4.5% more MR searches than polyalanine templates. For the same dataset of the 615 models, a workflow combining MR with predicted local accuracy of a model found 45% more correct solution than polyalanine templates. To predict such accuracy MetaMQAPclust, a “clustering MQAP” was used. Conclusions Using comparative models only marginally increases the MR success ratio in comparison to polyalanine structures of templates. However, the situation changes dramatically once comparative models are used together with their predicted local accuracy. A new functionality was added to the GeneSilico Fold Prediction Metaserver in order to build models that are more useful for MR searches. Additionally, we have developed a simple method, AmIgoMR (Am I good for MR?, to predict if an MR search with a template-based model for a given template is likely to find the correct solution.

  3. Marine-derived biological macromolecule-based biomaterials for wound healing and skin tissue regeneration.

    Science.gov (United States)

    Chandika, Pathum; Ko, Seok-Chun; Jung, Won-Kyo

    2015-01-01

    Wound healing is a complex biological process that depends on the wound condition, the patient's health, and the physicochemical support given through external materials. The development of bioactive molecules and engineered tissue substitutes to provide physiochemical support to enhance the wound healing process plays a key role in advancing wound-care management. Thus, identification of ideal molecules in wound treatment is still in progress. The discovery of natural products that contain ideal molecules for skin tissue regeneration has been greatly advanced by exploration of the marine bioenvironment. Consequently, tremendously diverse marine organisms have become a great source of numerous biological macromolecules that can be used to develop tissue-engineered substitutes with wound healing properties. This review summarizes the wound healing process, the properties of macromolecules from marine organisms, and the involvement of these molecules in skin tissue regeneration applications.

  4. Mitochondrial transit peptide exhibits cell penetration ability and efficiently delivers macromolecules to mitochondria.

    Science.gov (United States)

    Jain, Aastha; Chugh, Archana

    2016-09-01

    Mitochondrial malfunction under various circumstances can lead to a variety of disorders. Effective targeting of macromolecules (drugs) is important for restoration of mitochondrial function and treatment of related disorders. We have designed a novel cell-penetrating mitochondrial transit peptide (CpMTP) for delivery of macromolecules to mitochondria. Comparison between properties of cell-penetrating peptides (CPPs) and mitochondrial signal sequences enabled prediction of peptides with dual ability for cellular translocation and mitochondrial localization. Among the predicted peptides, CpMTP translocates across HeLa cells and shows successful delivery of noncovalently conjugated cargo molecules to mitochondria. CpMTP may have applications in transduction and transfection of mitochondria for therapeutics. © 2016 Federation of European Biochemical Societies.

  5. Recent Progress in the Design of Monodisperse, Sequence-Defined Macromolecules.

    Science.gov (United States)

    Solleder, Susanne C; Schneider, Rebekka V; Wetzel, Katharina S; Boukis, Andreas C; Meier, Michael A R

    2017-05-01

    This review describes different synthetic strategies towards sequence-defined, monodisperse macromolecules, which are built up by iterative approaches and lead to linear non-natural polymer structures. The review is divided in three parts: solution phase-, solid phase-, and fluorous- and polymer-tethered approaches. Moreover, synthesis procedures leading to conjugated and non-conjugated macromolecules are considered and discussed in the respective sections. A major focus in the evaluation is the applicability of the different approaches in polymer chemistry. In this context, simple procedures for monomer and oligomer synthesis, overall yields, scalability, purity of the oligomers, and the achievable level of control (side-chains, backbone, stereochemistry) are important benchmarks. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

    CERN Document Server

    Oliver, Robin; Harlen, Oliver G; Harris, Sarah A

    2012-01-01

    We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obt...

  7. Biomimetic Transmembrane Channels with High Stability and Transporting Efficiency from Helically Folded Macromolecules.

    Science.gov (United States)

    Lang, Chao; Li, Wenfang; Dong, Zeyuan; Zhang, Xin; Yang, Feihu; Yang, Bing; Deng, Xiaoli; Zhang, Chenyang; Xu, Jiayun; Liu, Junqiu

    2016-08-08

    Membrane channels span the cellular lipid bilayers to transport ions and molecules into cells with sophisticated properties including high efficiency and selectivity. It is of particular biological importance in developing biomimetic transmembrane channels with unique functions by means of chemically synthetic strategies. An artificial unimolecular transmembrane channel using pore-containing helical macromolecules is reported. The self-folding, shape-persistent, pore-containing helical macromolecules are able to span the lipid bilayer, and thus result in extraordinary channel stability and high transporting efficiency for protons and cations. The lifetime of this artificial unimolecular channel in the lipid bilayer membrane is impressively long, rivaling those of natural protein channels. Natural channel mimics designed by helically folded polymeric scaffolds will display robust and versatile transport-related properties at single-molecule level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Synthesis and mechanisms of formation of polymers composed of different macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Korshak, V.V.; Askadskii, A.A.; Vointseva, I.I.; Mustafaeva, B.B.; Slonimskii, G.L.; Suprun, A.P.

    1983-02-01

    The fundamental possibility of synthesizing soluble and fusible aggregates of different macromolecules was discovered in the reaction of chlorinated and aromatic polymers under the conditions of the Friedel-Crafts reaction. Such an approach opens the prospects of combining in one macromolecule two or more different types of chain, and of the synthesis of polymers with a new combination of properties. In this reaction poly-1,1,2-trichlorobutadiene (PTCB) and polyvinylcholoride can be used as chlorine-containing compounds, and polystyrene (PS), poly-..cap alpha..-methyl-styrene, polyarylates, polycarbonates, etc., as the aromatic polymers. The mechanism of the reaction of chlorinated and aromatic polymers was studied with PTCB and PS as the model pair of polymers.

  9. Spreading of a chain macromolecule onto a cell membrane by a computer simulation Model

    Science.gov (United States)

    Xie, Jun; Pandey, Ras

    2002-03-01

    Computer simulations are performed to study conformation and dynamics of a relatively large chain macromolecule at the surface of a model membrane - a preliminary attempt to ultimately realistic model for protein on a cell membrane. We use a discrete lattice of size Lx × L × L. The chain molecule of length Lc is modeled by consecutive nodes connected by bonds on the trail of a random walk with appropriate constraints such as excluded volume, energy dependent configurational bias, etc. Monte Carlo method is used to move chains via segmental dynamics, i.e., end-move, kink-jump, crank-shaft, reptation, etc. Membrane substrate is designed by a self-assemble biased short chains on a substrate. Large chain molecule is then driven toward the membrane by a field. We investigate the dynamics of chain macromolecule, spread of its density, and conformation.

  10. Load-release of small and macromolecules from elastomers with reversible gyroid mesoporosity

    DEFF Research Database (Denmark)

    Guo, Fengxiao; Schulte, Lars; Ndoni, Sokol

    2012-01-01

    . However, in the gel state in the presence of a good solvent the swollen matrix did show a nanoporous structure originated from the gyroid block copolymer precursor. Nanopores can be opened or closed depending on the presence or absence of a solvent. Macromolecules like PEG of different molecular weights...... or small molecules like the surfactant SDS were loaded into the opened nanoporous matrix in the presence of a solvent and remained trapped. The loaded molecules could be released again in the presence of a solvent. The load and release of the molecules in deuterated form were monitored by in situ time......-resolved small angle neutron scattering, SANS. The bicontinuous gyroid pore structure is accessible to macromolecules without the need for sample pre-alignment. The materials presented here are model systems for a novel type of load-delivery systems that could show great potential in e.g. diagnostics or drug...

  11. Ultrasound-enhanced penetration through sclera depends on frequency of sonication and size of macromolecules.

    Science.gov (United States)

    Chau, Ying; Suen, Wai Leung Langston; Tse, Ho Yan; Wong, Hoi Sang

    2017-03-30

    We previously employed ultrasound as a needleless approach to deliver macromolecules via the transscleral route to the back of the eye in live animals (Suen et al., 2013). Here, we investigated the nature of the ultrasound-enhanced transport through sclera, the outermost barrier in the transscleral route. Thus, the possible role of cavitation from ultrasound was explored; its effect during and after sonication on scleral penetration was measured; and the dependence on the size of macromolecules was determined. We applied ultrasound frequency from 40kHz to 3MHz at ISATA (spatial-average-temporal-average intensity) of 0.05W/cm(2) to fresh rabbit sclera ex vivo. Fluorescent dextran of size 20kDa to 150kDa was used as macromolecular probes. We measured the distance of penetration of the probes through the sclera over 30s during sonication and over 15min after sonication from cryosectioned tissue images. Deeper penetration in the sclera was observed with decreasing frequency. The presence of stable cavitation was further verified by passive acoustic detection. The effect during sonication increased penetration distance up to 20 fold and was limited to macromolecular probes ≤70kDa. The effect post sonication increased penetration distance up to 3 fold and attributed to the improved intrasscleral transport of macromolecules ≥70kDa. Post-sonication enhancement diminished gradually in 3h. As the extent of cavitation increased with decreasing frequency, the trend observed supports the contribution of (stable) cavitation to enhancing transport through sclera. Effect during sonication was attributed to flow associated with acoustic microstreaming. Effect post sonication was attributed to the temporary increase in scleral permeability. Flow-associated effect was more pronounced but only applied to smaller macromolecules. Copyright © 2017. Published by Elsevier B.V.

  12. Bioinformatic science and devices for computer analysis and visualization of macromolecules

    Directory of Open Access Journals (Sweden)

    Yu.B. Porozov

    2010-06-01

    Full Text Available The goals and objectives of bioinformatic science are presented in the article. The main methods and approaches used in computer biology are highlighted. Areas in which bioinformatic science can greatly facilitate and speed up the work of practical biologist and pharmacologist are revealed. The features of both the basic packages and software devices for complete, thorough analysis of macromolecules and for development and modeling of ligands and binding centers are described

  13. Asymmetrical flow field-flow fractionation in the study of water-soluble macromolecules

    OpenAIRE

    Yohannes, Gebrenegus

    2007-01-01

    Asymmetrical flow field-flow fractionation (AsFlFFF) was constructed, and its applicability to industrial, biochemical, and pharmaceutical applications was studied. The effect of several parameters, such as pH, ionic strength, temperature and the reactants mixing ratios on the particle sizes, molar masses, and the formation of aggregates of macromolecules was determined by AsFlFFF. In the case of industrial application AsFlFFF proved to be a valuable tool in the characterization of the hydrod...

  14. Crystal science fundamentals

    OpenAIRE

    Ramachandran, V.; Halfpenny, PJ; Roberts, KJ

    2017-01-01

    The fundamentals of crystal science notably crystallography, crystal chemistry, crystal defects, crystal morphology and the surface chemistry of crystals are introduced with particular emphasis on organic crystals.

  15. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    Science.gov (United States)

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  16. Application of Symmetry Adapted Function Method for Three-Dimensional Reconstruction of Octahedral Biological Macromolecules

    Directory of Open Access Journals (Sweden)

    Songjun Zeng

    2010-01-01

    Full Text Available A method for three-dimensional (3D reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions (OSAFs method, was introduced in this paper and a series of formulations for reconstruction by OSAF method were derived. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock protein Degp24 and the Red-cell L Ferritin, were utilized as examples to implement reconstruction by the OSAF method. The schedule for simulation was designed as follows: 2000 random orientated projections of single particles with predefined Euler angles and centers of origins were generated, then different levels of noises that is signal-to-noise ratio (S/N =0.1,0.5, and 0.8 were added. The structures reconstructed by the OSAF method were in good agreement with the standard models and the relative errors of the structures reconstructed by the OSAF method to standard structures were very little even for high level noise. The facts mentioned above account for that the OSAF method is feasible and efficient approach to reconstruct structures of macromolecules and have ability to suppress the influence of noise.

  17. Prevention of H-Aggregates Formation in Cy5 Labeled Macromolecules

    Directory of Open Access Journals (Sweden)

    Jing Kang

    2010-01-01

    Full Text Available H-aggregates of the cyanine dye Cy5 are formed during covalent linkage to the cationic macromolecule Poly(allylamine (PAH. The nonfluorescent H-aggregates strongly restrict the usage of the dye for analytical purposes and prevent a quantitative determination of the labeled macromolecules. The behavior of the H-aggregates has been studied by investigation of the absorption and fluorescence spectra of the dye polymer in dependence on solvent, label degree and additional sulfonate groups. H-aggregate formation is caused by an inhomogeneous distribution of the Cy5 molecules on the polymer chain. The H-aggregates can be destroyed by conformational changes of the PAH induced by interactions with polyanions or in organic solvents. It has been found that the polymer labeling process in high content of organic solvents can prevent the formation of H-aggregates. The results offer a better understanding and improvement of the use of the Cy5 dye for labeling purposes in fluorescence detection of macromolecules.

  18. Synthetic mimetics of the endogenous gastrointestinal nanomineral: Silent constructs that trap macromolecules for intracellular delivery.

    Science.gov (United States)

    Pele, Laetitia C; Haas, Carolin T; Hewitt, Rachel E; Robertson, Jack; Skepper, Jeremy; Brown, Andy; Hernandez-Garrido, Juan Carlos; Midgley, Paul A; Faria, Nuno; Chappell, Helen; Powell, Jonathan J

    2017-02-01

    Amorphous magnesium-substituted calcium phosphate (AMCP) nanoparticles (75-150nm) form constitutively in large numbers in the mammalian gut. Collective evidence indicates that they trap and deliver luminal macromolecules to mucosal antigen presenting cells (APCs) and facilitate gut immune homeostasis. Here, we report on a synthetic mimetic of the endogenous AMCP and show that it has marked capacity to trap macromolecules during formation. Macromolecular capture into AMCP involved incorporation as shown by STEM tomography of the synthetic AMCP particle with 5nm ultra-fine iron (III) oxohydroxide. In vitro, organic cargo-loaded synthetic AMCP was taken up by APCs and tracked to lysosomal compartments. The AMCP itself did not regulate any gene, or modify any gene regulation by its cargo, based upon whole genome transcriptomic analyses. We conclude that synthetic AMCP can efficiently trap macromolecules and deliver them to APCs in a silent fashion, and may thus represent a new platform for antigen delivery. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. Structure-Correlation NMR Spectroscopy for Macromolecules Using Repeated Bidirectional Photoisomerization of Azobenzene.

    Science.gov (United States)

    Nagashima, Toshio; Ueda, Keisuke; Nishimura, Chiaki; Yamazaki, Toshio

    2015-11-17

    Control over macromolecular structure offers bright potentials for manipulation of macromolecular functions. We here present structure-correlation NMR spectroscopy to analyze the correlation between polymorphic macromolecular structures driven by photoisomerization of azobenzene. The structural conversion of azobenzene was induced within the mixing time of a NOESY experiment using a colored light source, and the reverse structural conversion was induced during the relaxation delay using a light source of another color. The correlation spectrum between trans- and cis-azobenzene was then obtained. To maximize the efficiency of the bidirectional photoisomerization of azobenzene-containing macromolecules, we developed a novel light-irradiation NMR sample tube and method for irradiating target molecules in an NMR radio frequency (rf) coil. When this sample tube was used for photoisomerization of an azobenzene derivative at a concentration of 0.2 mM, data collection with reasonable sensitivity applicable to macromolecules was achieved. We performed isomerization of an azobenzene-cross-linked peptide within the mixing time of a NOESY experiment that produced cross-peaks between helix and random-coil forms of the peptide. Thus, these results indicate that macromolecular structure manipulation can be incorporated into an NMR pulse sequence using an azobenzene derivative and irradiation with light of two types of wavelengths, providing a new method for structural analysis of metastable states of macromolecules.

  20. Nasal Absorption of Macromolecules from Powder Formulations and Effects of Sodium Carboxymethyl Cellulose on Their Absorption.

    Science.gov (United States)

    Tanaka, Akiko; Furubayashi, Tomoyuki; Matsushita, Akifumi; Inoue, Daisuke; Kimura, Shunsuke; Katsumi, Hidemasa; Sakane, Toshiyasu; Yamamoto, Akira

    2016-01-01

    The nasal absorption of macromolecules from powder formulations and the effect of sodium carboxymethyl cellulose (CMC-Na) as a pharmaceutical excipient on their absorption were studied. Model macromolecules were fluorescein isothiocyanate-labeled dextran (average molecular weight of 4.4kDa, FD4) and insulin. The plasma concentration of FD4 after application of the powder containing 50% starch (control) was higher than that after application of the solution, and the absorption from 50% starch powder was enhanced by the substitution of starch with CMC-Na. The fractional absorption of FD4 after administration of the CMC-Na powder formulation was 30% and 40% higher than that after administration from the solution and the starch powder, respectively. The nasal absorption of insulin from the powder and the effect of CMC-Na were similar with those of FD4. The effective absorption of FD4 and insulin after application of powder with CMC-Na could be due to the increase in the nasal residence of FD4 and insulin. No damage in the nasal mucosa or dysfunction of the mucociliary clearance was observed after application of the drug powder and CMC-Na. The present findings indicate that nasal delivery of powder formulations with the addition of CMC-Na as an excipient is a promising approach for improving the nasal absorption of macromolecules.

  1. Ordinary-extraordinary transition in dynamics of solutions of charged macromolecules.

    Science.gov (United States)

    Muthukumar, Murugappan

    2016-10-24

    The occurrence of the ubiquitous and intriguing "ordinary-extraordinary" behavior of dynamics in solutions of charged macromolecules is addressed theoretically by explicitly considering counterions around the macromolecules. The collective and coupled dynamics of macromolecules and their counterion clouds in salt-free conditions are shown to lead to the "ordinary" behavior (also called the "fast" mode) where diffusion coefficients are independent of molar mass and polymer concentration and are comparable to those of isolated metallic ions in aqueous media, in agreement with experimental facts observed repeatedly over the past four decades. The dipoles arising from adsorbed counterions on polymer backbones can form many pairwise physical cross-links, leading to microgel-like aggregates. Balancing the swelling from excluded volume effects and counterion pressure with elasticity of the microgel, we show that there is a threshold value of a combination of polymer concentration and electrolyte concentration for the occurrence of the "extraordinary" phase (also called the "slow" mode) and the predicted properties of diffusion coefficient for this phase are in qualitative agreement with well-known experimental data.

  2. Immunomodulatory Properties of Taranjebin (Camel's Thorn) Manna and Its Isolated Carbohydrate Macromolecules.

    Science.gov (United States)

    Hamedi, Azadeh; Farjadian, Shirin; Karami, Mohammad Reza

    2015-10-01

    Taranjebin manna is a substance produced by Poophilus nebulosus Leth. (Aphrophoridae) larva that feed from host plant Alhagi maurorum (Leguminosae). In Persian ethnomedicine, it is used as an antipyretic, antiviral, antimicrobial, demulcent, and adaptogen. But it is contraindicated in acute fever and some infections. This controversy might be due to its immunomodulatory properties. This study evaluated immunomodulatory properties of Taranjebin and its macromolecules. Taranjebin solution was prepared as described in traditional literature. After dialysis and precipitation, the macromolecules were isolated on DEAE Sephadex A-25. The cytotoxic/proliferative properties of Taranjebin and its isolated macromolecules on human Jurkat E6.1 cells were investigated (15.62-1000 μg/mL) using WST-1 reagent. Three of 4 isolated acidic polysaccharides inhibited the proliferation of Jurkat cells in a dose-dependent manner at concentrations higher than 31.25 μg/mL (IC50 range of 44.81-147.97 μg/mL). The crude aqueous Taranjebin solution had proliferative effects. These results indicate the immunomodulatory properties of Taranjebin. © The Author(s) 2015.

  3. Silica-based systems for oral delivery of drugs, macromolecules and cells.

    Science.gov (United States)

    Diab, Roudayna; Canilho, Nadia; Pavel, Ileana A; Haffner, Fernanda B; Girardon, Maxime; Pasc, Andreea

    2017-04-20

    According to the US Food and Drug Administration and the European Food Safety Authority, amorphous forms of silica and silicates are generally recognized to be safe as oral delivery ingredients in amounts up to 1500mg per day. Silica is used in the formulation of solid dosage forms, e.g. tablets, as glidant or lubricant. The synthesis of silica-based materials depends on the payload nature, drug, macromolecule or cell, and on the target release (active or passive). In the literature, most of the examples deal with the encapsulation of drugs in mesoporous silica nanoparticles. Still to date limited reports concerning the delivery of encapsulated macromolecules and cells have been reported in the field of oral delivery, despite the multiple promising examples demonstrating the compatibility of the sol-gel route with biological entities, likewise the interest of silica as an oral carrier. Silica diatoms appear as an elegant, cost-effective and promising alternative to synthetic sol-gel-based materials. This review reports the latest advances silica-based systems and discusses the potential benefits and drawbacks of using silica for oral delivery of drugs, macromolecules or cells. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Diffusion profile of macromolecules within and between human skin layers for (trans)dermal drug delivery.

    Science.gov (United States)

    Römgens, Anne M; Bader, Dan L; Bouwstra, Joke A; Baaijens, Frank P T; Oomens, Cees W J

    2015-10-01

    Delivering a drug into and through the skin is of interest as the skin can act as an alternative drug administration route for oral delivery. The development of new delivery methods, such as microneedles, makes it possible to not only deliver small molecules into the skin, which are able to pass the outer layer of the skin in therapeutic amounts, but also macromolecules. To provide insight into the administration of these molecules into the skin, the aim of this study was to assess the transport of macromolecules within and between its various layers. The diffusion coefficients in the epidermis and several locations in the papillary and reticular dermis were determined for fluorescein dextran of 40 and 500 kDa using a combination of fluorescent recovery after photobleaching experiments and finite element analysis. The diffusion coefficient was significantly higher for 40 kDa than 500 kDa dextran, with median values of 23 and 9 µm(2)/s in the dermis, respectively. The values only marginally varied within and between papillary and reticular dermis. For the 40 kDa dextran, the diffusion coefficient in the epidermis was twice as low as in the dermis layers. The adopted method may be used for other macromolecules, which are of interest for dermal and transdermal drug delivery. The knowledge about diffusion in the skin is useful to optimize (trans)dermal drug delivery systems to target specific layers or cells in the human skin. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Formation and characterization of calcium orthophosphates in the presence of two different acidic macromolecules

    Science.gov (United States)

    Pelin, Irina M.; Maier, Vasilica; Suflet, Dana M.; Popescu, Irina; Darie-Nita, Raluca N.; Aflori, Magdalena; Butnaru, Maria

    2017-10-01

    The synthetic nanocrystalline calcium orthophosphates have a notable bioactivity due to the chemical similarity with biological apatite from calcified tissues. In mineralized tissues, the highly ordered structures come from organized assemblies of biomacromolecules and inorganic nanoparticles. One of the purposes of this work was to study the effect of two types of acidic macromolecules: atelocollagen and phosphorylated curdlan onto calcium orthophosphates formation after 30 days of maturation at 2 ± 2 °C. The resulted samples after a long aging time, either calcium orthophosphates or composites, were first investigated by FT-IR spectroscopy and X-ray diffractometry and the results indicated that precipitated hydroxyapatite with low crystallinity was obtained when the synthesis was performed in the presence of phosphorylated curdlan. The macromolecules influenced the morphology of the particles as shown by scanning and transmission electron microscopy. The presence of macromolecules as demonstrated by thermal investigation also influenced the rheological properties of the samples. The second purpose of the work was to evaluate the cytotoxicity of the samples using the MTT assay, and the results revealed very good cells viability. The preliminary results are encouraging regarding the use of these materials for further tests in order to develop injectable bone substitutes.

  6. Nasal Absorption of Macromolecules from Powder Formulations and Effects of Sodium Carboxymethyl Cellulose on Their Absorption

    Science.gov (United States)

    Tanaka, Akiko; Furubayashi, Tomoyuki; Matsushita, Akifumi; Inoue, Daisuke; Kimura, Shunsuke; Katsumi, Hidemasa; Sakane, Toshiyasu; Yamamoto, Akira

    2016-01-01

    The nasal absorption of macromolecules from powder formulations and the effect of sodium carboxymethyl cellulose (CMC-Na) as a pharmaceutical excipient on their absorption were studied. Model macromolecules were fluorescein isothiocyanate-labeled dextran (average molecular weight of 4.4kDa, FD4) and insulin. The plasma concentration of FD4 after application of the powder containing 50% starch (control) was higher than that after application of the solution, and the absorption from 50% starch powder was enhanced by the substitution of starch with CMC-Na. The fractional absorption of FD4 after administration of the CMC-Na powder formulation was 30% and 40% higher than that after administration from the solution and the starch powder, respectively. The nasal absorption of insulin from the powder and the effect of CMC-Na were similar with those of FD4. The effective absorption of FD4 and insulin after application of powder with CMC-Na could be due to the increase in the nasal residence of FD4 and insulin. No damage in the nasal mucosa or dysfunction of the mucociliary clearance was observed after application of the drug powder and CMC-Na. The present findings indicate that nasal delivery of powder formulations with the addition of CMC-Na as an excipient is a promising approach for improving the nasal absorption of macromolecules. PMID:27598527

  7. Size and average density spectra of macromolecules obtained from hydrodynamic data.

    Science.gov (United States)

    Pavlov, G M

    2007-02-01

    It is proposed to normalize the Mark-Kuhn-Houwink-Sakurada type of equation relating the hydrodynamic characteristics, such as intrinsic viscosity, velocity sedimentation coefficient and translational diffusion coefficient of linear macromolecules to their molecular masses for the values of linear density M(L) and the statistical segment length A. When the set of data covering virtually all known experimental information is normalized for M(L), it is presented as a size spectrum of linear polymer molecules. Further normalization for the A value reduces all data to two regions: namely the region exhibiting volume interactions and that showing hydrodynamic draining. For chains without intachain excluded volume effects these results may be reproduced using the Yamakawa-Fujii theory of wormlike cylinders. Data analyzed here cover a range of contour lengths of linear chains varying by three orders of magnitude, with the range of statistical segment lengths varying approximately 500 times. The plot of the dependence of [eta]M on M represents the spectrum of average specific volumes occupied by linear and branched macromolecules. Dendrimers and globular proteins for which the volume occupied by the molecule in solution is directly proportional to M have the lowest specific volume. The homologous series of macromolecules in these plots are arranged following their fractal dimensionality.

  8. High quality Y-type hexaferrite thick films for microwave applications by an economical and environmentally benign crystal growth technique

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Bolin; Chen, Yajie, E-mail: y.chen@neu.edu; Gillette, Scott; Su, Zhijuan; Harris, Vincent G. [Center for Microwave Magnetic Materials and Integrated Circuits and Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115 (United States); Wolf, Jason; McHenry, Michael E. [Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States)

    2014-02-17

    Thick barium hexaferrite Ba{sub 2}Zn{sub 2}Fe{sub 12}O{sub 22} (i.e., Zn{sub 2}Y) films having thicknesses of ∼100 μm were epitaxially grown on MgO (111) substrates using an environmentally benign ferrite-salt mixture by vaporizing the salt. X-ray diffraction pole figure analyses showed (00l) crystallographic alignment with little in plane dispersion confirming epitaxial growth. Saturation magnetization, 4πM{sub s}, was measured for as-grown films to be 2.51 ± 0.1 kG with an out of plane magnetic anisotropy field H{sub A} of 8.9 ± 0.1 kOe. Ferromagnetic resonance linewidth, as the peak-to-peak power absorption derivative at 9.6 GHz, was measured to be 62 Oe. These properties demonstrate a rapid, convenient, cost-effective, and nontoxic method of growing high quality thick crystalline ferrite films which could be used widely for microwave device applications.

  9. Nanometer-scale structure of alkali-soluble bio-macromolecules of maize plant residues explains their recalcitrance in soil.

    Science.gov (United States)

    Adani, Fabrizio; Salati, Silvia; Spagnol, Manuela; Tambone, Fulvia; Genevini, Pierluigi; Pilu, Roberto; Nierop, Klaas G J

    2009-07-01

    The quantity and quality of plant litter in the soil play an important role in the soil organic matter balance. Besides other pedo-climatic aspects, the content of recalcitrant molecules of plant residues and their chemical composition play a major role in the preservation of plant residues. In this study, we report that intrinsically resistant alkali-soluble bio-macromolecules extracted from maize plant (plant-humic acid) (plant-HA) contribute directly to the soil organic matter (OM) by its addition and conservation in the soil. Furthermore, we also observed that a high syringyl/guaiacyl (S/G) ratio in the lignin residues comprising the plant tissue, which modifies the microscopic structure of the alkali-soluble plant biopolymers, enhances their recalcitrance because of lower accessibility of molecules to degrading enzymes. These results are in agreement with a recent study, which showed that the humic substance of soil consists of a mixture of identifiable biopolymers obtained directly from plant tissues that are added annually by maize plant residues.

  10. Automation in biological crystallization

    Science.gov (United States)

    Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

    2014-01-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

  11. Automation in biological crystallization.

    Science.gov (United States)

    Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

    2014-06-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

  12. Detailed optical spectroscopy of hybridization gap and hidden-order transition in high-quality URu2Si2 single crystals

    Science.gov (United States)

    Bachar, N.; Stricker, D.; Muleady, S.; Wang, K.; Mydosh, J. A.; Huang, Y. K.; van der Marel, D.

    2016-12-01

    We present a detailed temperature and frequency dependence of the optical conductivity measured on clean high-quality single crystals of URu2Si2 of a c - and a b -plane surfaces. Our data demonstrate the itinerant character of the narrow 5 f bands, becoming progressively coherent as the temperature is lowered below a crossover temperature T*˜75 K. T* is higher than in previous reports as a result of a different sample preparation, which minimizes residual strain. We furthermore present the density-response (energy-loss) function of this compound, and determine the energies of the heavy-fermion plasmons with a - and c -axis polarization. Our observation of a suppression of optical conductivity below 50 meV along both the a and c axes, along with a heavy-fermion plasmon at 18 meV, points toward the emergence of a band of coherent charge carriers crossing the Fermi energy and the emergence of a hybridization gap on part of the Fermi surface. The evolution towards coherent itinerant states is accelerated below the hidden order temperature THO=17.5 K. In the hidden order phase the low-frequency optical conductivity shows a single gap at ˜6.5 meV, which closes at THO.

  13. Availability and chemical quality of ground water in the Crystal River and Cattle Creek Drainage Basins near Glenwood Springs, west-central Colorado

    Science.gov (United States)

    Brogden, Robert E.; Giles, T.F.

    1976-01-01

    Parts of the Crystal River and cattle Creek drainage basins near Glenwood Springs, Colo., have undergone rapid population growth in recent years. This growth has resulted in an increased demand for information for additional domestic, industrial, and municipal water supplies. A knowledge of the occurrence of ground water will permit a more efficient allocation of the resource. Aquifers in the two drainage basins include: alluvium, basalts, the Mesa Verde Formation, Mancos Shale, Dakota Sandstone, Morrison Formation, Entrada Sandstone, Maroon Formation, Eagle Valley Evaporite, and undifferentiated formations. Except for aquifers in the alluvium, and basalt, well yields are generally low and are less than 25 gallons per minute. Well yields form aquifers in the alluvium and basalt can be as much as several hundred gallons per minute. Water quality is dependent of rock type. Calcium bicarbonate is the predominant type of water in the study area. However, calcium sulfate type water may be found in aquifers in the Eagle Valley Evaporite and in the alluvium where the alluvial material has been derived from the Eagle Valley Evaporite. Concentrations of selenium in excess of U.S. Public Health Service standards for drinking water can be found locally in aquifers in the Eagle Valley Evaporite. (Woodard-USGS)

  14. Investigating the nucleation of protein crystals with hydrostatic pressure

    Energy Technology Data Exchange (ETDEWEB)

    Kadri, A [Departement ' Mecanismes et Macromolecules de la Synthese Proteique et Cristallogenese' UPR 9002, Institut de Biologie Moleculaire et Cellulaire du CNRS, 15 rue Rene Descartes, F-67084 Strasbourg Cedex (France); Damak, M [Laboratoire de Chimie des Substances Naturelles, Faculte des Sciences de Sfax, BP 802, 3018 Sfax (Tunisia); Jenner, G [Laboratoire de Piezochimie Organique, UMR 7123, Faculte de Chimie, Universite Louis Pasteur, 1 rue Blaise Pascal, F-67008 Strasbourg Cedex (France); Lorber, B [Departement ' Mecanismes et Macromolecules de la Synthese Proteique et Cristallogenese' UPR 9002, Institut de Biologie Moleculaire et Cellulaire du CNRS, 15 rue Rene Descartes, F-67084 Strasbourg Cedex (France); Giege, R [Departement ' Mecanismes et Macromolecules de la Synthese Proteique et Cristallogenese' UPR 9002, Institut de Biologie Moleculaire et Cellulaire du CNRS, 15 rue Rene Descartes, F-67084 Strasbourg Cedex (France)

    2003-12-17

    Hydrostatic pressure in the 0.1-75 MPa range has been used as a non-invasive tool to study the crystallization process of the tetragonal crystal form of the protein thaumatin (M{sub r} 22 200). Crystals were prepared within agarose gel and at temperatures in the range from 283 to 303 K. The solubility, i.e. the concentration of soluble macromolecules remaining in equilibrium with the crystals, decreases when the pressure increases and when the temperature decreases. High pressure was used to probe the nucleation behaviour of thaumatin. The pressure dependence of the nucleation rate leads to an activation volume of -46.5cm{sup 3} mol{sup -1}. It is shown that an increase in pressure decreases the enthalpy, the entropy and the free energy of crystallization of thaumatin. The data are discussed in the light of the results of crystallographic analyses and of the structure of the protein.

  15. Hypersonic phononic crystals.

    Science.gov (United States)

    Gorishnyy, T; Ullal, C K; Maldovan, M; Fytas, G; Thomas, E L

    2005-03-25

    In this Letter we propose the use of hypersonic phononic crystals to control the emission and propagation of high frequency phonons. We report the fabrication of high quality, single crystalline hypersonic crystals using interference lithography and show that direct measurement of their phononic band structure is possible with Brillouin light scattering. Numerical calculations are employed to explain the nature of the observed propagation modes. This work lays the foundation for experimental studies of hypersonic crystals and, more generally, phonon-dependent processes in nanostructures.

  16. The role of the fast motion of the spin label in the interpretation of EPR spectra for spin-labeled macromolecules.

    Science.gov (United States)

    Timofeev, Vladimir P; Nikolsky, Dmitriy O

    2003-12-01

    The spin label method was used to observe the nature of the fast motions of side chains in protein monocrystals. The EPR spectra of spin-labeled lysozyme monocrystals (with different orientations of the tetragonal protein crystal in relation to the direction of the magnetic field) were interpreted using the method of molecular dynamics (MD). Within the proposed simple model, MD calculations of the spin label motion trajectories are performed in a reasonable real time. The model regards the protein molecule as frozen as a whole and the spin-labeled amino acid residue as unfrozen. To calculate the trajectories in vacuum, a model of spin-labeled lysozyme was assembled, and the parameters of the force fields were specified for atoms of the protein molecule, including the spin label. The calculations show that the protein environment sterically limits the area of the possible angular reorientations for the NO reporter group of the nitroxide (within the spin label), and this, in turn, affects the shape of the EPR spectrum. However, it turned out that the spread in the positions of the reporter group in the angle space strictly adheres to the Gaussian distribution. Using the coordinates of the spin label atoms obtained by the MD method within a selected time range and considering the distribution of the spin label states over the ensemble of spin-labeled macromolecules in a crystal, the EPR spectra of spin-labeled lysozyme monocrystals were simulated. The resultant theoretical EPR spectra appeared to be similar to experimental ones.

  17. Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering.

    Science.gov (United States)

    Tria, Giancarlo; Mertens, Haydyn D T; Kachala, Michael; Svergun, Dmitri I

    2015-03-01

    Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving the function and molecular interactions of 'unstructured' and flexible molecules requires alternative approaches to those traditionally employed in structural biology. Small-angle X-ray scattering (SAXS) is an established method for structural characterization of biological macromolecules in solution, and is directly applicable to the study of flexible systems such as intrinsically disordered proteins and multi-domain proteins with unstructured regions. The Ensemble Optimization Method (EOM) [Bernadó et al. (2007 ▶). J. Am. Chem. Soc. 129, 5656-5664] was the first approach introducing the concept of ensemble fitting of the SAXS data from flexible systems. In this approach, a large pool of macromolecules covering the available conformational space is generated and a sub-ensemble of conformers coexisting in solution is selected guided by the fit to the experimental SAXS data. This paper presents a series of new developments and advancements to the method, including significantly enhanced functionality and also quantitative metrics for the characterization of the results. Building on the original concept of ensemble optimization, the algorithms for pool generation have been redesigned to allow for the construction of partially or completely symmetric oligomeric models, and the selection procedure was improved to refine the size of the ensemble. Quantitative measures of the flexibility of the system studied, based on the characteristic integral parameters of the selected ensemble, are introduced. These improvements are implemented in the new EOM version 2.0, and the capabilities as well as inherent limitations of the ensemble approach in SAXS, and of EOM 2.0 in particular, are discussed.

  18. Aqueous self-assembly of hydrophobic macromolecules with adjustable rigidity of the backbone.

    Science.gov (United States)

    Guan, Zhou; Liu, Dapeng; Lin, Jiaping; Wang, Xiaosong

    2017-08-02

    P(FpC3P) (Fp: CpFe(CO)2; C3P: propyl diphenyl phosphine) has a helical backbone, resulting from piano stool metal coordination geometry, which is rigid with intramolecular aromatic interaction of the phenyl groups. The macromolecule is hydrophobic, but the polarized CO groups can interact with water for aqueous self-assembly. The stiffness of P(FpC3P), which is adjustable by temperature, is an important factor influencing the morphologies of kinetically trapped assemblies. P(FpC3P)7 self-assembles in DMSO/water (10/90 by volume) into lamellae at 25 °C, vesicles at 40 °C and irregular aggregates at higher temperatures (60 and 70 °C). The colloidal stability decreases in the order of lamellae, vesicles and irregular aggregates. Dissipative particle dynamics (DPD) simulation reveals the same temperature-dependent self-assembled morphologies with an interior of hydrophobic aromatic groups covered with the metal coordination units. The rigid backbone at 25 °C accounts for the formation of the layered morphology, while the reduced rigidity of the same P(FpC3P)7 at 40 °C curves up the lamellae into vesicles. At a higher temperature (60 or 70 °C), P(FpC3P)7 behaves as a random coil without obvious amphiphilic segregation, resulting in irregular aggregates. The stiffness is, therefore, a crucial factor for the aqueous assembly of macromolecules without obvious amphiphilic segregation, which is reminiscent of the solution behavior observed for many hydrophobic biological macromolecules such as proteins.

  19. Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering

    Directory of Open Access Journals (Sweden)

    Giancarlo Tria

    2015-03-01

    Full Text Available Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving the function and molecular interactions of `unstructured' and flexible molecules requires alternative approaches to those traditionally employed in structural biology. Small-angle X-ray scattering (SAXS is an established method for structural characterization of biological macromolecules in solution, and is directly applicable to the study of flexible systems such as intrinsically disordered proteins and multi-domain proteins with unstructured regions. The Ensemble Optimization Method (EOM [Bernadó et al. (2007. J. Am. Chem. Soc. 129, 5656–5664] was the first approach introducing the concept of ensemble fitting of the SAXS data from flexible systems. In this approach, a large pool of macromolecules covering the available conformational space is generated and a sub-ensemble of conformers coexisting in solution is selected guided by the fit to the experimental SAXS data. This paper presents a series of new developments and advancements to the method, including significantly enhanced functionality and also quantitative metrics for the characterization of the results. Building on the original concept of ensemble optimization, the algorithms for pool generation have been redesigned to allow for the construction of partially or completely symmetric oligomeric models, and the selection procedure was improved to refine the size of the ensemble. Quantitative measures of the flexibility of the system studied, based on the characteristic integral parameters of the selected ensemble, are introduced. These improvements are implemented in the new EOM version 2.0, and the capabilities as well as inherent limitations of the ensemble approach in SAXS, and of EOM 2.0 in particular, are discussed.

  20. Impacts of Organic Macromolecules, Chlorophyll and Soot on Arctic Sea Ice

    Science.gov (United States)

    Ogunro, O. O.; Wingenter, O. W.; Elliott, S.; Flanner, M.; Dubey, M. K.

    2014-12-01

    Recent intensification of Arctic amplification can be strongly connected to positive feedback relating black carbon deposition to sea ice surface albedo. In addition to soot deposition on the ice and snow pack, ice algal chlorophyll is likely to compete as an absorber and redistributor of energy. Hence, solar radiation absorption by chlorophyll and some components of organic macromolecules in/under the ice column is currently being examined to determine the level of influence on predicted rate of ice loss. High amounts of organic macromolecules and chlorophyll are produced in global sea ice by the bottom microbial community and also in vertically distributed layers where substantial biological activities take place. Brine channeling in columnar ice can allow for upward flow of nutrients which leads to greater primary production in the presence of moderate light. Modeling of the sea-ice processes in tandem with experiments and field observations promises rapid progress in enhancing Arctic ice predictions. We are designing and conducting global climate model experiments to determine the impact of organic macromolecules and chlorophyll on Arctic sea ice. Influences on brine network permeability and radiation/albedo will be considered in this exercise. Absorption by anthropogenic materials such as soot and black carbon will be compared with that of natural pigments. We will indicate areas of soot and biological absorption dominance in the sense of single scattering, then couple into a full radiation transfer scheme to attribute the various contributions to polar climate change amplification. The work prepares us to study more traditional issues such as chlorophyll warming of the pack periphery and chemical effects of the flow of organics from ice internal communities. The experiments started in the Arctic will broaden to include Antarctic sea ice and shelves. Results from the Arctic simulations will be presented.

  1. High quality factor and high sensitivity photonic crystal rectangular holes slot nanobeam cavity with parabolic modulated lattice constant for refractive index sensing

    Science.gov (United States)

    Sun, Fujun; Zhou, Jian; Huang, Lijun; Fu, Zhongyuan; Tian, Huiping

    2017-09-01

    In this paper, we present a novel optical sensor based on photonic crystal slot nanobeam cavity (PCSNC) with rectangular air holes. By introducing a continuous slot and quadratically modulated hole spacing (lattice constant a) structure, the majority of the optical field is localized in the slot region, which enhances the light-matter interaction. With applying the three dimensional finite-difference time-domain (3D-FDTD) simulations, three key geometric parameters (hole width wx, slot width ws and the number of the holes N) are optimized to achieve a high sensitivity (S) while keeping a high quality (Q) factor. The highest S over 1000 nm/RIU (refractive index unit) is achieved when the slot width equals to 200 nm. The highest Q-factor of 2.15×107 is obtained when 30 holes are placed on both sides of the host waveguide with the slot width of 80 nm. Considering the transmission efficiency and the trade-off between S and Q-factor, the slot width and the number of the tapered region are chosen as 80 nm and 20, respectively. A high S approximately 835 nm/RIU and a Q-factor about 5.50×105 with small effective mode volume of 0.03(λ/nair)3 are achieved simultaneously, resulting in an ultra-high figure-of-merit (FOM) above 2.92×105. Furthermore, the active sensing region of the optimized structure occupies only about 12 μm×0.08 μm, which makes the device attractive for realizing on-chip integrated sensor arrays.

  2. Image quality performance of liquid crystal display systems: influence of display resolution, magnification and window settings on contrast-detail detection.

    Science.gov (United States)

    Bacher, Klaus; Smeets, Peter; De Hauwere, An; Voet, Tony; Duyck, Philippe; Verstraete, Koenraad; Thierens, Hubert

    2006-06-01

    The aim of this study was to investigate the combined effects of liquid crystal display (LCD) resolution, image magnification and window/level adjustment on the low-contrast performance in soft-copy image interpretation in digital radiography and digital mammography. In addition, the effect of a new LCD noise reduction mechanism on the low-contrast detectability was studied. Digital radiographs and mammograms of two dedicated contrast-detail phantoms (CDRAD 2.0 and CDMAM 3.4) were scored on five LCD devices with varying resolutions (1-3- and 5-megapixel) and one dedicated 5-megapixel cathode ray tube monitor. Two 5-megapixel LCDs were included. The first one was a standard 5-megapixel LCD and the second had a new (Per Pixel Uniformity) noise reduction mechanism. A multi-variate analysis of variance revealed a significant influence of LCD resolution, image magnification and window/level adjustment on the image quality performance assessed with both the CDRAD 2.0 and the CDMAM 3.4 phantoms. The interactive adjustment of brightness and contrast of digital images did not affect the reading time, whereas magnification to full resolution resulted in a significantly slower soft-copy interpretation. For digital radiography applications, a 3-megapixel LCD is comparable with a 5-megapixel CRT monitor in terms of low-contrast performance as well as in reading time. The use of a 2-megapixel LCD is only warranted when radiographs are analysed in full resolution and when using the interactive window/level adjustment. In digital mammography, a 5-megapixel monitor should be the first choice. In addition, the new PPU noise reduction system in the 5-megapixel LCD devices provides significantly better results for mammography reading as compared to a standard 5-magapixel LCD or CRT. If a 3-megapixel LCD is used in mammography setting, a very time-consuming magnification of the digital mammograms would be necessary.

  3. Image quality performance of liquid crystal display systems: Influence of display resolution, magnification and window settings on contrast-detail detection

    Energy Technology Data Exchange (ETDEWEB)

    Bacher, Klaus [Department of Medical Physics and Radiation Protection, Ghent University, Proeftuinstraat 86, B-9000 Gent (Belgium)]. E-mail: klaus.bacher@ugent.be; Smeets, Peter [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); De Hauwere, An [Department of Medical Physics and Radiation Protection, Ghent University, Proeftuinstraat 86, B-9000 Gent (Belgium); Voet, Tony [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); Duyck, Philippe [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); Verstraete, Koenraad [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); Thierens, Hubert [Department of Medical Physics and Radiation Protection, Ghent University, Proeftuinstraat 86, B-9000 Gent (Belgium)

    2006-06-15

    The aim of this study was to investigate the combined effects of liquid crystal display (LCD) resolution, image magnification and window/level adjustment on the low-contrast performance in soft-copy image interpretation in digital radiography and digital mammography. In addition, the effect of a new LCD noise reduction mechanism on the low-contrast detectability was studied. Digital radiographs and mammograms of two dedicated contrast-detail phantoms (CDRAD 2.0 and CDMAM 3.4) were scored on five LCD devices with varying resolutions (1-3- and 5-megapixel) and one dedicated 5-megapixel cathode ray tube monitor. Two 5-megapixel LCDs were included. The first one was a standard 5-megapixel LCD and the second had a new (Per Pixel Uniformity) noise reduction mechanism. A multi-variate analysis of variance revealed a significant influence of LCD resolution, image magnification and window/level adjustment on the image quality performance assessed with both the CDRAD 2.0 and the CDMAM 3.4 phantoms. The interactive adjustment of brightness and contrast of digital images did not affect the reading time, whereas magnification to full resolution resulted in a significantly slower soft-copy interpretation. For digital radiography applications, a 3-megapixel LCD is comparable with a 5-megapixel CRT monitor in terms of low-contrast performance as well as in reading time. The use of a 2-megapixel LCD is only warranted when radiographs are analysed in full resolution and when using the interactive window/level adjustment. In digital mammography, a 5-megapixel monitor should be the first choice. In addition, the new PPU noise reduction system in the 5-megapixel LCD devices provides significantly better results for mammography reading as compared to a standard 5-magapixel LCD or CRT. If a 3-megapixel LCD is used in mammography setting, a very time-consuming magnification of the digital mammograms would be necessary.

  4. Small and Wide Angle X-ray Scattering studies of biological macromolecules in solution.

    Science.gov (United States)

    Liu, Li; Boldon, Lauren; Urquhart, Melissa; Wang, Xiangyu

    2013-01-08

    In this paper, Small and Wide Angle X-ray Scattering (SWAXS) analysis of macromolecules is demonstrated through experimentation. SWAXS is a technique where X-rays are elastically scattered by an inhomogeneous sample in the nm-range at small angles (typically 0.1 - 5°) and wide angles (typically > 5°). This technique provides information about the shape, size, and distribution of macromolecules, characteristic distances of partially ordered materials, pore sizes, and surface-to-volume ratio. Small Angle X-ray Scattering (SAXS) is capable of delivering structural information of macromolecules between 1 and 200 nm, whereas Wide Angle X-ray Scattering (WAXS) can resolve even smaller Bragg spacing of samples between 0.33 nm and 0.49 nm based on the specific system setup and detector. The spacing is determined from Bragg's law and is dependent on the wavelength and incident angle. In a SWAXS experiment, the materials can be solid or liquid and may contain solid, liquid or gaseous domains (so-called particles) of the same or another material in any combination. SWAXS applications are very broad and include colloids of all types: metals, composites, cement, oil, polymers, plastics, proteins, foods, and pharmaceuticals. For solid samples, the thickness is limited to approximately 5 mm. Usage of a lab-based SWAXS instrument is detailed in this paper. With the available software (e.g., GNOM-ATSAS 2.3 package by D. Svergun EMBL-Hamburg and EasySWAXS software) for the SWAXS system, an experiment can be conducted to determine certain parameters of interest for the given sample. One example of a biological macromolecule experiment is the analysis of 2 wt% lysozyme in a water-based aqueous buffer which can be chosen and prepared through numerous methods. The preparation of the sample follows the guidelines below in the Preparation of the Sample section. Through SWAXS experimentation, important structural parameters of lysozyme, e.g. the radius of gyration, can be analyzed.

  5. Key factors regulating the mass delivery of macromolecules to model cell membranes

    DEFF Research Database (Denmark)

    Campbell, Richard A.; Watkins, Erik B.; Jagalski, Vivien

    2014-01-01

    We show that both gravity and electrostatics are key factors regulating interactions between model cell membranes and self-assembled liquid crystalline aggregates of dendrimers and phospholipids. The system is a proxy for the trafficking of reservoirs of therapeutic drugs to cell membranes for slow...... diffusion and continuous delivery. Neutron reflectometry measurements were carried out on supported lipid bilayers of varying charge and on hydrophilic silica surfaces. Translocation of the macromolecule across the membrane and adsorption of the lamellar aggregates occur only when the membrane (1...... of the aggregates to activate endocytosis pathways on specific cell types is discussed in the context of targeted drug delivery applications....

  6. Controlled uniform coating from the interplay of Marangoni flows and surface-adsorbed macromolecules

    CERN Document Server

    Kim, Hyoungsoo; Um, Eujin; Jacobi, Ian; Button, Ernie; Stone, Howard A

    2016-01-01

    Surface coatings and patterning technologies are essential for various physicochemical applications. In this Letter, we describe key parameters to achieve uniform particle coatings in binary solutions: First, multiple sequential Marangoni flows, set by solute and surfactant simultaneously, prevent non-uniform particle distributions and continuously mix suspended materials during droplet evaporation. Second, we show the importance of particle-surface interactions that can be established by surface-adsorbed macromolecules. To achieve a uniform deposit in a binary mixture a small concentration of surfactant and surface-adsorbed polymer (0.05 wt% each) is sufficient, which offers a new physicochemical avenue for control of coatings.

  7. Differential scanning calorimetry: An invaluable tool for a detailed thermodynamic characterization of macromolecules and their interactions

    Directory of Open Access Journals (Sweden)

    Michael H Chiu

    2011-01-01

    Full Text Available Differential Scanning Calorimetry (DSC is a highly sensitive technique to study the thermotropic properties of many different biological macromolecules and extracts. Since its early development, DSC has been applied to the pharmaceutical field with excipient studies and DNA drugs. In recent times, more attention has been applied to lipid-based drug delivery systems and drug interactions with biomimetic membranes. Highly reproducible phase transitions have been used to determine values, such as, the type of binding interaction, purity, stability, and release from a drug delivery mechanism. This review focuses on the use of DSC for biochemical and pharmaceutical applications.

  8. Isolation of cell nuclei using inert macromolecules to mimic the crowded cytoplasm.

    Directory of Open Access Journals (Sweden)

    Ronald Hancock

    Full Text Available Cell nuclei are commonly isolated and studied in media which include millimolar concentrations of cations, which conserve the nuclear volume by screening the negative charges on chromatin and maintaining its compaction. However, two factors question if these ionic conditions correctly reproduce the environment of nuclei in vivo: the small-scale motion and conformation of chromatin in vivo are not reproduced in isolated nuclei, and experiments and theory suggest that small ions in the cytoplasm are not free in the soluble phase but are predominantly bound to macromolecules. We studied the possible role in maintaining the structure and functions of nuclei in vivo of a further but frequently overlooked property of the cytoplasm, the crowding or osmotic effects caused by diffusible macromolecules whose concentration, measured in several studies, is in the range of 130 mg/ml. Nuclei which conserved their volume in the cell and their ultrastructure seen by electron microscopy were released from K562 cells in media containing the inert polymer 70 kDa Ficoll (50% w/v or 70 kDa dextran (35% w/v to replace the diffusible cytoplasmic molecules which were dispersed on cell lysis with digitonin, with 100 microM K-Hepes buffer as the only source of ions. Immunofluorescence labelling and experiments using cells expressing GFP-fusion proteins showed that internal compartments (nucleoli, PML and coiled bodies, foci of RNA polymerase II were conserved in these nuclei, and nascent RNA transcripts could be elongated. Our observations are consistent with the hypothesis that crowding by diffusible cytoplasmic macromolecules is a crucial but overlooked factor which supports the nucleus in vivo by equilibrating the opposing osmotic pressure cause by the high concentration of macromolecules in the nucleus, and suggest that crowded media provide more physiological conditions to study nuclear structure and functions. They may also help to resolve the long-standing paradox

  9. Cluster of red blood cells in microcapillary flow: hydrodynamic versus macromolecule induced interaction

    CERN Document Server

    Clavería, Viviana; Thiébaud, Marine; Abkarian, Manouk; Coupier, Gwennou; Misbah, Chaouqi; John, Thomas; Wagner, Christian

    2016-01-01

    We present experiments on RBCs that flow through microcapillaries under physiological conditions. We show that the RBC clusters form as a subtle imbrication between hydrodynamics interaction and adhesion forces because of plasma proteins. Clusters form along the capillaries and macromolecule-induced adhesion contribute to their stability. However, at high yet physiological flow velocities, shear stresses overcome part of the adhesion forces, and cluster stabilization due to hydrodynamics becomes the only predominant mechanism. For the case of pure hydrodynamic interaction, cell-to-cell distances have a pronounced bimodal distribution. Our 2D-numerical simulations on vesicles captures the transition between adhesive and non-adhesive clusters at different flow velocities.

  10. Differential scanning calorimetry: An invaluable tool for a detailed thermodynamic characterization of macromolecules and their interactions

    Science.gov (United States)

    Chiu, Michael H.; Prenner, Elmar J.

    2011-01-01

    Differential Scanning Calorimetry (DSC) is a highly sensitive technique to study the thermotropic properties of many different biological macromolecules and extracts. Since its early development, DSC has been applied to the pharmaceutical field with excipient studies and DNA drugs. In recent times, more attention has been applied to lipid-based drug delivery systems and drug interactions with biomimetic membranes. Highly reproducible phase transitions have been used to determine values, such as, the type of binding interaction, purity, stability, and release from a drug delivery mechanism. This review focuses on the use of DSC for biochemical and pharmaceutical applications. PMID:21430954

  11. Macromolecules Mimicking Backbones of Nucleic and Teichoic Acids.Synthesis,Some Properties and Applications

    Institute of Scientific and Technical Information of China (English)

    Stanislaw; Penczek; Julia; B.Pretula; Krzysztof; Kaluzynski

    2007-01-01

    1 Results Several methods have been elaborated in this laboratory allowing preparation of macromolecules with phosphodiester bonds,and having sequence of atoms similar as in the chains of biomacromolecules - nucleic or teichoic acids (TA),namely:-(C)n-O-PO-,where n=2 (for teichoic acids) or 3.These methods,to be discussed in the lecture,are based on the ring-opening polymerization,transesterification,and recently elaborated direct addition of phosphoric acid to diepoxides.For the first time an attempt h...

  12. Interactions between macromolecule-bound antioxidants and Trolox during liposome autoxidation

    DEFF Research Database (Denmark)

    Celik, Ecem Evrim; Amigo Rubio, Jose Manuel; Andersen, Mogens Larsen

    2017-01-01

    The interactions between free and macromolecule-bound antioxidants were investigated in order to evaluate their combined effects on the antioxidant environment. Dietary fiber (DF), protein and lipid-bound antioxidants, obtained from whole wheat, soybean and olive oil products, respectively...... of the simple addition effects of Trolox and bound antioxidants with measured values on lipid oxidation revealed synergetic interactions for DF and refined olive oil-bound antioxidants, and antagonistic interactions for protein and extra virgin olive oil-bound antioxidants with Trolox. A generalized version...

  13. Advanced Crystal Growth Technology

    Energy Technology Data Exchange (ETDEWEB)

    Land, T A; Hawley-Fedder, R A

    2005-03-01

    Although the fundamental mechanism of crystal growth has received and continues to receive deserved attention as a research activity, similar research efforts addressing the need for advanced materials and processing technology required to grow future high quality crystals has been sorely lacking. The purpose of this research effort is to develop advanced rapid growth processing technologies and materials suitable for providing the quality of products needed for advanced laser and photonics applications. In particular we are interested in developing a methodology for growing high quality KDP crystals based on an understanding of the fundamental mechanisms affecting growth. One problem in particular is the issue of control of impurities during the growth process. Many unwanted impurities are derived from the growth system containers and can adversely affect the optical quality and aspect ratio (shape) of the crystals. Previous studies have shown that even trace concentrations ({approx}10{sup -9} M) of impurities affect growth and even 'insignificant' species can have a large impact. It is also known that impurities affect the two growth faces of KDP very differently. Traces of trivalent metal impurities such as Fe{sup 3+}, Cr{sup 3+}, and Al{sup 3+} in solution are known to inhibit growth of the prismatic {l_brace}100{r_brace} faces of KDP while having little effect on the growth of the pyramidal {l_brace}101{r_brace} faces. This differentiation opens the possibility of intentionally adding select ions to control the aspect ratio of the crystal to obtain a more advantageous shape. This document summarizes our research efforts to improve KDP crystal growth. The first step was to control unwanted impurity addition from the growth vessel by developing an FEP liner to act as a barrier to the glass container. The other focus to develop an understanding of select impurities on growth rates in order to be able to use them to control the habit or shape of the

  14. Effect of ZnI2 cosolute on quality and performance of γ-CuI ultrafast scintillation crystal grown via evaporation method in acetonitrile solvent

    Science.gov (United States)

    Yue, Shuangqiang; Gu, Mu; Liu, Xiaolin; Zhang, Juannan; Huang, Shiming; Liu, Bo; Ni, Chen

    2017-04-01

    γ-CuI single crystal was grown via evaporation method in ZnI2 acetonitrile solvent. The ZnI2 plays a unique role which can not only increase the solubility of CuI in acetonitrile but also introduce the Zn and I ions in the crystal. The γ-CuI crystal grown in ZnI2 acetonitrile is regular and transparent. Its size reaches up to 18 × 11 × 2 mm3 which is larger than that of the crystal grown in pure acetonitrile. In terms of the photoluminescence, the intensity of the emission at 411 nm of the crystal grown with ZnI2 as a cosolute is much higher than that of the crystal grown without ZnI2, which implies that the crystallinity of the crystal can be improved by ZnI2 doping. The X-ray excited luminescence of the crystal shows that the emission at 435 nm can be significantly enhanced and the emission near 680 nm can be suppressed by introducing Zn and I in the natural non-stoichiometry γ-CuI crystal. The nature of the phenomena is discussed. The decay time of the emission at 435 nm similar to that of the emission at 411 nm is faster than the detection limit of the instrument, i.e. less than 1 ns, and the average decay time of the emission near 680 nm is about 183 ns. The results can provide a useful guide to optimize the scintillation properties of γ-CuI single crystal.

  15. Configurational diffusion of coal macromolecules. Final technical report, September 15, 1986--September 14, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Guin, J.A.; Curtis, C.W.; Tarrer, A.R.; Kim, S.; Hwang, D.; Chen, C.C.; Chiou, Z.

    1991-12-31

    The objective of our research was to obtain fundamental information regarding the functional dependence of the diffusion coefficient of coal molecules on the ratio of molecule to pore diameter. That is, the objective of our study was to examine the effect of molecule size and configuration on hindered diffusion of coal macromolecules through as porous medium. To best accomplish this task, we circumvented the complexities of an actual porous catalyst by using a well defined porous matrix with uniform capillaric pores, i.e., a track-etched membrane. In this way, useful information was obtained regarding the relationship of molecular size and configuration on the diffusion rate of coal derived macromolecules through a pore structure with known geometry. Similar studies were performed using a pellet formed of porous alumina, to provide a link between the idealized membranes and the actual complex pore structure of real catalyst extrudates. The fundamental information from our study will be useful toward the tailoring of catalysts to minimize diffusional influences and thereby increase coal conversion and selectivity for desirable products. (VC)

  16. Toward detecting and identifying macromolecules in a cellular context: Template matching applied to electron tomograms

    Science.gov (United States)

    Böhm, Jochen; Frangakis, Achilleas S.; Hegerl, Reiner; Nickell, Stephan; Typke, Dieter; Baumeister, Wolfgang

    2000-01-01

    Electron tomography is the only technique available that allows us to visualize the three-dimensional structure of unfixed and unstained cells currently with a resolution of 6–8 nm, but with the prospect to reach 2–4 nm. This raises the possibility of detecting and identifying specific macromolecular complexes within their cellular context by virtue of their structural signature. Templates derived from the high-resolution structure of the molecule under scrutiny are used to search the reconstructed volume. Here we outline and test a computationally feasible two-step procedure: In a first step, mean-curvature motion is used for segmentation, yielding subvolumes that contain with a high probability macromolecules in the expected size range. Subsequently, the particles contained in the subvolumes are identified by cross-correlation, using a set of three-dimensional templates. With simulated and real tomographic data we demonstrate that such an approach is feasible and we explore the detection limits. Even structurally similar particles, such as the thermosome, GroEL, and the 20S proteasome can be identified with high fidelity. This opens up exciting prospects for mapping the territorial distribution of macromolecules and for analyzing molecular interactions in situ. PMID:11087814

  17. Development of a Non-Aqueous Dispersion to Improve Intestinal Epithelial Flux of Poorly Permeable Macromolecules.

    Science.gov (United States)

    Maher, Sam; Medani, Mekki; Carballeira, Nestor N; Winter, Desmond C; Baird, Alan W; Brayden, David J

    2017-01-01

    Intestinal permeation enhancers (PEs) offer an attractive strategy to enable oral peptide administration. However, optimal presentation of peptide and PE from solid-dosage forms is offset by slow dissolution rates in the small intestine, which reduces the likelihood that the PE can reach the threshold concentration for sufficient permeability enhancement. The purpose of this study was to design a PE-based liquid dispersion that can improve intestinal permeation of macromolecules across Caco-2 monolayers and isolated rat/human intestinal mucosae mounted in Ussing chambers. An enhancer screen in monolayers based on permeability (TEER, Papp [(14)C]-mannitol) and cytotoxicity (MTT assay) initially identified methyl 10-hydroxydecanoate (10-OHC10CH3) as a candidate. 10-OHC10CH3 (20 mM) increased the Papp of fluorescent dextran of 4 kDa (FD4) (167-fold), 10 kDa (FD10) (429-fold), and 40 kDa (FD40) (520-fold) across monolayers. Blends of 10-OHC10CH3 with low molecular weight PEGs (0.2-1 kDa) formed liquid dispersions in which enhancement capacity across monolayers of 10-OHC10CH3 was increased over 10-OHC10CH3 alone in the order PEG200 macromolecules.

  18. Cryo-electron microscopy for structural analysis of dynamic biological macromolecules.

    Science.gov (United States)

    Murata, Kazuyoshi; Wolf, Matthias

    2017-07-27

    Since the introduction of what became today's standard for cryo-embedding of biological macromolecules at native conditions more than 30years ago, techniques and equipment have been drastically improved and the structure of biomolecules can now be studied at near atomic resolution by cryo-electron microscopy (cryo-EM) while capturing multiple dynamic states. Here we review the recent progress in cryo-EM for structural studies of dynamic biological macromolecules. We provide an overview of the cryo-EM method and introduce contemporary studies to investigate biomolecular structure and dynamics, including examples from the recent literature. Cryo-EM is a powerful tool for the investigation of biological macromolecular structures including analysis of their dynamics by using advanced image-processing algorithms. The method has become even more widely applicable with present-day single particle analysis and electron tomography. The cryo-EM method can be used to determine the three-dimensional structure of biomacromolecules in near native condition at close to atomic resolution, and has the potential to reveal conformations of dynamic molecular complexes. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  19. Coupled Segmentation of Nuclear and Membrane-bound Macromolecules through Voting and Multiphase Level Set.

    Science.gov (United States)

    Chang, Hang; Wen, Quan; Parvin, Bahram

    2015-03-01

    Membrane-bound macromolecules play an important role in tissue architecture and cell-cell communication, and is regulated by almost one-third of the genome. At the optical scale, one group of membrane proteins expresses themselves as linear structures along the cell surface boundaries, while others are sequestered; and this paper targets the former group. Segmentation of these membrane proteins on a cell-by-cell basis enables the quantitative assessment of localization for comparative analysis. However, such membrane proteins typically lack continuity, and their intensity distributions are often very heterogeneous; moreover, nuclei can form large clump, which further impedes the quantification of membrane signals on a cell-by-cell basis. To tackle these problems, we introduce a three-step process to (i) regularize the membrane signal through iterative tangential voting, (ii) constrain the location of surface proteins by nuclear features, where clumps of nuclei are segmented through a delaunay triangulation approach, and (iii) assign membrane-bound macromolecules to individual cells through an application of multi-phase geodesic level-set. We have validated our method using both synthetic data and a dataset of 200 images, and are able to demonstrate the efficacy of our approach with superior performance.

  20. Effect of poly-L-arginine on intestinal absorption of hydrophilic macromolecules in rats.

    Science.gov (United States)

    Yamaki, Tsutomu; Uchida, Masaki; Kuwahara, Yusuke; Shimazaki, Yohei; Ohtake, Kazuo; Kimura, Mitsutoshi; Uchida, Hiroyuki; Kobayashi, Jun; Ogihara, Masahiko; Morimoto, Yasunori; Natsume, Hideshi

    2013-01-01

    We have already reported that poly-L-arginine (PLA) remarkably enhanced the in vivo nasal absorption of hydrophilic macromolecules without producing any significant epithelial damage in rats. In the present study, we examined whether PLA could enhance the absorption of a model hydrophilic macromolecule, fluorescein isothiocyanate-dextran (FD-4), across the intestinal mucosa, as well as the nasal mucosa, by an in situ closed-loop method using the rat intestine. PLA was found to enhance the intestinal absorption of FD-4 in a concentration-dependent manner within the concentrations investigated in this study, but segment-specific differences were found to be associated with this effect (ileum>jejunum>duodenum≧colon). The factors responsible for the segment-specific differences were also investigated by intestinal absorption studies using aprotinin, a trypsin inhibitor, and an analysis of the expression of occludin, a tight junction protein. In the small intestine, the differences in the effect of PLA on the absorption of FD-4 may be related to the enzymatic degradation of PLA. In the colon, the reduced effect of PLA on the absorption of FD-4 may be related to the smaller surface area for absorption and the higher expression of occludin compared with other segments.

  1. Complexation between a macromolecule and an amphiphile by Monte Carlo technique.

    Science.gov (United States)

    Gharibi, Hussein; Behjatmanesh-Ardakani, Reza; Hashemianzadeh, Majid; Mousavi-Khoshdel, Morteza

    2006-07-13

    Using a simple modified version of Larson's model, we studied the complexation between a macromolecule and an amphiphile in a dilute range of concentrations. The main characteristic of amphiphile molecules, that is, the hydrophobicity of the tails and hydrophilicity of the heads, is used to model the self-assembling process. Contrary to the molecular thermodynamics approaches, no prior shape was considered for the aggregates and the system was allowed to choose the most stable structure. For true ensemble averaging, without any synthetic results, configurational bias Monte Carlo and reptation moves are used to produce a Markov chain of configurations. From the results, it is found that the macromolecule causes the clusters of surfactants to be formed at a concentration much lower than the critical micelle concentration. Furthermore, the shape of the clusters tends to be more spherical, which is in line with theory and experiments. From the results, it is learned how a polymer can change the behavior of an amphiphilic molecule. All of the results are in good qualitative agreement with experimental and molecular thermodynamics results. Furthermore, the model predicts network formation between bound clusters at high concentrations of the surfactant.

  2. Combining modular ligation and supramolecular self-assembly for the construction of star-shaped macromolecules.

    Science.gov (United States)

    Altintas, Ozcan; Muller, Thierry; Lejeune, Elise; Plietzsch, Oliver; Bräse, Stefan; Barner-Kowollik, Christopher

    2012-06-14

    A well-defined random copolymer of styrene (S) and chloromethylstyrene (CMS) featuring lateral chlorine moieties with an alkyne terminal group is prepared (P(S-co-CMS), M(n) = 5500 Da, PDI = 1.13). The chloromethyl groups are converted into Hamilton wedge (HW) entities (P(S-co-HWS), M(n) = 6200 Da, PDI = 1.13). The P(S-co-HWS) polymer is subsequently ligated with tetrakis(4-azidophenyl)methane to give HW-functional star-shaped macromolecules (P(S-co-HWS))(4), M(n) = 25,100 Da, PDI = 1.08). Supramolecular star-shaped copolymers are then prepared via self-assembly between the HW-functionalized four-arm star-shaped macromolecules (P(S-co-HW))(4) and cyanuric acid (CA) end-functionalized PS (PS-CA, M(n) = 3700 Da, PDI = 1.04), CA end-functionalized poly(methyl methacrylate) (PMMA-CA, M(n) = 8500 Da, PDI = 1.13) and CA end-functionalized polyethylene glycol (PEG-CA, M(n) = 1700 Da, PDI = 1.05). The self-assembly is monitored by (1)H NMR spectroscopy and light scattering analyses.

  3. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.

    Science.gov (United States)

    Ashkenazy, Haim; Abadi, Shiran; Martz, Eric; Chay, Ofer; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir

    2016-07-08

    The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree.

  4. Smooth deuterated cellulose films for the visualisation of adsorbed bio-macromolecules.

    Science.gov (United States)

    Su, Jielong; Raghuwanshi, Vikram S; Raverty, Warwick; Garvey, Christopher J; Holden, Peter J; Gillon, Marie; Holt, Stephen A; Tabor, Rico; Batchelor, Warren; Garnier, Gil

    2016-10-31

    Novel thin and smooth deuterated cellulose films were synthesised to visualize adsorbed bio-macromolecules using contrast variation neutron reflectivity (NR) measurements. Incorporation of varying degrees of deuteration into cellulose was achieved by growing Gluconacetobacter xylinus in deuterated glycerol as carbon source dissolved in growth media containing D2O. The derivative of deuterated cellulose was prepared by trimethylsilylation(TMS) in ionic liquid(1-butyl-3-methylimidazolium chloride). The TMS derivative was dissolved in toluene for thin film preparation by spin-coating. The resulting film was regenerated into deuterated cellulose by exposure to acidic vapour. A common enzyme, horseradish peroxidase (HRP), was adsorbed from solution onto the deuterated cellulose films and visualized by NR. The scattering length density contrast of the deuterated cellulose enabled accurate visualization and quantification of the adsorbed HRP, which would have been impossible to achieve with non-deuterated cellulose. The procedure described enables preparing deuterated cellulose films that allows differentiation of cellulose and non-deuterated bio-macromolecules using NR.

  5. Smooth deuterated cellulose films for the visualisation of adsorbed bio-macromolecules

    Science.gov (United States)

    Su, Jielong; Raghuwanshi, Vikram S.; Raverty, Warwick; Garvey, Christopher J.; Holden, Peter J.; Gillon, Marie; Holt, Stephen A.; Tabor, Rico; Batchelor, Warren; Garnier, Gil

    2016-10-01

    Novel thin and smooth deuterated cellulose films were synthesised to visualize adsorbed bio-macromolecules using contrast variation neutron reflectivity (NR) measurements. Incorporation of varying degrees of deuteration into cellulose was achieved by growing Gluconacetobacter xylinus in deuterated glycerol as carbon source dissolved in growth media containing D2O. The derivative of deuterated cellulose was prepared by trimethylsilylation(TMS) in ionic liquid(1-butyl-3-methylimidazolium chloride). The TMS derivative was dissolved in toluene for thin film preparation by spin-coating. The resulting film was regenerated into deuterated cellulose by exposure to acidic vapour. A common enzyme, horseradish peroxidase (HRP), was adsorbed from solution onto the deuterated cellulose films and visualized by NR. The scattering length density contrast of the deuterated cellulose enabled accurate visualization and quantification of the adsorbed HRP, which would have been impossible to achieve with non-deuterated cellulose. The procedure described enables preparing deuterated cellulose films that allows differentiation of cellulose and non-deuterated bio-macromolecules using NR.

  6. STUDY ON THE EFFECT OF POLYSTYRENE SULFONIC ACID MACROMOLECULES ON THE POLYMERIZATION OF ACRYLAMIDE

    Institute of Scientific and Technical Information of China (English)

    WANG Shenguo; XI Fu; LI Zhifen

    1983-01-01

    The effect of polystyrene sulfonic acid (PSSA) macromolecules on the polymerization of acrylamide (AM) has been studied. It was found that the rates of polymerization of AM were greatly increased in the presence of PSSA in the polymerization system. The maximum value of the rate of polymerization of AM was obtained when the ratio of[-SO3H]: [AM] reached 3:1. When the insoluble crosslinked PSSA was used instead of the soluble one, this effect decreased considerably. The interaction between molecules of PSSA and AM was determined by infrared spectroscopy, elementary analysis and X-ray photoelectron spectroscopy.The combination form, -SO3-NH3+ CO-, formed between sulfonic group and amide group was found to be existed since the infrared absorption band of -NH2 shifted from 3400 cm-1 to 3150cm-1, the binding energy of electron N1S changed from 399.7 eV to 401.3 eV, and the atomic ratio of N to S of the products was similar to the ratio of reagents. Based on these experimental results, the mechanism of AM polymerization in the presence of PSSA is proposed. The initial step is the combination of AM with sulfonic group to form -CONH3+, then followed by polymerization on the PSSA macromolecule. The role of PSSA on the polymerization of AM is discussed.

  7. Food macromolecule based nanodelivery systems for enhancing the bioavailability of polyphenols

    Directory of Open Access Journals (Sweden)

    Bing Hu

    2017-01-01

    Full Text Available Diet polyphenols—primarily categorized into flavonoids (e.g., flavonols, flavones, flavan-3-ols, anthocyanidins, flavanones, and isoflavones and nonflavonoids (with major subclasses of stilbenes and phenolic acids—are reported to have health-promoting effects, such as antioxidant, antiinflammatory, anticarcinoma, antimicrobial, antiviral, and cardioprotective properties. However, their applications in functional foods or medicine are limited because of their inefficient systemic delivery and poor oral bioavailability. Epigallocatechin-3-gallate, curcumin, and resveratrol are the well-known representatives of the bioactive diet polyphenols but with poor bioavailability. Food macromolecule based nanoparticles have been fabricated using reassembled proteins, crosslinked polysaccharides, protein–polysaccharide conjugates (complexes, as well as emulsified lipid via safe procedures that could be applied in food. The human gastrointestinal digestion tract is the first place where the food grade macromolecule nanoparticles exert their effects on improving the bioavailability of diet polyphenols, via enhancing their solubility, preventing their degradation in the intestinal environment, elevating the permeation in small intestine, and even increasing their contents in the bloodstream. We contend that the stability and structure behaviors of nanocarriers in the gastrointestinal tract environment and the effects of nanoencapsulation on the metabolism of polyphenols warrant more focused attention in further studies.

  8. Ordered mesoporous polymer-silica hybrid nanoparticles as vehicles for the intracellular controlled release of macromolecules.

    Science.gov (United States)

    Kim, Tae-Wan; Slowing, Igor I; Chung, Po-Wen; Lin, Victor Shang-Yi

    2011-01-25

    A two-dimensional hexagonal ordered mesoporous polymer-silica hybrid nanoparticle (PSN) material was synthesized by polymerization of acrylate monomers on the surface of SBA-15 mesoporous silica nanoparticles. The structure of the PSN material was analyzed using a series of different techniques, including transmission electron microscopy, powder X-ray diffraction, and N(2) sorption analysis. These structurally ordered mesoporous polymer-silica hybrid nanoparticles were used for the controlled release of membrane-impermeable macromolecules inside eukaryotic cells. The cellular uptake efficiency and biocompatibility of PSN with human cervical cancer cells (HeLa) were investigated. Our results show that the inhibitory concentration (IC(50)) of PSN is very high (>100 μg/mL per million cells), while the median effective concentration for the uptake (EC(50)) of PSN is low (EC(50) = 4.4 μg/mL), indicating that PSNs are fairly biocompatible and easily up-taken in vitro. A membrane-impermeable macromolecule, 40 kDa FITC-Dextran, was loaded into the mesopores of PSNs at low pH. We demonstrated that the PSN material could indeed serve as a transmembrane carrier for the controlled release of FITC-Dextran at the pH level inside live HeLa cells. We believe that further developments of this PSN material will lead to a new generation of nanodevices for intracellular controlled delivery applications.

  9. Distribution volumes of macromolecules in human ovarian and endometrial cancers--effects of extracellular matrix structure.

    Science.gov (United States)

    Haslene-Hox, Hanne; Oveland, Eystein; Woie, Kathrine; Salvesen, Helga B; Tenstad, Olav; Wiig, Helge

    2015-01-01

    Elements of the extracellular matrix (ECM), notably collagen and glucosaminoglycans, will restrict part of the space available for soluble macromolecules simply because the molecules cannot occupy the same space. This phenomenon may influence macromolecular drug uptake. To study the influence of steric and charge effects of the ECM on the distribution volumes of macromolecules in human healthy and malignant gynecologic tissues we used as probes 15 abundant plasma proteins quantified by high-resolution mass spectrometry. The available distribution volume (VA) of albumin was increased in ovarian carcinoma compared with healthy ovarian tissue. Furthermore, VA of plasma proteins between 40 and 190 kDa decreased with size for endometrial carcinoma and healthy ovarian tissue, but was independent of molecular weight for the ovarian carcinomas. An effect of charge on distribution volume was only found in healthy ovaries, which had lower hydration and high collagen content, indicating that a condensed interstitium increases the influence of negative charges. A number of earlier suggested biomarker candidates were detected in increased amounts in malignant tissue, e.g., stathmin and spindlin-1, showing that interstitial fluid, even when unfractionated, can be a valuable source for tissue-specific proteins. We demonstrate that the distribution of abundant plasma proteins in the interstitium can be elucidated by mass spectrometry methods and depends markedly on hydration and ECM structure. Our data can be used in modeling of drug uptake, and give indications on ECM components to be targeted to increase the uptake of macromolecular substances.

  10. Bionic design for surface optimization combining hydrophilic and negative charged biological macromolecules.

    Science.gov (United States)

    Ran, Fen; Song, Haiming; Niu, Xiaoqin; Yang, Aimei; Nie, Shengqiang; Wang, Lingren; Li, Jie; Sun, Shudong; Zhao, Changsheng

    2014-06-01

    While polyethersulfone (PES) membrane represents a promising option for blood purification, the blood compatibility must be dramatically enhanced to meet today's ever-increasing demands for many emerging application. In this study, we report a bionic design for optimization and development of a modified PES membrane combining hydrophilic and negative charged biological macromolecules on its surface. The hydrophilic and ionic charged biological macromolecules sulfonated poly(styrene)-b-poly(methyl methacrylate)-b-poly-(styrene) (PSSMSS) and poly(vinyl pyrrolidone)-b-poly(methyl methacrylate)-b-poly-(vinyl pyrrolidone) were synthesized via reversible addition-fragmentation chain transfer polymerization and used together to modify PES membranes by blending method. A hydrophilic membrane surface with negative charged surface coating was obtained, imitating the hydrophilic and negatively charged structure feature of heparin. The modified PES membranes showed suppressed platelet adhesion, and a prolonged blood clotting time, and thereby improved blood compatibility. In addition, the blood clotting time of the modified membranes increased with the blended PSSMSS amounts increment, indicating that both the hydrophilic and negative charged groups play important roles in improving the blood compatibility of PES membranes.

  11. A dural lymphatic vascular system that drains brain interstitial fluid and macromolecules.

    Science.gov (United States)

    Aspelund, Aleksanteri; Antila, Salli; Proulx, Steven T; Karlsen, Tine Veronica; Karaman, Sinem; Detmar, Michael; Wiig, Helge; Alitalo, Kari

    2015-06-29

    The central nervous system (CNS) is considered an organ devoid of lymphatic vasculature. Yet, part of the cerebrospinal fluid (CSF) drains into the cervical lymph nodes (LNs). The mechanism of CSF entry into the LNs has been unclear. Here we report the surprising finding of a lymphatic vessel network in the dura mater of the mouse brain. We show that dural lymphatic vessels absorb CSF from the adjacent subarachnoid space and brain interstitial fluid (ISF) via the glymphatic system. Dural lymphatic vessels transport fluid into deep cervical LNs (dcLNs) via foramina at the base of the skull. In a transgenic mouse model expressing a VEGF-C/D trap and displaying complete aplasia of the dural lymphatic vessels, macromolecule clearance from the brain was attenuated and transport from the subarachnoid space into dcLNs was abrogated. Surprisingly, brain ISF pressure and water content were unaffected. Overall, these findings indicate that the mechanism of CSF flow into the dcLNs is directly via an adjacent dural lymphatic network, which may be important for the clearance of macromolecules from the brain. Importantly, these results call for a reexamination of the role of the lymphatic system in CNS physiology and disease.

  12. Czochralski crystal growth: Modeling study

    Science.gov (United States)

    Dudukovic, M. P.; Ramachandran, P. A.; Srivastava, R. K.; Dorsey, D.

    1986-01-01

    The modeling study of Czochralski (Cz) crystal growth is reported. The approach was to relate in a quantitative manner, using models based on first priniciples, crystal quality to operating conditions and geometric variables. The finite element method is used for all calculations.

  13. High-quality photonic crystals with a nearly complete band gap obtained by direct inversion of woodpile templates with titanium dioxide

    CERN Document Server

    Marichy, Catherine; Froufe-Pérez, Luis S; Scheffold, Frank

    2015-01-01

    Photonic crystal materials are based on a periodic modulation of the dielectric constant on length scales comparable to the wavelength of light. These materials can exhibit photonic band gaps; frequency regions for which the propagation of electromagnetic radiation is forbidden due to the depletion of the density of states. In order to exhibit a full band gap, 3D PCs must present a threshold refractive index contrast that depends on the crystal structure. In the case of the so-called woodpile photonic crystals this threshold is comparably low, approximately 1.9 for the direct structure. Therefore direct or inverted woodpiles made of high refractive index materials like silicon, germanium or titanium dioxide are sought after. Here we show that, by combining multiphoton lithography and atomic layer deposition, we can achieve a direct inversion of polymer templates into TiO$_{2}$ based photonic crystals. The obtained structures show remarkable optical properties in the near-infrared region with almost perfect sp...

  14. Self-assembly of an amphiphilic macromolecule under spherical confinement: An efficient route to generate hollow nanospheres

    Science.gov (United States)

    Glagoleva, A. A.; Vasilevskaya, V. V.; Yoshikawa, K.; Khokhlov, A. R.

    2013-12-01

    In general, bio-macromolecules are composed of hydrophilic and hydrophobic moieties and are confined within small cavities, such as cell membranes and intracellular organelles. Here, we studied the self-organization of macromolecules having groups with different affinities to solvents under spherical nano-scale confinement by means of computer modeling. It is shown that depending on the interaction parameters of monomer units composed of side- and main-chain monomer groups along a single linear macromolecule and on cavity size, such amphiphilic polymers undergo the conformational transitions between hollow nanospheres, rod-like and folded cylindrical structures, and a necklace conformation with and without a particular ordering of beads. The diagram of the conformations in the variables the incompatibility parameter of monomer units and the cavity radius is constructed.

  15. Axion Crystals

    CERN Document Server

    Ozaki, Sho

    2016-01-01

    The low-energy effective theories for gapped insulators are classified by three parameters: permittivity $\\epsilon$, permeability $\\mu$, and theta angle $\\theta$. Crystals with periodic $\\epsilon$ are known as photonic crystals. We here study the band structure of photons in a new type of crystals with periodic $\\theta$ (modulo $2\\pi$) in space, which we call the axion crystals. We find that the axion crystals have a number of new properties that the usual photonic crystals do not possess, such as the helicity-dependent photonic band gaps and the nonrelativistic gapless dispersion relation at small momentum. We briefly discuss possible realizations of axion crystals in condensed matter systems as well as high-energy physics.

  16. Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

    Science.gov (United States)

    Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

    2002-11-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately

  17. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Bruetzel, Linda K.; Fischer, Stefan; Salditt, Annalena; Sedlak, Steffen M.; Nickel, Bert; Lipfert, Jan, E-mail: Jan.Lipfert@lmu.de [Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich (Germany)

    2016-02-15

    We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 10{sup 6} photons/s at a beam size of 1.2 × 1.2 mm{sup 2} at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å{sup −1} down to 0.009 Å{sup −1} in SAXS configuration and of 0.26 Å{sup −1} up to 5.7 Å{sup −1} in wide-angle X-ray scattering (WAXS) mode. To determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ∼12 to 69 kDa and concentrations of 1.5–24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ∼0.2 Å{sup −1} allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources.

  18. Engineering crystal growth of calcium hydrogenphosphate dihydrate

    Energy Technology Data Exchange (ETDEWEB)

    Sikiric, M.; Babic-Ivancic, V. [Institut Rudjer Boskovic, Zagreb (Croatia); Milat, O. [Zagreb Univ. (Croatia). Inst. za Fiziku; Sarig, S.; Fueredi-Milhofer, H. [Hebrew Univ., Jerusalem (Israel). Inst. of Applied Chemistry

    2001-07-01

    The factors underlying calcium hydrogenphosphate dihydrate (CaHPO{sub 4}.2H{sub 2}O, DCPD) interactions with several structurally different additives: glutamic and aspartic acid, sodium citrate, hexaammonium tetrapolyphosphate, calcium phytate and polyaspartic acid were studied. DCPD crystals were prepared under controlled conditions by fast mixing of the anionic and cationic reactant solutions and subsequent growth without further stirring in the course of 24 hours at 37 C. The initial conditions were c(CaCl{sub 2}) = c(Na{sub 2}HPO{sub 4}) = 0.021 mol dm{sup -3}, c(NaCl) = 0.3 mol dm{sup -3}, pH{sub i} 5.5. The respective additive was added to the anionic component prior to pH adjustment. Crystals were characterized by X-ray diffraction, while their morphology was observed by optical and scanning electron microscopy (SEM). The Miller indices of the crystal faces were determined from SEM micrographs, after the orientation of the most prominent face was ascertained by the Weissenberg method. Mechanism of additive-DCPD crystals interaction depends on size and structure of additive molecule, structural fit between organic molecule and the ionic structure of particular crystal face. Small molecules (ions) specifically adsorb on lateral faces by electrostatic interactions, while macromolecules and molecules with hindered structure specifically adsorb on dominant (010) face, for which certain degree of structural fit is necessary. (orig.)

  19. Growing Organic Crystals By The Czochralski Method

    Science.gov (United States)

    Shields, Angela; Frazier, Donald O.; Penn, Benjamin G.; Aggarwal, M. D.; Wang, W. S.

    1994-01-01

    Apparatus grows high-quality single crystals of organic compounds by Czochralski method. In Czochralski process, growing crystal lifted from middle of molten material without touching walls. Because of low melting temperatures of organic crystals, glass vessels usable. Traditional method for inorganic semiconductors adapted to optically nonlinear organic materials.

  20. Protein Crystallization

    Science.gov (United States)

    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.

  1. NATO Advanced Research Workshop on Nuclear Magnetic Resonance of Paramagnetic Macromolecules

    CERN Document Server

    1995-01-01

    Since A. Kowalsky's first report of the spectrum of cytochrome c in 1965, interest in the detection, assignment and interpretation of paramagnetic molecules has surged, especially in the last decade. Two classes of systems have played a key role in the development of the field: heme proteins and iron-sulfur proteins. These two systems are unique in many respects, one of which is that they contain well-defined chromophores, each of which can be studied in detail outside the protein matrix. They are the most successfully studied macromolecules, and the first eight and last six of the seventeen contributions to this book deal with heme and/or iron-sulfur proteins. The middle three chapters survey the progress on, and significant promise of, more difficult systems which do not possess a chromophore, but which have nevertheless yielded remarkable insights into their structure.

  2. [Diffusion and diffusion-osmosis models of the charged macromolecule transfer in barriers of biosystems].

    Science.gov (United States)

    Varakin, A I; Mazur, V V; Arkhipova, N V; Serianov, Iu V

    2009-01-01

    Mathematical models of the transfer of charged macromolecules have been constructed on the basis of the classical equations of electromigration diffusion of Helmholtz-Smolukhovskii, Goldman, and Goldman-Hodgkin-Katz. It was shown that ion transfer in placental (mimicking lipid-protein barriers) and muscle barriers occurs by different mechanisms. In placental barriers, the electromigration diffusion occurs along lipid-protein channels formed due to the conformational deformation of phospholipid and protein molecules with the coefficients of diffusion D = (2.6-3.6) x 10(-8) cm2/s. The transfer in muscle barriers is due to the migration across charged interfibrillar channels with the negative diffusion activation energy, which is explained by changes in the structure of muscle fibers and expenditures of thermal energy for the extrusion of Cl- from channel walls with the diffusion coefficient D = (6.0-10.0) x 10(-6) cm2/s.

  3. Enhanced ileal absorption of a hydrophilic macromolecule, pentosan polysulfate sodium (PPS).

    Science.gov (United States)

    Dong, Liang; Yum, Alicia; Nguyen, Joe; Wong, Pat

    2004-01-01

    An in situ gelling, bioadhesive liquid formulation was developed to enhance the bioavailbility (BA) of a polysaccharide, pentosan polysulfate sodium (PPS). The formulation was tested to determine its bioavailability enhancement in a non-flush/non-ligated rat ileal model. A potent synergistic effect was found with a gelling agent Cremophor and a permeation enhancer sodium salicylate. The absolute bioavailabilities were 1.9%, 4.6%, 6.3% and 46.4%, respectively, for the PPS solution in saline, sodium salicylate/PPS, Cremophor/PPS and Cremophor/sodium salicylate/PPS. Therefore, we successfully demonstrated the approach of utilizing an in situ gelling/bioadhesive liquid carrier to enhancing the bioavailability of a hydrophilic macromolecule at the distal small intestine.

  4. Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions.

    Science.gov (United States)

    Smirnov, A V; Entelis, N S; Krasheninnikov, I A; Martin, R; Tarassov, I A

    2008-12-01

    Small non-coding RNAs are today a topic of great interest for molecular biologists because they can be regarded as relicts of a hypothetical "RNA world" which, apparently, preceded the modern stage of organic evolution on Earth. The small molecule of 5S rRNA (approximately 120 nucleotides) is a component of large ribosomal subunits of all living beings (5S rRNAs are not found only in mitoribosomes of fungi and metazoans). This molecule interacts with various protein factors and 23S (28S) rRNA. This review contains the accumulated data to date concerning 5S rRNA structure, interactions with other biological macromolecules, intracellular traffic, and functions in the cell.

  5. Dielectric many-body effects in arrays of charged cylindrical macromolecules

    Science.gov (United States)

    Sinkovits, Daniel W.; Barros, Kipton; Dobnikar, Jure; Kandu&{Caron; C}, Matej; Naji, Ali; Podgornik, Rudolf; Luijten, Erik

    2012-02-01

    Nonuniform dielectric constants are a ubiquitous aspect of condensed-matter systems, but nevertheless widely ignored in simulations. Analytical work suggests that the polarization effects resulting from these inhomogeneities can produce many-body interactions that qualitatively alter the behavior of systems driven by electrostatic interactions, but such work relies on approximations. Recently, we have developed an algorithm that computes the fluctuating polarization charge at the interface between dielectric materials during a molecular dynamics simulation, without approximation. Here, we apply this approach to investigate arrays of charged cylindrical macromolecules in the presence of explicit counterions. We study the dielectric many-body effects as a function of separation, dielectric constant variation, and counterion valency. Our findings have implications for the aggregation of polyelectrolytes such as F-actin or DNA.

  6. A Biology Laboratory Exercise Using Macromolecule Assays to Distinguish Four Types of Milk

    Directory of Open Access Journals (Sweden)

    Charlotte W. Pratt

    2011-03-01

    Full Text Available One of the drawbacks of cookbook-style laboratory exercises for General Biology courses is that students are not challenged to develop skills in scientific reasoning, such as formulating hypotheses and designing and carrying out experiments. Several traditional laboratory curricula include exercises involving semi-quantitative colorimetric assays to detect proteins (biuret test, reducing sugars (Benedict’s test, starch (Lugol’s test, and lipids (Sudan red test in a variety of easily prepared solutions (glucose, albumin, glycine, etc. and familiar food items (lemon juice, cornstarch, egg white, etc.. An extension of this lab exercise was developed to allow students to use their knowledge of the macromolecule assays to design an experiment to distinguish four types of “milk”: whole milk, skim milk, cream, and soy milk (rice milk or almond milk could also be included.

  7. Spirulina cultivation with a CO2 absorbent: Influence on growth parameters and macromolecule production.

    Science.gov (United States)

    Rosa, Gabriel Martins da; Moraes, Luiza; de Souza, Michele da Rosa Andrade Zimmermann; Costa, Jorge Alberto Vieira

    2016-01-01

    The objective of this study was to select a concentration of CO2 absorbents to supplement Spirulina sp. LEB 18 cultivation and to evaluate the effect of these compounds on the growth and production of macromolecules. Three initial biomass concentrations (X0), eight concentrations of monoethanolamine (MEA), and three NaOH concentrations were tested. The selected MEA concentrations did not inhibit the growth of Spirulina and doubled the dissolved inorganic carbon concentration in the assay medium in relation to the concentration of NaOH. The protein concentration in the biomass grown with MEA was, on average, 17% higher than that obtained with NaOH. Thus, it was found that MEA did not reduce the productivity of Spirulina sp. LEB 18, and its use can be further explored as a means for converting the carbon dissolved in the medium to biomolecules.

  8. Enzyme kinetics and transport in a system crowded by mobile macromolecules.

    Science.gov (United States)

    Echeverria, Carlos; Kapral, Raymond

    2015-11-21

    The dynamics of an elastic network model for the enzyme 4-oxalocrotonate tautomerase is studied in a system crowded by mobile macromolecules, also modeled by elastic networks. The system includes a large number of solvent molecules, as well as substrate and product molecules which undergo catalytic reactions with this hexameric protein. The time evolution of the entire system takes place through a hybrid dynamics that combines molecular dynamics for solute species and multiparticle collision dynamics for the solvent. It is shown that crowding leads to subdiffusive dynamics for the protein, in accord with many studies of diffusion in crowded environments, and increases orientational relaxation times. The enzyme reaction kinetics is also modified by crowding. The effective Michaelis constant decreases with crowding volume fraction, and this decrease is attributed to excluded volume effects, which dominate over effects due to reduced substrate diffusion that would cause the Michaelis constant to increase.

  9. Microwave-assisted extraction of Shenfu coal and its macromolecule structure

    Institute of Scientific and Technical Information of China (English)

    CHEN Hong; LI Jian-wei; LEI Zhao; GE Ling-mei

    2009-01-01

    Coals consist of some molecules trapped within an organic matrix from which some organic compounds can be extracted by solvents. The Soxhlet technique has been widely used for extracting organic compounds. Microwave heating methods may be successfully applied in the field of coal science. Acetone extraction yields and the chemical composition of the extract were inves-tigated using a typical Chinese coal, Shenfu coal, with microwave-assisted extraction. The acetone extract and residue were ana-lyzed by GC/MS and carbon-13 nuclear magnetic resonance spectroscopy respectively. The carbon spectra were converted into several numerical parameters, fa, Ha, Xb, which indicate the difference in macromolecular structure between Shenfu coal and its residue. Furthermore, a hybrid genetic algorithm was employed using these parameters to approximate a coal macromolecule by assembling the structural fragments or functional groups into a large and complicated structure.

  10. Computational crystallization.

    Science.gov (United States)

    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.

  11. Ex vitro experimental study on concentration polarization of macromolecules (LDL) at an arterial stenosis.

    Science.gov (United States)

    Zhang, ZhiGuo; Deng, XiaoYan; Fan, YuBo; Li, DeYu

    2007-08-01

    To verify the previous theoretical prediction that the disturbed flow distal to a stenosis enhances lipid accumulation at the blood/arterial wall interface, we designed a canine carotid arterial stenosis model and measured ex vitro the luminal surface concentration of bovine serum albumin (as a tracer macromolecule) by directly taking liquid samples from the luminal surface of the artery. The experimental results showed that due to the presence of a filtration flow, the luminal surface albumin concentration c(w) was higher than the bulk concentration c(0) as predicted by our theory. The measurement revealed that the luminal surface concentration of macromolecules was indeed enhanced significantly in regions of the disturbed flow. At Re = 50, the relative luminal surface concentration c(w)/c(0) was 1.66 +/- 0.10 in the vortex region, while the c(w)/c(0) was 1.37 +/- 0.06 in the laminar flow region. When Re increased to 100, the c(w)/c(0) in the vortex flow region and the laminar flow region reduced to 1.39 +/- 0.07 and 1.24 +/- 0.04, respectively. The effect of the filtration rate, v(w), on the luminal surface concentration of albumin was remarkably apparent. At Re = 50 and 100, when v(w) = 8.9 +/- 1.7 x 10(-6) cm/s, c(w) in the vortex region was 77% and 52% higher than c(0) respectively, meanwhile when v(w) = 4.8 +/- 0.6 x 10(-6) cm/s, c(w) in the vortex region was only 66% and 39% higher than c(0) respectively. In summary, the present study has provided further experimental evidence that concentration polarization can occur in the arterial system and fluid layer with highly concentrated lipids in the area of flow separation point may be responsible for the formation and development of atherosclerosis.

  12. Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

    Science.gov (United States)

    Grazioli, Gianmarc

    Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

  13. Opinion: hazards faced by macromolecules when confined to thin aqueous films.

    Science.gov (United States)

    Glaeser, Robert M; Han, Bong-Gyoon

    2017-01-01

    Samples prepared for single-particle electron cryo-microscopy (cryo-EM) necessarily have a very high surface-to-volume ratio during the short period of time between thinning and vitrification. During this time, there is an obvious risk that macromolecules of interest may adsorb to the air-water interface with a preferred orientation, or that they may even become partially or fully unfolded at the interface. In addition, adsorption of macromolecules to an air-water interface may occur even before thinning. This paper addresses the question whether currently used methods of sample preparation might be improved if one could avoid such interfacial interactions. One possible way to do so might be to preemptively form a surfactant monolayer over the air-water interfaces, to serve as a structure-friendly slide and coverslip. An alternative is to immobilize particles of interest by binding them to some type of support film, which-to continue using the analogy-thus serves as a slide. In this case, the goal is not only to prevent the particles of interest from diffusing into contact with the air-water interface but also to increase the number of particles seen in each image. In this direction, it is natural to think of developing various types of affinity grids as structure-friendly alternatives to thin carbon films. Perhaps ironically, if precautions are not taken against adsorption of particles to air-water interfaces, sacrificial monolayers of denatured protein may take the roles of slide, coverslip, or even both.

  14. A mathematical model for filtration and macromolecule transport across capillary walls.

    Science.gov (United States)

    Facchini, L; Bellin, A; Toro, E F

    2014-07-01

    Metabolic substrates, such as oxygen and glucose, are rapidly delivered to the cells of large organisms through filtration across microvessels walls. Modelling this important process is complicated by the strong coupling between flow and transport equations, which are linked through the osmotic pressure induced by the colloidal plasma proteins. The microvessel wall is a composite media with the internal glycocalyx layer exerting a strong sieving effect on macromolecules, with respect to the external layer composed by the endothelial cells. The physiological structure of the microvessel is represented as the superimposition of two membranes with different properties; the inner membrane represents the glycocalyx, while the outer membrane represents the surrounding endothelial cells. Application of the mass conservation principle and thermodynamic considerations lead to a model composed of two coupled second-order ordinary differential equations for the hydrostatic and osmotic pressures, one, expressing volumetric mass conservation and the other, which is non-linear in the unknown osmotic pressure, expressing macromolecules mass conservation. Despite the complexity of the system, the assumption that the properties of the layers are piece-wise constant allows us to obtain analytical solutions for the two pressures. This solution is in agreement with experimental observations, which contrary to common belief, show that flow reversal cannot occur in steady-state conditions unless the hydrostatic pressure in the lumen drops below physiologically plausible values. The observed variations of the volumetric flux and the solute mass flux in case of a significant reduction of the hydrostatic pressure at the lumen are in qualitative agreement with observed variations during detailed experiments reported in the literature. On the other hand, homogenising the microvessel wall into a single-layer membrane with equivalent properties leads to a very different distribution of

  15. Ex vitro experimental study on concentration polari-zation of macromolecules (LDL) at an arterial stenosis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    To verify the previous theoretical prediction that the disturbed flow distal to a stenosis enhances lipid accumulation at the blood/arterial wall interface, we designed a canine carotid arterial stenosis model and measured ex vitro the luminal surface concentration of bovine serum albumin (as a tracer mac-romolecule) by directly taking liquid samples from the luminal surface of the artery. The experimental results showed that due to the presence of a filtration flow, the luminal surface albumin concentration cw was higher than the bulk concentration co as predicted by our theory. The measurement revealed that the luminal surface concentration of macromolecules was indeed enhanced significantly in re-gions of the disturbed flow. At Re = 50, the relative luminal surface concentration cw/co was 1.66 ± 0.10 in the vortex region, while the cw/co was 1.37 ± 0.06 in the laminar flow region. When Re increased to 100, the cw/co in the vortex flow region and the laminar flow region reduced to 1.39 ± 0.07 and 1.24 ± 0.04, respectively. The effect of the filtration rate, vw, on the luminal surface concentration of albumin was remarkably apparent. At Re = 50 and 100, when vw = 8.9 ± 1.7 × 10-6 cm/s, cw in the vortex region was 77% and 52% higher than co respectively, meanwhile when vw = 4.8 ± 0.6 × 10-6 cm/s, cw in the vortex region was only 66 % and 39% higher than co respectively. In summary, the present study has provided further experimental evidence that concentration polarization can occur in the arterial system and fluid layer with highly concentrated lipids in the area of flow separation point may be responsible for the formation and development of atherosclerosis.

  16. Ex vitro experimental study on concentration polarization of macromolecules (LDL) at an arterial stenosis

    Institute of Scientific and Technical Information of China (English)

    ZHANG ZhiGuo; DENG XiaoYan; FAN YuBo; LI DeYu

    2007-01-01

    To verify the previous theoretical prediction that the disturbed flow distal to a stenosis enhances lipid accumulation at the blood/arterial wall interface, we designed a canine carotid arterial stenosis model and measured ex vitro the luminal surface concentration of bovine serum albumin (as a tracer macromolecule) by directly taking liquid samples from the luminal surface of the artery. The experimental results showed that due to the presence of a filtration flow, the luminal surface albumin concentration cw was higher than the bulk concentration co as predicted by our theory. The measurement revealed that the luminal surface concentration of macromolecules was indeed enhanced significantly in regions of the disturbed flow. At Re = 50, the relative luminal surface concentration cw/co was 1.66±0.10 in the vortex region, while the cw/co was 1.37±0.06 in the laminar flow region. When Re increased to 100,the cw/co in the vortex flow region and the laminar flow region reduced to 1.39±0.07 and 1.24±0.04,respectively. The effect of the filtration rate, vw, on the luminal surface concentration of albumin was remarkably apparent. At Re=50 and 100, when vw=8.9±1.7×10-6 cm/s, cw in the vortex region was 77% and 52% higher than co respectively, meanwhile when vw = 4.8±0.6×10-6 cm/s, cw in the vortex region was only 66% and 39% higher than co respectively. In summary, the present study has provided further experimental evidence that concentration polarization can occur in the arterial system and fluid layer with highly concentrated lipids in the area of flow separation point may be responsible for the formation and development of atherosclerosis.

  17. Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

    Science.gov (United States)

    Li, Hao; Wu, Chao; Malinin, Sergey V.; Tretiak, Sergei; Chernyak, Vladimir Y.

    2016-12-01

    The exciton scattering (ES) technique is a multiscale approach based on the concept of a particle in a box and developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, electronic excitations in molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph whose edges and nodes stand for the molecular linear segments and vertices, respectively. Exciton propagation on the linear segments is characterized by the exciton dispersion, whereas exciton scattering at the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized "particle in a box" problems on the graph that represents the molecule. Similarly, unique energy-dependent ES dipolar parameters permit calculations of the corresponding oscillator strengths, thus, completing optical spectra modeling. Both the energetic and dipolar parameters can be extracted from quantum-chemical computations in small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within a considered molecular family could be performed with negligible numerical effort. We demonstrate the ES method application to molecular families of branched conjugated phenylacetylenes and ladder poly-para-phenylenes, as well as structures with electron donor and acceptor chemical substituents. Time-dependent density functional theory (TD-DFT) is used as a reference model for electronic structure. The ES calculations accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

  18. Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate.

    Science.gov (United States)

    Lebedeva, Natalia V; Nese, Alper; Sun, Frank C; Matyjaszewski, Krzysztof; Sheiko, Sergei S

    2012-06-12

    Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C ─ C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (k(B)T) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V(0)(1 - e(-βx))(2) - fx, we determined the depth and width of the potential to be V(0) = 141 ± 19 kJ/mol and β(-1) = 0.18 ± 0.03 Å, respectively. Whereas the V(0) value is in reasonable agreement with the activation energy E(a) = 80-220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C ─ C bond D(e) = 350 kJ/mol. Moreover, the force constant K(x) = 2β(2)V(0) = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C ─ C bond K(l) = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains.

  19. Do column frits contribute to the on-column, flow-induced degradation of macromolecules?

    Science.gov (United States)

    Striegel, André M

    2014-09-12

    Flow-induced, on-column degradation is a major hindrance to the accurate characterization of ultra-high molar mass macromolecules and colloids. This degradation is a direct result of the large shear rates which are generated within the column, which cause chain scission to occur both in the interstitial medium and, it has been postulated, at the packing particle pore boundary. An additional putative source of degradation has been the column frits, though little experimental evidence exists to either support or refute this claim. To this effect, the present experiments examine the role of the frits in the degradation of high molar mass macromolecules. Two narrow dispersity polystyrene standards, the molar mass of which differs by a factor of two, were analyzed on three different size-exclusion chromatography (SEC) columns, each with frits of different pore size, at various flow rates. In the smallest pore size column, which also contained the smallest frits and which was packed with the smallest diameter particles, the larger standard was forced to degrade by increasing the flow rate of the mobile phase. During the course of the latter portion of the study, the inlet and the outlet frits were removed from the column, in stepwise fashion. It was concluded that neither frit played any appreciable role in the degradation. Results of our studies were applied to explain previously observed degradation in ultra-high pressure liquid chromatography of polymers. The general conclusion arrived at herein is that the column frits are likely to have a secondary role (as compared to interstitial and pore boundary stresses), or no role at all, in polymer degradation for cases where the frit radius is larger than or equal to the hydraulic radius rcof the column.

  20. The fluid phenomena in the crystallization of the protein crystal

    Institute of Scientific and Technical Information of China (English)

    Duan Li; Kang Qi

    2008-01-01

    This paper reports that an optical diagnostic system consisting of Maeh-Zehnder interferometer with a phase shift device and image processor has been used for study of the kinetics of protein crystal growing process. The crystallization process of protein crystal by vapour diffusion is investigated. The interference fringes are observed in real time. The present experiment demonstrates that the diffusion and the sedimentation influence the crystallization of protein crystal which grows in solution, and the concentration capillary convection associated with surface tension occurs at the vicinity of free surface of the protein mother liquor, and directly affects on the outcome of protein crystallization. So far the detailed analysis and the important role of the fluid phenomena in protein crystallization have been discussed a little in both space- and ground-based crystal growth experiments. It is also found that these fluid phenomena affect theoutcome of protein crystallization, regular growth, and crystal quality. This may explain the fact that many results of space-based investigation do not show overall improvement.

  1. Comparison of gold nanoparticle mediated photoporation: vapor nanobubbles outperform direct heating for delivering macromolecules in live cells.

    Science.gov (United States)

    Xiong, Ranhua; Raemdonck, Koen; Peynshaert, Karen; Lentacker, Ine; De Cock, Ine; Demeester, Jo; De Smedt, Stefaan C; Skirtach, Andre G; Braeckmans, Kevin

    2014-06-24

    There is a great interest in delivering macromolecular agents into living cells for therapeutic purposes, such as siRNA for gene silencing. Although substantial effort has gone into designing nonviral nanocarriers for delivering macromolecules into cells, translocation of the therapeutic molecules from the endosomes after endocytosis into the cytoplasm remains a major bottleneck. Laser-induced photoporation, especially in combination with gold nanoparticles, is an alternative physical method that is receiving increasing attention for delivering macromolecules in cells. By allowing gold nanoparticles to bind to the cell membrane, nanosized membrane pores can be created upon pulsed laser illumination. Depending on the laser energy, pores are created through either direct heating of the AuNPs or by vapor nanobubbles (VNBs) that can emerge around the AuNPs. Macromolecules in the surrounding cell medium can then diffuse through the pores directly into the cytoplasm. Here we present a systematic evaluation of both photoporation mechanisms in terms of cytotoxicity, cell loading, and siRNA transfection efficiency. We find that the delivery of macromolecules under conditions of VNBs is much more efficient than direct photothermal disturbance of the plasma membrane without any noticeable cytotoxic effect. Interestingly, by tuning the laser energy, the pore size could be changed, allowing control of the amount and size of molecules that are delivered in the cytoplasm. As only a single nanosecond laser pulse is required, we conclude that VNBs are an interesting photoporation mechanism that may prove very useful for efficient high-throughput macromolecular delivery in live cells.

  2. Application of flow field-flow fractionation for the characterization of macromolecules of biological interest: a review

    NARCIS (Netherlands)

    Qureshi, R.N.; Kok, W.T.

    2011-01-01

    An overview is given of the recent literature on (bio) analytical applications of flow field-flow fractionation (FlFFF). FlFFF is a liquid-phase separation technique that can separate macromolecules and particles according to size. The technique is increasingly used on a routine basis in a variety

  3. Effect of adsorption of charged macromolecules on streaming and membrane potential values measured with a microporous polysulfone membrane

    DEFF Research Database (Denmark)

    Benavente, J.; Jonsson, Gunnar Eigil

    1997-01-01

    Changes in streaming and membrane potentials measured across a commercial microporous polysulfone membrane as a result of the adsorption of differently charged macromolecules were studied. Measurements were carried out with different NaCl solutions (10(-3) M to 5 x 10(-2) M) and their mixtures...

  4. Hydroxycinnamic acids are ester-linked directly to glucosyl moieties within the lignan macromolecule from flaxseed hulls

    NARCIS (Netherlands)

    Struijs, K.; Vincken, J.P.; Verhoef, R.P.; Voragen, A.G.J.; Gruppen, H.

    2008-01-01

    In flaxseed hulls, lignans are present in an oligomeric structure. Secoisolariciresinol diglucoside (SDG), ester-linked to hydroxy-methyl-glutaric acid (HMGA), forms the backbone of this lignan macromolecule. The hydroxycinnamic acids p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeA

  5. Application of flow field-flow fractionation for the characterization of macromolecules of biological interest: a review

    NARCIS (Netherlands)

    R.N. Qureshi; W.T. Kok

    2011-01-01

    An overview is given of the recent literature on (bio) analytical applications of flow field-flow fractionation (FlFFF). FlFFF is a liquid-phase separation technique that can separate macromolecules and particles according to size. The technique is increasingly used on a routine basis in a variety o

  6. Crystallization-induced properties from morphology-controlled organic crystals.

    Science.gov (United States)

    Park, Chibeom; Park, Ji Eun; Choi, Hee Cheul

    2014-08-19

    dissimilar molecular arrangements. Recently, researchers have proposed several approaches for the vapor and solution phase synthesis of high quality organic crystals with various morphologies. In this Account, we focus on methodologies for the synthesis of various organic- and metal-containing highly conjugated molecular crystals. We also examine the new optical and chemical properties of these materials. In addition, we introduce recent experimental results demonstrating that high crystallinity and specific molecular arrangements lead to crystallization-induced property changes. We believe that the understanding of the crystallization-induced property changes in organic crystals will provide both fundamental knowledge of the chemical processes occurring at various interfaces and opportunities for researchers to take advantage of crystallization-induced property changes in the development of high-performance organic devices.

  7. Crystal Data

    Science.gov (United States)

    SRD 3 NIST Crystal Data (PC database for purchase)   NIST Crystal Data contains chemical, physical, and crystallographic information useful to characterize more than 237,671 inorganic and organic crystalline materials. The data include the standard cell parameters, cell volume, space group number and symbol, calculated density, chemical formula, chemical name, and classification by chemical type.

  8. Measurements of Protein Crystal Face Growth Rates

    Science.gov (United States)

    Gorti, S.

    2014-01-01

    Protein crystal growth rates will be determined for several hyperthermophile proteins.; The growth rates will be assessed using available theoretical models, including kinetic roughening.; If/when kinetic roughening supersaturations are established, determinations of protein crystal quality over a range of supersaturations will also be assessed.; The results of our ground based effort may well address the existence of a correlation between fundamental growth mechanisms and protein crystal quality.

  9. Last crystals for the CMS chandelier

    CERN Multimedia

    2008-01-01

    In March, the last crystals for CMS’s electromagnetic calorimeter arrived from Russia and China. Like dedicated jewellers crafting an immense chandelier, the CMS ECAL collaborators are working extremely hard to install all the crystals before the start-up of the LHC. One of the last CMS end-cap crystals, complete with identification bar code. Lead tungstate crystals mounted onto one section of the CMS ECAL end caps. Nearly 10 years after the first production crystal arrived at CERN in September 1998, the very last shipment has arrived. These final crystals will be used to complete the end-caps of the electromagnetic calorimeter (ECAL) at CMS. All in all, there are more than 75,000 crystals in the ECAL. The huge quantity of CMS lead tungstate crystals used in the ECAL corresponds to the highest volume ever produced for a single experiment. The excellent quality of the crystals, both in ter...

  10. Extracting trends from two decades of microgravity macromolecular crystallization history

    Science.gov (United States)

    Judge, Russell A.; Snell, Edward H.; van der Woerd, Mark J.

    2005-01-01

    Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.

  11. Macromolecular crystallization and crystal perfection

    CERN Document Server

    Chayen, Naomi E; Snell, Edward H

    2010-01-01

    Structural biology is key to our understanding of the mechanisms of biological processes. This text describes current methods and future frontiers in crystal growth and use of X-ray and neutron crystallography, in the context of automation of crystallization and generation of synchrotron X-ray and neutron beams.

  12. Liquid crystal tunable photonic crystal dye laser

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  13. Synthesis and application of functional branched macromolecules: From site isolation and energy harvesting to catalysis

    Science.gov (United States)

    Hecht, Stefan

    The symbiosis of our understanding of structure property relationships in many biological macromolecules and our increased ability to prepare large synthetic macromolecules with exquisite structural precision has generated a new area of research where chemistry and materials science join with biology. For example, numerous biological systems utilize the concept of site isolation whereby an active center or catalytic site is encapsulated, frequently within a protein, to afford properties that would not be encountered in the bulk state. The ability of a dendritic shell to encapsulate functional core moieties and to create specific site-isolated nanoenvironments, thereby affecting molecular properties, not only mimics natural systems but affords novel materials with unique characteristics. Furthermore, introduction of donor chromophores at periphery of dendrimers having a central acceptor dye enables spatial and spectral energy concentration at the core. Continuing the effort towards designing bio-inspired macromolecules, this dissertation describes the use of different polymer architectures to encapsulate active sites that have either photophysical, photochemical, or catalytic functions and the evaluation of site isolation using a variety of different techniques. While the first part is mainly concerned with different synthetic approaches towards site isolation of porphyrin moieties, the second part describes the design of light-driven catalytic systems incorporating both light harvesting and energy conversion. The fundamental knowledge that can be gleaned from such investigations has implications that range from the preliminary design of artificial enzymes to the construction of molecular-scale devices. After an overview of dendritically encapsulated functions (Chapter 1) and a brief account of a novel synthetic approach to benzene core dendrimers (Chapter 2), site isolation of porphyrin moieties within dendrimers, their linear structural isomers, and branched star

  14. Crystal Dislocations

    Directory of Open Access Journals (Sweden)

    Ronald W. Armstrong

    2016-01-01

    Full Text Available Crystal dislocations were invisible until the mid-20th century although their presence had been inferred; the atomic and molecular scale dimensions had prevented earlier discovery. Now they are normally known to be just about everywhere, for example, in the softest molecularly-bonded crystals as well as within the hardest covalently-bonded diamonds. The advent of advanced techniques of atomic-scale probing has facilitated modern observations of dislocations in every crystal structure-type, particularly by X-ray diffraction topography and transmission electron microscopy. The present Special Issue provides a flavor of their ubiquitous presences, their characterizations and, especially, their influence on mechanical and electrical properties.

  15. Surface behavior and kinetic analysis of macromolecules separated from beer in aqueous solution; Biru yori bunrishita kobunshi no suiyoeki deno hyomen kyodo to sono sokudo ronteki kaiseki

    Energy Technology Data Exchange (ETDEWEB)

    Segawa, S.; Mitani, Y. [Sapporo Breweries Ltd., Tokyo (Japan). Brewing Research Lab.; Ogaki, K. [Osaka Univ., Osaka (Japan). Division of Chemical Engineering

    2000-09-10

    In a solution of macromolecules such as proteins that have surface activity, the macromolecules stabilize the foam by adsorbing at the bubble surface. These surface-active macromolecules at the gas/liquid interface lower surface energy. The macromolecules adhere to the gas/liquid interface, and then change their shapes. Hydrophobic groups in the molecule turn to the gas phase and hydrophilic groups turn to the liquid phase. The macromolecules separated from beer were dissolved in an acetic acid buffer solution, and then the surface behavior was speculated by the surface tension change. Their surface tension did not reach a constant value for several seconds, not like the low molecular solutions such as ethanol. The decrease in this surface tension could be kinetically analyzed. The surface tension decreased by the adsorption of macromolecules on the liquid surface, and by the shape changes in the molecule (the extension of molecule at the surface). In the {beta}-casein solution, the surface tension decreased in 2 steps that were more clear than in the beer macromolecule solution. This surface tension decrease is also supposed to show the adsorption of protein molecules and the shape change at the liquid surface. (author)

  16. The chain length of lignan macromolecule from flaxseed hulls is determined by the incorporation of coumaric acid glucosides and ferulic acid glucosides.

    Science.gov (United States)

    Struijs, Karin; Vincken, Jean-Paul; Doeswijk, Timo G; Voragen, Alphons G J; Gruppen, Harry

    2009-01-01

    Lignan macromolecule from flaxseed hulls is composed of secoisolariciresinol diglucoside (SDG) and herbacetin diglucoside (HDG) moieties ester-linked by 3-hydroxy-3-methylglutaric acid (HMGA), and of p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) moieties ester-linked directly to SDG. The linker molecule HMGA was found to account for 11% (w/w) of the lignan macromolecule. Based on the extinction coefficients and RP-HPLC data, it was determined that SDG contributes for 62.0% (w/w) to the lignan macromolecule, while CouAG, FeAG, and HDG contribute for 12.2, 9.0, and 5.7% (w/w), respectively. Analysis of fractions of lignan macromolecule showed that the higher the molecular mass, the higher the proportion of SDG was. An inverse relation between the molecular mass and the proportion (%) CouAG+FeAG was found. Together with the structural information of oligomers of lignan macromolecule obtained after partial saponification, it is hypothesized that the amount of CouAG+FeAG present during biosynthesis determines the chain length of lignan macromolecule. Furthermore, the chain length was estimated from a model describing lignan macromolecule based on structural and compositional data. The average chain length of the lignan macromolceule was calculated to be three SDG moieties with CouAG or FeAG at each of the terminal positions, with a variation between one and seven SDG moieties.

  17. Systematic Procedure for Generating Operational Policies to Achieve Target Crystal Size Distribution (CSD) in Batch Cooling Crystallization

    DEFF Research Database (Denmark)

    Abdul Samad, Noor Asma Fazli; Singh, Ravendra; Sin, Gürkan

    Batch cooling crystallization is one of the important unit operations involving separation of solid-liquid phases. Usually the most common crystal product qualities are directly related to the crystal size distribution (CSD). However the main difficulty in batch crystallization is to obtain a uni...

  18. Effect of cAMP on macromolecule synthesis in the pathogenic protozoa Trypanosoma cruzi

    Directory of Open Access Journals (Sweden)

    Dilvani O. Santos

    1988-09-01

    Full Text Available Macromolecule synthesis of Trypanosoma cruzi in culture was monitored using radioactive tracers. Cells of different days in culture displayed a preferential incorporation of precursors as follows: 1 day for (³H-thymidine cells; 3 days for (³H-uridine cells, and 4 days for (³H-leucine cells. Autoradiographic studies showed that (³H-thymidine was incorporated in the DNA of both kinetoplast and nucleus in this order. Shifts in the intracellular content of cAMP either by addition of dibutyryl-cAMP or by stimulation of the adenylcyclase by isoproterenol, caused an inhibition in the synthesis of DNA, RNA and proteins. Addition to the T. cruzi cultures of these agents which elevate the intracellular content ofcAMP provoked an interruption of cell proliferation as a result of the impairment of macromolecule synthesis. A discrimination was observed among the stereoisomers of isoproterenol, the L configuration showing to be most active.A síntese de macromoléculas de T. cruzi em cultura foi monitorada usando traçadores radioativos. Células de diferentes dias em cultura mostraram uma incorporação preferencial de precursores comco se seguez: 1 dia para (3H-timidina; 3 dias para (3H-uridina e 4 dias para (3H-leucina. Estudos autoradiográficos mostraram que (3H-leucina. Estudos autoradiográficos mostraram que (3H-timidina foi incorporada no DNA de ambos, cinetoplasto e núcleo, nesta ordem. Alterações no conteúdo intracelular de cAMP seja por adição de dibutiril-cAMP ou por estimulação de adenilciclase por isoproterenol, causav am inibição na síntese de DNA, RNA e proteínas. A adição destes agentes que elevam o conteúdo intracelular de cAMP em culturas de T.cruzi provocou inibição de crescimento, com resultado da síntese macromolecular imperfeita. Foi observada uma discriminação entre os estereoisômeros de isoproterenol, sendo a configuração L, a mais ativa.

  19. A statistical model of macromolecules dynamics for Fluorescence Correlation Spectroscopy data analysis

    Directory of Open Access Journals (Sweden)

    Dmitri Koroliouk

    2016-08-01

    Full Text Available In this paper, we propose a new mathematical model to describe the mechanisms of biological macromolecules interactions. Our model consists of a discrete stationary random sequence given by a solution of difference stochastic equation, characterized by a drift predictive component and by a diffusion term. The relative statistical estimations are very simple and effective, promising to be a good tool for the mathematical description of collective biological reactions. This paper presents the mathematical model and its verification on a simulated data set, obtained on the basis of the well-known Stokes-Einsteinmodel. In particular, we considered several mix of particles of different diffusion coefficient, respectively: D1=10 mm2/sec and D2=100 mm2/sec. The parameters evaluated by this new mathematical model on simulated data show good estimation accuracy, in comparison with the prior parameters used in the simulations. Furthermore, when analyzing the data for the mix of particles with different diffusion coefficient, the proposed model parameters  (regression and  (square variance of the stochastic component have a good discriminative ability for the molar fraction determination.  In this paper, we propose a new mathematical model to describe the mechanisms of biological macromolecules interactions. Our model consists of a discrete stationary random sequence given by a solution of difference stochastic equation, characterized by a drift predictive component and by a diffusion term. The relative statistical estimations are very simple and effective, promising to be a good tool for mathematical description of collective biological reactions. This paper presents the mathematical model and its verification on simulated data set, obtained on the basis of the well-known Stokes-Einsteinmodel. In particular we considered several mix of particles of different diffusion coefficient, respectively: D1=10 mm2/sec and D2=100 mm2/sec. The parameters

  20. The MORPHEUS II protein crystallization screen.

    Science.gov (United States)

    Gorrec, Fabrice

    2015-07-01

    High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

  1. Cobalt-mediated radical coupling (CMRC): an unusual route to midchain-functionalized symmetrical macromolecules.

    Science.gov (United States)

    Debuigne, Antoine; Poli, Rinaldo; De Winter, Julien; Laurent, Pascal; Gerbaux, Pascal; Dubois, Philippe; Wathelet, Jean-Paul; Jérôme, Christine; Detrembleur, Christophe

    2010-02-01

    Cobalt-mediated radical coupling (CMRC) is a straightforward approach to the synthesis of symmetrical macromolecules that relies on the addition of 1,3-diene compounds onto polymer precursors preformed by cobalt-mediated radical polymerization (CMRP). Mechanistic features that make this process so efficient for radical polymer coupling are reported here. The mechanism was established on the basis of NMR spectroscopy and MALDI-MS analyses of the coupling product and corroborated by DFT calculations. A key feature of CMRC is the preferential insertion of two diene units in the middle of the chain of the coupling product mainly according to a trans-1,4-addition pathway. The large tolerance of CMRC towards the diene structure is demonstrated and the impact of this new coupling method on macromolecular engineering is discussed, especially for midchain functionalization of polymers. It is worth noting that the interest in CMRC goes beyond the field of polymer chemistry, since it constitutes a novel carbon-carbon bond formation method that could be applied to small organic molecules.

  2. Controlled method of reducing electrophoretic mobility of macromolecules, particles, or cells

    Science.gov (United States)

    Vanalstine, James M. (Inventor)

    1992-01-01

    A method of reducing electrophoretic mobility of macromolecules, particles, cells, and other substances is provided which comprises interacting in a conventional electrophoretic separating procedure, the substances with a polymer-linked affinity compound comprised of a hydrophilic neutral polymer such as polyethylene glycol bound to a second component such as a hydrophobic compound, an immunocompound such as an antibody or antibody active fragment, or a ligand such as a hormone, drug, antigen, or a hapten. The reduction of electrophoretic mobility achieved is directly proportional to the concentration of the polymer-linked affinity compound employed, and such reduction can comprise up to 100 percent for particular particles and cells. The present invention is advantageous in that electrophoretic separation can now be achieved for substances whose native surface charge structure had prevented them from being separated by normal electrophoretic means. Depending on the affinity component utilized, separation can be achieved on the basis of the specific/irreversible, specific/reversible, semi-specific/reversible, relatively nonspecific/reversible, or relatively nonspecific/irreversible ligand-substance interactions.

  3. Glycoxidation of biological macromolecules: a critical approach to halt the menace of glycation.

    Science.gov (United States)

    Ahmad, Saheem; Khan, M Salman; Akhter, Firoz; Khan, Mohd Sajid; Khan, Amir; Ashraf, J M; Pandey, Ramendra Pati; Shahab, Uzma

    2014-11-01

    Glycation is the result of covalent bonding of a free amino group of biological macromolecules with a reducing sugar, which results in the formation of a Schiff base that undergoes rearrangement, dehydration and cyclization to form a more stable Amadori product. The final products of nonenzymatic glycation of biomacromolecules like DNA, proteins and lipids are known as advanced glycation end products (AGEs). AGEs may be generated rapidly or over long times stimulated by distinct triggering mechanisms, thereby accounting for their roles in multiple settings and disease states. Both Schiff base and Amadori glycation products generate free radicals resulting in decline of antioxidant defense mechanisms and can damage cellular organelles and enzymes. This critical review primarily focuses on the mechanistic insight of glycation and the most probable route for the formation of glycation products and their therapeutic interventions. Furthermore, the prevention of glycation reaction using therapeutic drugs such as metformin, pyridoxamine and aminoguanidine (AG) are discussed with special emphasis on the novel concept of the bioconjugation of these drugs like, AG with gold nanoparticles (GNPs). At or above 10 mM concentration, AG is found to be toxic and therefore has serious health concerns, and the study warrants doing this novel bioconjugation of AG with GNPs. This approach might increase the efficacy of the AG at a reduced concentration with low or no toxicity. Using the concept of synthesis of GNPs with abovementioned drugs, it is assumed that toxicity of various drugs which are used at high doses can be minimized more effectively.

  4. Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

    Science.gov (United States)

    Skolnick, Jeffrey

    2016-01-01

    An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes. PMID:27634243

  5. Antioxidant, antimicrobial, cell viability and enzymatic inhibitory of antioxidant polymers as biological macromolecules.

    Science.gov (United States)

    Hashemi Gahruie, Hadi; Niakousari, Mehrdad

    2017-11-01

    Polymeric antioxidants such as Catechinaldehyde Polycondensates, Catechin-acelaldehydepolycondensates, Flavonoid-grafted chitosan fibers, Ferulate hydrogel, Dextran ferulate hydrogel, Starch-quercetin conjugate, Gallic acid- and Caffeic acid-functionalized chitosan, Gallic acid - chitosan conjugate, Poly(rutin), Gallic acid grafted chitosan, Dextran-Catechin Conjugate belong to biological macromolecules. These kinds of compounds have stronger antioxidant potential and pharmacokinetic activities, as compared to similar low molecular weight preservatives. Most of these compounds sources are either antioxidants with low molecules polymerization, or polymers conjugation such as synthetic or natural preservatives. Additives are well known as being an important ingredient of food products due to their strong preservative potential. Many researchers and industries attempt to find synthesize materials with the same antioxidant potential and higher stability than the similar compounds with low molecular weight. Recently, macromolecular antioxidants have received wide attention as food additives and dietary supplements in functional foods. It seems that the main usage of these compounds is in the food packaging industry. Most of these compounds have strong antioxidant, antimicrobial, cell viability and enzymatic inhibitory properties. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Coupling of the fusion and budding of giant phospholipid vesicles containing macromolecules.

    Science.gov (United States)

    Terasawa, Hidetoshi; Nishimura, Kazuya; Suzuki, Hiroaki; Matsuura, Tomoaki; Yomo, Tetsuya

    2012-04-17

    Mechanisms that enabled primitive cell membranes to self-reproduce have been discussed based on the physicochemical properties of fatty acids; however, there must be a transition to modern cell membranes composed of phospholipids [Budin I, Szostak JW (2011) Proc Natl Acad Sci USA 108:5249-5254]. Thus, a growth-division mechanism of membranes that does not depend on the chemical nature of amphiphilic molecules must have existed. Here, we show that giant unilamellar vesicles composed of phospholipids can undergo the coupled process of fusion and budding transformation, which mimics cell growth and division. After gaining excess membrane by electrofusion, giant vesicles spontaneously transform into the budded shape only when they contain macromolecules (polymers) inside their aqueous core. This process is a result of the vesicle maximizing the translational entropy of the encapsulated polymers (depletion volume effect). Because the cell is a lipid membrane bag containing highly concentrated biopolymers, this coupling process that is induced by physical and nonspecific interactions may have a general importance in the self-reproduction of the early cellular compartments.

  7. Preparation, characterization and application of a novel biodegradable macromolecule: carboxymethyl zein.

    Science.gov (United States)

    Yin, Huayue; Lu, Tao; Liu, Li; Lu, Chuanhua

    2015-01-01

    Zein, a naturally biocompatible and biodegradable macromolecule, is widely used as plastic film material; however, the poor water solubility limits its other applications. In this study, we aimed to obtain carboxymethyl zein (CM-zein) by modifying it with sodium monochloroacetate in weakly basic environment. CM-zein showed a new FTIR peak of C-O-C bond at 1080 cm(-1), with a new signal region appearing at 4.0-4.05 ppm that assigned to the protons of the CH2 group from a carboxymethyl on (1)H NMR and a Tg of 168.0 °C by thermal analysis. Compared with the -12.3 mV of zeta potential of unmodified zein, CM-zein increased it significantly to -23.9 mV as a consequence of carboxymethylation. 5-Fluorouracil (5-FU), a model drug used in CM-zein-based tablet, was rarely detected in 0.1 mol/L HCl (pH 1.0) but it was released massively and quickly in phosphates buffer (pH 6.8) in vitro assays. The unmodified zein-based tablet illustrated much lower release level in these two fluids. Furthermore, the pharmacokinetic study of rats showed that CM-zein released 5-FU in intestine but not in stomach after dissolving. These findings indicated that CM-zein has the potential to be used for enteric preparation as a novel pH-selective biomaterial.

  8. Introduction to 3D reconstruction of macromolecules using single particle electron microscopy

    Institute of Scientific and Technical Information of China (English)

    Oscar LLORCA

    2005-01-01

    Single-particle electron microscopy has now reached maturity, becoming a commonly used method in the examination ofmacromolecular structure. Using a small amount of purified protein, isolated molecules are observed under the electron microscope and the data collected can be averaged into a 3D reconstruction.Single-particle electron microscopy is an appropriate tool for the analysis of proteins that can only be obtained in modest quantities, like many of the large complexes currently of interest in biomedicine. Whilst the use of electron microscopy expands, new methods are being developed and improved to deal with further challenges, such as reaching higher resolutions and the combination of information at different levels of structural detail. More importantly, present methodology is still not robust enough when studying certain "tricky" proteins like those displaying extensive conformational flexibility and a great deal of user expertise is required, posing a threat to the consistency of the final structure. This mini review describes a brief outline of the methods currently used in the 3D analysis of macromolecules using single-particle electron microscopy, intended for those first approaching this field. A summary of methods, techniques, software, and some recent work is presented. The spectacular improvements to the technique in recent years, its advantages and limitations compared to other structural methods,and its future developments are discussed.

  9. Correction: Membrane-active macromolecules resensitize NDM-1 gram-negative clinical isolates to tetracycline antibiotics.

    Directory of Open Access Journals (Sweden)

    Divakara S S M Uppu

    Full Text Available Gram-negative 'superbugs' such as New Delhi metallo-beta-lactamase-1 (blaNDM-1 producing pathogens have become world's major public health threats. Development of molecular strategies that can rehabilitate the 'old antibiotics' and halt the antibiotic resistance is a promising approach to target them. We report membrane-active macromolecules (MAMsthat restore the antibacterial efficacy (enhancement by >80-1250 fold of tetracycline antibiotics towards blaNDM-1 Klebsiella pneumonia and blaNDM-1 Escherichia coli clinical isolates.Organismic studies showed that bacteria had an increased and faster uptake of tetracyclinein the presence of MAMs which is attributed to the mechanism of re-sensitization. Moreover,bacteria did not develop resistance to MAMs and MAMs stalled the development of bacterial resistance to tetracycline. MAMs displayed membrane-active properties such as dissipation of membrane potential and membrane-permeabilization that enabled higher uptake of tetracycline in bacteria. In-vivo toxicity studies displayed good safety profiles and preliminary in-vivo antibacterial efficacy studies showed that mice treated with MAMs in combination with antibiotics had significantly decreased bacterial burden compared to the untreated mice. This report of re-instating the efficacy of the antibiotics towards blaNDM-1 pathogens using membrane-active molecules advocates their potential for synergistic co-delivery of antibiotics to combat Gram-negative superbugs.

  10. Membrane-active macromolecules resensitize NDM-1 gram-negative clinical isolates to tetracycline antibiotics.

    Directory of Open Access Journals (Sweden)

    Divakara S S M Uppu

    Full Text Available Gram-negative 'superbugs' such as New Delhi metallo-beta-lactamase-1 (blaNDM-1 producing pathogens have become world's major public health threats. Development of molecular strategies that can rehabilitate the 'old antibiotics' and halt the antibiotic resistance is a promising approach to target them. We report membrane-active macromolecules (MAMs that restore the antibacterial efficacy (enhancement by >80-1250 fold of tetracycline antibiotics towards blaNDM-1 Klebsiella pneumonia and blaNDM-1 Escherichia coli clinical isolates. Organismic studies showed that bacteria had an increased and faster uptake of tetracycline in the presence of MAMs which is attributed to the mechanism of re-sensitization. Moreover, bacteria did not develop resistance to MAMs and MAMs stalled the development of bacterial resistance to tetracycline. MAMs displayed membrane-active properties such as dissipation of membrane potential and membrane-permeabilization that enabled higher uptake of tetracycline in bacteria. In-vivo toxicity studies displayed good safety profiles and preliminary in-vivo antibacterial efficacy studies showed that mice treated with MAMs in combination with antibiotics had significantly decreased bacterial burden compared to the untreated mice. This report of re-instating the efficacy of the antibiotics towards blaNDM-1 pathogens using membrane-active molecules advocates their potential for synergistic co-delivery of antibiotics to combat Gram-negative superbugs.

  11. Suspendable macromolecules are responsible for ice nucleation activity of birch and conifer pollen

    Directory of Open Access Journals (Sweden)

    B. G. Pummer

    2012-03-01

    Full Text Available The ice nucleation of bioaerosols (bacteria, pollen, spores, etc. is a topic of growing interest, since their impact on ice cloud formation and thus on radiative forcing, an important parameter in global climate, is not yet fully understood. Here we show that pollen of different species strongly differ in their ice nucleation behaviour. The average freezing temperatures in laboratory experiments range from 240 to 255 K. As the most efficient nuclei (silver birch, Scots pine and common juniper pollen have a distribution area up to the Northern timberline, their ice nucleation activity might be a cryoprotective mechanism. Far more intriguingly, it has turned out that water, which has been in contact with pollen and then been separated from the bodies, nucleates as good as the pollen grains themselves. The ice nuclei have to be easily-suspendable macromolecules located on the pollen. Once extracted, they can be distributed further through the atmosphere than the heavy pollen grains and so presumably augment the impact of pollen on ice cloud formation even in the upper troposphere. Our experiments lead to the conclusion that pollen ice nuclei, in contrast to bacterial and fungal ice nucleating proteins, are non-proteinaceous compounds.

  12. Oxidative damage to macromolecules in human Parkinson disease and the rotenone model.

    Science.gov (United States)

    Sanders, Laurie H; Greenamyre, J Timothy

    2013-09-01

    Parkinson disease (PD), the most common neurodegenerative movement disorder, is associated with selective degeneration of nigrostriatal dopamine neurons. Although the underlying mechanisms contributing to neurodegeneration in PD seem to be multifactorial, mitochondrial impairment and oxidative stress are widely considered to be central to many forms of the disease. Whether oxidative stress is a cause or a consequence of dopaminergic death, there is substantial evidence for oxidative stress both in human PD patients and in animal models of PD, especially using rotenone, a complex I inhibitor. There are many indices of oxidative stress, but this review covers the recent evidence for oxidative damage to nucleic acids, lipids, and proteins in both the brain and the peripheral tissues in human PD and in the rotenone model. Limitations of the existing literature and future perspectives are discussed. Understanding how each particular macromolecule is damaged by oxidative stress and the interplay of secondary damage to other biomolecules may help us design better targets for the treatment of PD. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Film Self-Assembly of Oppositely Charged Macromolecules Triggered by Electrochemistry through a Morphogenic Approach.

    Science.gov (United States)

    Dochter, Alexandre; Garnier, Tony; Pardieu, Elodie; Chau, Nguyet Trang Thanh; Maerten, Clément; Senger, Bernard; Schaaf, Pierre; Jierry, Loïc; Boulmedais, Fouzia

    2015-09-22

    The development of new surface functionalization methods that are easy to use, versatile, and allow local deposition represents a real scientific challenge. Overcoming this challenge, we present here a one-pot process that consists in self-assembling, by electrochemistry on an electrode, films made of oppositely charged macromolecules. This method relies on a charge-shifting polyanion, dimethylmaleic-modified poly(allylamine) (PAHd), that undergoes hydrolysis at acidic pH, leading to an overall switching of its charge. When a mixture of the two polyanions, PAHd and poly(styrenesulfonate) (PSS), is placed in contact with an electrode, where the pH is decreased locally by electrochemistry, the transformation of PAHd into a polycation (PAH) leads to the continuous self-assembly of a nanometric PAH/PSS film by electrostatic interactions. The pH decrease is obtained by the electrochemical oxidation of hydroquinone, which produces protons locally over nanometric distances. Using a negatively charged enzyme, alkaline phosphatase (AP), instead of PSS, this one-pot process allows the creation of enzymatically active films. Under mild conditions, self-assembled PAH/AP films have an enzymatic activity which is adjustable simply by controlling the self-assembly time. The selective functionalization of microelectrode arrays by PAH/AP was achieved, opening the route toward miniaturized biosensors.

  14. A new force-extension formula for stretched macromolecules and polymers based on the Ising model

    Science.gov (United States)

    Chan, Yue; Haverkamp, Richard G.

    2016-12-01

    In this paper, we derive a new force-extension formula for stretched macromolecules and homogeneous polymer matrices. The Ising model arising from paramagnetism is employed, where the magnetic force is replaced by the external force, and the resistance energy is addressed in this model instead of the usual persistent length arising from the freely jointed chain and worm-like chain models. While the force-extension formula reveals the distinctive stretching features for stretched polymers, the resistance energy is found to increase almost linearly with the external force for our two polysaccharides stretching examples with and without ring conformational changes. In particular, a jump in the resistance energy which is caused by a conformational transition is investigated, and the gap between the jump determines the energy barrier between two conformational configurations. Our theoretical model matches well with experimental results undergoing no and single conformational transitions, and a Monte Carlo simulation has also been performed to ensure the correctness of the resistance energy. This technique might also be employed to determine the binding energy from other causes during molecular stretching and provide vital information for further theoretical investigations.

  15. Quantum propagation of electronic excitations in macromolecules: A computationally efficient multiscale approach

    Science.gov (United States)

    Schneider, E.; a Beccara, S.; Mascherpa, F.; Faccioli, P.

    2016-07-01

    We introduce a theoretical approach to study the quantum-dissipative dynamics of electronic excitations in macromolecules, which enables to perform calculations in large systems and cover long-time intervals. All the parameters of the underlying microscopic Hamiltonian are obtained from ab initio electronic structure calculations, ensuring chemical detail. In the short-time regime, the theory is solvable using a diagrammatic perturbation theory, enabling analytic insight. To compute the time evolution of the density matrix at intermediate times, typically ≲ps , we develop a Monte Carlo algorithm free from any sign or phase problem, hence computationally efficient. Finally, the dynamics in the long-time and large-distance limit can be studied combining the microscopic calculations with renormalization group techniques to define a rigorous low-resolution effective theory. We benchmark our Monte Carlo algorithm against the results obtained in perturbation theory and using a semiclassical nonperturbative scheme. Then, we apply it to compute the intrachain charge mobility in a realistic conjugated polymer.

  16. Electric double layer and electrokinetic potential of pectic macromolecules in sugar beet

    Directory of Open Access Journals (Sweden)

    Kuljanin Tatjana A.

    2008-01-01

    Full Text Available Electrokinetic potential is an important property of colloidal particles and, regarding the fact that it is a well defined and easily measurable property, it is considered to be a permanent characteristic of a particular colloidal system. In fact, it is a measure of electrokinetic charge that surrounds the colloidal particle in a solution and is in direct proportion with the mobility of particles in an electric field. Gouy-Chapman-Stern-Graham's model of electric double layer was adopted and it was proven experimentally that the addition of Cu++ ions to sugar beet pectin caused a reduction in the negative electrokinetic potential proportional to the increase of Cu++ concentration. Higher Cu++ concentrations increased the proportion of cation specific adsorption (Cu++ and H+ with regard to electrostatic Coulombic forces. Consequently, there is a shift in the shear plane between the fixed and diffuse layers directed towards the diffuse layer, i.e. towards its compression and decrease in the electrokinetic potential or even charge inversion of pectin macromolecules.

  17. Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution.

    Science.gov (United States)

    Pernot, Petra; Round, Adam; Barrett, Ray; De Maria Antolinos, Alejandro; Gobbo, Alexandre; Gordon, Elspeth; Huet, Julien; Kieffer, Jerôme; Lentini, Mario; Mattenet, Muriel; Morawe, Christian; Mueller-Dieckmann, Christoph; Ohlsson, Staffan; Schmid, Werner; Surr, John; Theveneau, Pascal; Zerrad, Louiza; McSweeney, Sean

    2013-07-01

    Small-angle X-ray scattering (SAXS) measurements of proteins in solution are becoming increasingly popular with biochemists and structural biologists owing to the presence of dedicated high-throughput beamlines at synchrotron sources. As part of the ESRF Upgrade program a dedicated instrument for performing SAXS from biological macromolecules in solution (BioSAXS) has been installed at the renovated BM29 location. The optics hutch has been equipped with new optical components of which the two principal elements are a fixed-exit double multilayer monochromator and a 1.1 m-long toroidal mirror. These new dedicated optics give improved beam characteristics (compared with the previous set-up on ID14-3) regarding the energy tunability, flux and focusing at the detector plane leading to reduced parasitic scattering and an extended s-range. User experiments on the beamline have been successfully carried out since June 2012. A description of the new BioSAXS beamline and the set-up characteristics are presented together with examples of obtained data.

  18. Detection of Macromolecules in Desert Cyanobacteria Mixed with a Lunar Mineral Analogue After Space Simulations

    Science.gov (United States)

    Baqué, Mickael; Verseux, Cyprien; Rabbow, Elke; de Vera, Jean-Pierre Paul; Billi, Daniela

    2014-09-01

    In the context of future exposure missions in Low Earth Orbit and possibly on the Moon, two desert strains of the cyanobacterium Chroococcidiopsis, strains CCMEE 029 and 057, mixed or not with a lunar mineral analogue, were exposed to fractionated fluencies of UVC and polychromatic UV (200-400 nm) and to space vacuum. These experiments were carried out within the framework of the BIOMEX (BIOlogy and Mars EXperiment) project, which aims at broadening our knowledge of mineral-microorganism interaction and the stability/degradation of their macromolecules when exposed to space and simulated Martian conditions. The presence of mineral analogues provided a protective effect, preserving survivability and integrity of DNA and photosynthetic pigments, as revealed by testing colony-forming abilities, performing PCR-based assays and using confocal laser scanning microscopy. In particular, DNA and pigments were still detectable after 500 kJ/m2 of polychromatic UV and space vacuum (10-4 Pa), corresponding to conditions expected during one-year exposure in Low Earth Orbit on board the EXPOSE-R2 platform in the presence of 0.1 % Neutral Density (ND) filter. After exposure to high UV fluencies (800 MJ/m2) in the presence of minerals, however, altered fluorescence emission spectrum of the photosynthetic pigments were detected, whereas DNA was still amplified by PCR. The present paper considers the implications of such findings for the detection of biosignatures in extraterrestrial conditions and for putative future lunar missions.

  19. New beamline dedicated to solution scattering from biological macromolecules at the ESRF

    Energy Technology Data Exchange (ETDEWEB)

    Pernot, P; Theveneau, P; Giraud, T; Fernandes, R Nogueira; Nurizzo, D; Spruce, D; Surr, J; McSweeney, S [ESRF, BP 220, Grenoble (France); Round, A; Felisaz, F; Foedinger, L; Gobbo, A; Huet, J; Villard, C; Cipriani, F, E-mail: rejma@esrf.f, E-mail: around@embl.f [EMBL Grenoble, BP 181, Grenoble (France)

    2010-10-01

    The new bio-SAXS beamline (ID14-3 at the ESRF, Grenoble, France) is dedicated exclusively to small-angle scattering experiments of biological macromolecules in solution and has been in user operation since November 2008. Originally a protein crystallography beamline, ID14-3 was refurbished, still as a part of the ESRF Structural Biology group, with the main aim to provide a facility with 'quick and easy' access to satisfy rapidly growing demands from crystallographers, biochemists and structural biologists. The beamline allows manual and automatic sample loading/unloading, data collection, processing (conversion of a 2D image to a normalized 1D X-ray scattering profile) and analysis. The users obtain on-line standard data concerning the size (radius of gyration, maximum dimension and volume) and molecular weight of samples which allow on-the fly ab-inito shape reconstruction in order to provide feedback enabling the data collection strategies to be optimized. Automation of sample loading is incorporated on the beamline using a device constructed in collaboration between the EMBL (Grenoble and Hamburg outstations) and the ESRF. Semi/automated data analysis is implemented following the model of the SAXS facility at X33, EMBL Hamburg. This paper describes the bio-SAXS beamline and set-up characteristics together with the examples of user data obtained.

  20. Electrospun ECM macromolecules as biomimetic scaffold for regenerative medicine: challenges for preserving conformation and bioactivity

    Directory of Open Access Journals (Sweden)

    Chiara Emma Campiglio

    2017-05-01

    Full Text Available The extracellular matrix (ECM, the physiological scaffold for cells in vivo, provides structural support to cells and guaranties tissue integrity. At the same time, however, it represents an extremely complex and finely tuned signaling environment that contributes in regulating tissue homeostasis and repair. ECM can bind, release and activate signaling molecules and also modulate cell reaction to soluble factors. Cell-ECM interactions, as a result, are recognized to be critical for physiological wound healing, and consequently in guiding regeneration. Due to its complexity, mimicking ECM chemistry and architecture appears a straightforward strategy to exploit the benefits of a biologically recognizable and cell-instructive environment. As ECM consists primarily of sub-micrometric fibers, electrospinning, a simple and versatile technique, has attracted the majority efforts aimed at reprocessing of biologically occurring molecules. However, the ability to trigger specific cellular behavior is likely to depend on both the chemical and conformational properties of biological molecules. As a consequence, when ECM macromolecules are electrospun, investigating the effect of processing on their structure, and the extent to which their potential in directing cellular behavior is preserved, appears crucial. In this perspective, this review explores the electrospinning of ECM molecules specifically focusing on the effect of processing on polymer structure and on in vitro or in vivo experiments designed to confirm the maintenance of their instructive role.

  1. Electronic method for autofluorography of macromolecules on two-D matrices

    Science.gov (United States)

    Davidson, Jackson B.; Case, Arthur L.

    1983-01-01

    A method for detecting, localizing, and quantifying macromolecules contained in a two-dimensional matrix is provided which employs a television-based position sensitive detection system. A molecule-containing matrix may be produced by conventional means to produce spots of light at the molecule locations which are detected by the television system. The matrix, such as a gel matrix, is exposed to an electronic camera system including an image-intensifier and secondary electron conduction camera capable of light integrating times of many minutes. A light image stored in the form of a charge image on the camera tube target is scanned by conventional television techniques, digitized, and stored in a digital memory. Intensity of any point on the image may be determined from the number at the memory address of the point. The entire image may be displayed on a television monitor for inspection and photographing or individual spots may be analyzed through selected readout of the memory locations. Compared to conventional film exposure methods, the exposure time may be reduced 100-1000 times.

  2. Microfiberoptic fluorescence photobleaching reveals size-dependent macromolecule diffusion in extracellular space deep in brain.

    Science.gov (United States)

    Zador, Zsolt; Magzoub, Mazin; Jin, Songwan; Manley, Geoffrey T; Papadopoulos, Marios C; Verkman, A S

    2008-03-01

    Diffusion in brain extracellular space (ECS) is important for nonsynaptic intercellular communication, extracellular ionic buffering, and delivery of drugs and metabolites. We measured macromolecular diffusion in normally light-inaccessible regions of mouse brain by microfiberoptic epifluorescence photobleaching, in which a fiberoptic with a micron-size tip is introduced deep in brain tissue. In brain cortex, the diffusion of a noninteracting molecule [fluorescein isothiocyanate (FITC)-dextran, 70 kDa] was slowed 4.5 +/- 0.5-fold compared with its diffusion in water (D(o)/D), and was depth-independent down to 800 microm from the brain surface. Diffusion was significantly accelerated (D(o)/D of 2.9+/-0.3) in mice lacking the glial water channel aquaporin-4. FITC-dextran diffusion varied greatly in different regions of brain, with D(o)/D of 3.5 +/- 0.3 in hippocampus and 7.4 +/- 0.3 in thalamus. Remarkably, D(o)/D in deep brain was strongly dependent on solute size, whereas diffusion in cortex changed little with solute size. Mathematical modeling of ECS diffusion required nonuniform ECS dimensions in deep brain, which we call "heterometricity," to account for the size-dependent diffusion. Our results provide the first data on molecular diffusion in ECS deep in brain in vivo and demonstrate previously unrecognized hindrance and heterometricity for diffusion of large macromolecules in deep brain.

  3. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J

    2007-04-27

    The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both functional and pathological mineral tissues. The results reveal a consistent picture of shape modification in which stereochemical matching of modifiers to specific atomic steps drives shape modification. Inhibition and other changes in growth kinetics are shown to be due to a range of mechanisms that depend on chemistry and molecular size. Some effects are well described by classic crystal growth theories, but others, such as step acceleration due to peptide charge and hydrophylicity, were previously unrealized

  4. Combining Two Methods of Sequence Definition in a Convergent Approach: Scalable Synthesis of Highly Defined and Multifunctionalized Macromolecules.

    Science.gov (United States)

    Solleder, Susanne C; Martens, Steven; Espeel, Pieter; Du Prez, Filip; Meier, Michael A R

    2017-08-23

    The straightforward convergent synthesis of sequence-defined and multifunctionalized macromolecules is described herein. The first combination of two efficient approaches for the synthesis of sequence-defined macromolecules is reported: thiolactone chemistry and the Passerini three-component reaction (P-3CR). The thiolactone moiety was used as protecting group for the thiol, allowing the synthesis of a library of sequence-defined α,ω-functionalized building blocks. These building blocks were subsequently efficiently coupled to oligomers with carboxylic acid functionalities in a P-3CR. Thus, larger oligomers with molecular weights of up to 4629.73 g mol(-1) were obtained in gram quantities in a convergent approach along with the introduction of independently selectable side chains (up to 15), thus clearly demonstrating the high versatility and the efficiency of the reported approach. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Coil-globule transition of macromolecules in mixed solvent: A semi-grand canonical molecular dynamics approach

    Science.gov (United States)

    Mukherji, Debashish; Kremer, Kurt

    2014-03-01

    Conformational transition of macromolecules in mixed solvents are intimately linked to large local concentration fluctuations of solvent components. The numerical studies in the field are limited to the closed boundary schemes, which, however, suffer from severe system size effects. To overcome this discrepancy, we have developed a semi-grand canonical molecular dynamics scheme for complex fluids. Our method makes use of the adaptive resolution scheme (AdResS) with a metropolis particle exchange criterion. In AdResS, an all-atom region, containing macromolecule, is coupled to a coarse-grained (CG) reservoir. The semi-grand canonical particle exchange is performed in the CG region. As the applications of the method, we study the concentration driven reentrant collapse and swelling transition of poly(N-isopropylacrylamide) (PNIPAm) and poly(N,N-diethylacrylamide) (PDEAm) in aqueous methanol and demonstrate the role of the delicate interplay of the different intermolecular interactions.

  6. Facile synthesis of CuSe nanoparticles and high-quality single-crystal two-dimensional hexagonal nanoplatelets with tunable near-infrared optical absorption

    Science.gov (United States)

    Wu, Yimin; Korolkov, Ilia; Qiao, Xvsheng; Zhang, Xianghua; Wan, Jun; Fan, Xianping

    2016-06-01

    A rapid injection approach is used to synthesize the copper selenide nanoparticles and two-dimensional single crystal nanoplates. This technique excludes the use of toxic or expensive materials, increasing the availability of two-dimensional binary chalcogenide semiconductors. The structure of the nanocrystals has been studied and the possible formation mechanism of the nanoplates has been proposed. The optical absorption showed that the nanoplates demonstrated wide and tuneable absorption band in the visible and near infrared region. These nanoplates could be interesting for converting solar energy and for nanophotonic devices operating in the near infrared.

  7. Correlation between intrinsic defects and electrical properties in the high-quality Cu2ZnSnS4 single crystal

    Science.gov (United States)

    Nagaoka, Akira; Miyake, Hideto; Taniyama, Tomoyasu; Kakimoto, Koichi; Yoshino, Kenji

    2013-09-01

    Temperature dependent Hall effect measurements from 20 to 300 K have been performed on the quaternary compounds Cu2ZnSnS4 (CZTS) single crystals. The conductivity mechanisms can be described by a two-path system using Mott variable range hopping and typical thermal activation conduction. The center level of the acceptor band is 132 meV above the valence band maximum and is of width 40 meV. A correlation between the activation energy and acceptor concentration in CZTS is observed.

  8. [The contribution of magnetic resonance spectroscopy to the classification of high grade gliomas. The predictive value of macromolecules].

    Science.gov (United States)

    Martínez-Bisbal, M C; Celda-Muñoz, B; Martí-Bonmatí, L; Ferrer-Ripollés, P; Revert-Ventura, A J; Piquer-Belloch, J; Mollá-Olmos, E; Arana-Fernández de Moya, E; Dosdá-Muñoz, R

    1H MRS allows the study of metabolite concentration changes in intracranial tumours, relating them, more or less successfully, to the histological type and grade of the tumour. To analyse the patterns which are useful for classifying the grades of cerebral gliomas by means of various ratios obtained using 1H MRS with two echo times (ET), with and without water suppression, paying special attention to the macromolecules. We studied 8 gliomas (1 grade II, 2 grade III and 5 grade IV) with single volume 1H MRS at ET 31 ms (8/8) and 136 ms (7/8). The intensities of the metabolites, including macromolecules (MMA, 0.9 ppm; MMB, 1.3 ppm), were normalised to water signal intensity for ET 31, to Cr at ET 31 and 136 ms and NAA/Cho for both ET and the ratio MMA/MMB at ET 31. There were significant differences between the three grades on the ratios MMA/MMB (p= 0.000) with descent of the MMA/MMB coefficient as the grade increases, and NNA/Cho at ET 136 (p= 0.018). We found an inverse relationship between the quantity in mI and the increase in grade. No macromolecules were found at ET 136 in any of the tumours of grade II or III. The spectra of gliomas with ET 31 showed macromolecules around 0.9 and 1.3 ppm with different relative ratios for each tumour grade. The ET 136 spectra informs about the content of NNA and Cho. Apart from the increase in MMB (0.9 ppm), with short ET the higher grades showed lower content of mI. The study of gliomas using 1H MRS with ET 31 and 136 ms contributes to the diagnosis of the grade of tumour.

  9. Synthesis of CaCO3 crystals using hydroxypropylmethyl cellulose hydrogel as template

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jin; LI YanJun; CHENG GuoXiang

    2007-01-01

    Calcium carbonate crystallization was performed in hydrogel of hydroxypropylmethyl cellulose (HPMC). Results showed that the polyhydroxy functionalities in HPMC gel network facilitated the nucleation of aragonite which was not found in experiment without HPMC hydrogel and in experiment using methylcellulose (MC) hydrogel as template. On the other hand,due to the unique assembly of the macromolecules in HPMC hydrogel network,which was different from other hydrogels used in some previous reports,particular crystal morphology,corncob-like CaCO3,was obtained for the first time.

  10. Crystallization, recrystallization, and melting lines in syndiotactic polypropylene crystallized from quiescent melt and semicrystalline state due to stress-induced localized melting and recrystallization.

    Science.gov (United States)

    Lu, Ying; Wang, Yaotao; Fu, Lianlian; Jiang, Zhiyong; Men, Yongfeng

    2014-11-13

    Crystalline lamellar thickness in syndiotactic polypropylene (sPP) during crystallization from either isothermal molten or stretching induced localized melt states and during subsequent heating was investigated by means of temperature dependent small-angle X-ray scattering techniques. Well-defined crystallization lines where the reciprocal lamellar thickness is linearly dependent on crystallization temperature were observed. Unlike in the case of polybutene-1 where stretching crystallization line was shifted to direction of much smaller lamellar thickness (Macromolecules 2013, 46, 7874), the stretching induced crystallization line for sPP deviates from its corresponding isothermal crystallization line only slightly. Such phenomenon could be attributed to the fact that both crystallization processes from quiescent melt and stress induced localized melt are mediated in a mesomorphic phase in sPP. Subsequent heating of sPP after crystallization revealed the same melting behavior in both systems for the two kinds of crystallites obtained from either quiescent melt or stretching induced localized melt. Both of them underwent melting and recrystallization when the lamellar thickness was smaller than a critical value and melting directly without changing in thickness when the lamellar thickness was larger than the critical value. The melting behavior in sPP systems can be understood by considering the chain relaxation ability within crystalline phase and also can be used as evidence that the crystallization from molten state and stress-induced crystallization passed through the intermediate phase before forming crystallites.

  11. A Redox-Activatable Fluorescent Sensor for the High-Throughput Quantification of Cytosolic Delivery of Macromolecules.

    Science.gov (United States)

    Wang, Zhaohui; Luo, Min; Mao, Chengqiong; Wei, Qi; Zhao, Tian; Li, Yang; Huang, Gang; Gao, Jinming

    2017-01-24

    Efficient delivery of biomacromolecules (e.g., proteins, nucleic acids) into cell cytosol remains a critical challenge for the development of macromolecular therapeutics or diagnostics. To date, most common approaches to assess cytosolic delivery rely on fluorescent labeling of macromolecules with an "always on" reporter and subcellular imaging of endolysosomal escape by confocal microscopy. This strategy is limited by poor signal-to-noise ratio and only offers low throughput, qualitative information. Herein we describe a quantitative redox-activatable sensor (qRAS) for the real-time monitoring of cytosolic delivery of macromolecules. qRAS-labeled macromolecules are silent (off) inside the intact endocytic organelles, but can be turned on by redox activation after endolysosomal disruption and delivery into the cytosol, thereby greatly improving the detection accuracy. In addition to confocal microscopy, this quantitative sensing technology allowed for a high-throughput screening of a panel of polymer carriers toward efficient cytosolic delivery of model proteins on a plate reader. The simple and versatile qRAS design offers a useful tool for the investigation of new strategies for endolysosomal escape of biomacromolecules to facilitate the development of macromolecular therapeutics for a variety of disease indications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules.

    Science.gov (United States)

    Costa, Luca; Andriatis, Alexander; Brennich, Martha; Teulon, Jean-Marie; Chen, Shu-Wen W; Pellequer, Jean-Luc; Round, Adam

    2016-10-27

    Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. By employing atomic force microscopy, another common technique to determine the shape of biological macromolecules when deposited on flat substrates, we present a protocol to evaluate and characterize consequences of radiation damage. It requires the acquisition of images of irradiated samples at the single molecule level in a timely manner while using minimal amounts of protein. The protocol has been tested on two different molecular systems: a large globular tetremeric enzyme (β-Amylase) and a rod-shape plant virus (tobacco mosaic virus). Radiation damage on the globular enzyme leads to an apparent increase in molecular sizes whereas the effect on the long virus is a breakage into smaller pieces resulting in a decrease of the average long-axis radius. These results show that radiation damage can appear in different forms and strongly support the need to check the effect of radiation damage at synchrotron sources using the presented protocol.

  13. Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

    Science.gov (United States)

    Xia, Hongwei; Fu, Hailin; Zhang, Yanfeng; Shih, Kuo-Chih; Ren, Yuan; Anuganti, Murali; Nieh, Mu-Ping; Cheng, Jianjun; Lin, Yao

    2017-08-16

    Supramolecular polymerization or assembly of proteins or large macromolecular units by a homogeneous nucleation mechanism can be quite slow and require specific solution conditions. In nature, protein assembly is often regulated by molecules that modulate the electrostatic interactions of the protein subunits for various association strengths. The key to this regulation is the coupling of the assembly process with a reversible or irreversible chemical reaction that occurs within the constituent subunits. However, realizing this complex process by the rational design of synthetic molecules or macromolecules remains a challenge. Herein, we use a synthetic polypeptide-grafted comb macromolecule to demonstrate how the in situ modulation of interactions between the charged macromolecules affects their resulting supramolecular structures. The kinetics of structural formation was studied and can be described by a generalized model of nucleated polymerization containing secondary pathways. Basic thermodynamic analysis indicated the delicate role of the electrostatic interactions between the charged subunits in the reaction-induced assembly process. This approach may be applicable for assembling a variety of ionic soft matters that are amenable to chemical reactions in situ.

  14. Membrane-active macromolecules kill antibiotic-tolerant bacteria and potentiate antibiotics towards Gram-negative bacteria.

    Science.gov (United States)

    Uppu, Divakara S S M; Konai, Mohini M; Sarkar, Paramita; Samaddar, Sandip; Fensterseifer, Isabel C M; Farias-Junior, Celio; Krishnamoorthy, Paramanandam; Shome, Bibek R; Franco, Octávio L; Haldar, Jayanta

    2017-01-01

    Chronic bacterial biofilms place a massive burden on healthcare due to the presence of antibiotic-tolerant dormant bacteria. Some of the conventional antibiotics such as erythromycin, vancomycin, linezolid, rifampicin etc. are inherently ineffective against Gram-negative bacteria, particularly in their biofilms. Here, we report membrane-active macromolecules that kill slow dividing stationary-phase and antibiotic tolerant cells of Gram-negative bacteria. More importantly, these molecules potentiate antibiotics (erythromycin and rifampicin) to biofilms of Gram-negative bacteria. These molecules eliminate planktonic bacteria that are liberated after dispersion of biofilms (dispersed cells). The membrane-active mechanism of these molecules forms the key for potentiating the established antibiotics. Further, we demonstrate that the combination of macromolecules and antibiotics significantly reduces bacterial burden in mouse burn and surgical wound infection models caused by Acinetobacter baumannii and Carbapenemase producing Klebsiella pneumoniae (KPC) clinical isolate respectively. Colistin, a well-known antibiotic targeting the lipopolysaccharide (LPS) of Gram-negative bacteria fails to kill antibiotic tolerant cells and dispersed cells (from biofilms) and bacteria develop resistance to it. On the contrary, these macromolecules prevent or delay the development of bacterial resistance to known antibiotics. Our findings emphasize the potential of targeting the bacterial membrane in antibiotic potentiation for disruption of biofilms and suggest a promising strategy towards developing therapies for topical treatment of Gram-negative infections.

  15. Using a water-confined carbon nanotube to probe the electricity of sequential charged segments of macromolecules

    Institute of Scientific and Technical Information of China (English)

    Wang Yu; Zhao Yan-Jiao; Huang Ji-Ping

    2012-01-01

    The detection of macromolecular conformation is particularly important in many physical and biological applications.Here we theoretically explore a method for achieving this detection by probing the electricity of sequential charged segments of macromolecules.Our analysis is based on molecular dynamics simulations,and we investigate a single file of water molecules confined in a half-capped single-walled carbon nanotube (SWCNT) with an external electric charge of +e or -e (e is the elementary charge).The charge is located in the vicinity of the cap of the SWCNT and along the centerline of the SWCNT.We reveal the picosecond timescaie for the re-orientation (namely,from one unidirectional direction to the other) of the water molecules in response to a switch in the charge signal,-e → +e or +e → e.Our results are well understood by taking into account the electrical interactions between the water molecules and between the water molecules and the external charge.Because such signals of re-orientation can be magnified and transported according to Tu et al.[2009 Proc.Natl.Acad.Sci.USA 106 18120],it becomes possible to record fingerprints of electric signals arising from sequential charged segments of a macromolecule,which are expected to be useful for recognizing the conformations of some particular macromolecules.

  16. Diffusion and partitioning of macromolecules in casein microgels: evidence for size-dependent attractive interactions in a dense protein system.

    Science.gov (United States)

    Peixoto, Paulo D S; Bouchoux, Antoine; Huet, Sébastien; Madec, Marie-Noëlle; Thomas, Daniel; Floury, Juliane; Gésan-Guiziou, Geneviève

    2015-02-10

    Understanding the mechanisms that determine the diffusion and interaction of macromolecules (such as proteins and polysaccharides) that disperse through dense media is an important fundamental issue in the development of innovative technological and medical applications. In the current work, the partitioning and diffusion of macromolecules of different sizes (from 4 to 10 nm in diameter) and shapes (linear or spherical) within dispersions of casein micelles (a protein microgel) is studied. The coefficients for diffusion and partition are measured using FRAP (fluorescence recovery after photobleaching) and analyzed with respect to the structural characteristics of the microgel determined by the use of TEM (transmission electron microscopy) tomography. The results show that the casein microgel displays a nonspecific attractive interaction for all macromolecules studied. When the macromolecular probes are spherical, this affinity is clearly size-dependent, with stronger attraction for the larger probes. The current data show that electrostatic effects cannot account for such an attraction. Rather, nonspecific hydration molecular forces appear to explain these results. These findings show how weak nonspecific forces affect the diffusion and partitioning of proteins and polysaccharides in a dense protein environment. These results could be useful to better understand the mechanisms of diffusion and partitioning in other media such as cells and tissues. Furthermore, there arises the possibility of using the casein micelle as a size-selective molecular device.

  17. Liquid Crystals

    Science.gov (United States)

    1990-01-01

    Thermochromic liquid crystals, or TLCs, are a type of liquid crystals that react to changes in temperature by changing color. The Hallcrest/NASA collaboration involved development of a new way to visualize boundary layer transition in flight and in wind tunnel testing of aircraft wing and body surfaces. TLCs offered a new and potentially better method of visualizing the boundary layer transition in flight. Hallcrest provided a liquid crystal formulation technique that afforded great control over the sensitivity of the liquid crystals to varying conditions. Method is of great use to industry, government and universities for aerodynamic and hydrodynamic testing. Company's principal line is temperature indicating devices for industrial use, such as non-destructive testing and flaw detection in electric/electronic systems, medical application, such as diagnostic systems, for retail sale, such as room, refrigerator, baby bath and aquarium thermometers, and for advertising and promotion specials. Additionally, Hallcrest manufactures TLC mixtures for cosmetic applications, and liquid crystal battery tester for Duracell batteries.

  18. Protein Crystal Growth in Microgravity

    Institute of Scientific and Technical Information of China (English)

    毕汝昌; 桂璐璐; 师珂; 王耀萍; 陈世芝; 韩青; 胡永林; 沈福苓; 牛秀田; 华子谦; 卢光莹; 张健; 李松林; 龚为民; 牛立文; 黄其辰

    1994-01-01

    Protein crystal growth is quite important for the determination of protein structureswhich are essential to the understanding of life at molecular level as well as to the development of molecu-lar biotechnology.The microgravity environment of space is an ideal place to study the complicated pro-tein crystallization and to grow good-quality protein crystals.A number of crystal-growth experiments of10 different proteins were carried out in August,1992 on the Chinese re-entry satellite FSW-2 in spaceusing a tube crystallization equipment made in China.A total of 25 samples from 6 proteins producedcrystals,and the effects of microgravity on protein crystal growth were observed,especially for an acidicphospholipase A2 and henegg-white lysozyme which gave better crystals in space than earth-grown crys-tals in ground control experiments.The results have shown that the microgravity in space favors the im-provement of the size,perfection,morphology and internal order of the grown protein crytals.

  19. Photoelastic sphenoscopic analysis of crystals

    Energy Technology Data Exchange (ETDEWEB)

    Montalto, L. [DIISM, Dip. Di Ingegneria Industriale e Scienze Matematiche—Università Politecnica delle Marche, Ancona (Italy); SIMAU, Dip. Di Scienze e Ingegneria della Materia, dell’ambiente ed Urbanistica—Università Politecnica delle Marche, Ancona (Italy); Rinaldi, D. [SIMAU, Dip. Di Scienze e Ingegneria della Materia, dell’ambiente ed Urbanistica—Università Politecnica delle Marche, Ancona (Italy); Scalise, L.; Paone, N. [DIISM, Dip. Di Ingegneria Industriale e Scienze Matematiche—Università Politecnica delle Marche, Ancona (Italy); Davì, F. [DICEA, Dip. Di Ingegneria Civile, Edile e Architettura—Università Politecnica delle Marche, Ancona (Italy)

    2016-01-15

    Birefringent crystals are at the basis of various devices used in many fields, from high energy physics to biomedical imaging for cancer detection. Since crystals are the main elements of those devices, a great attention is paid on their quality and properties. Here, we present a methodology for the photoelastic analysis of birefringent crystals, based on a modified polariscope. Polariscopes using conoscopic observation are used to evaluate crystals residual stresses in a precise but time consuming way; in our methodology, the light beam shape, which impinges on the crystal surface, has been changed from a solid cone (conoscopy) to a wedge (sphenoscopy). Since the polarized and coherent light is focused on a line rather than on a spot, this allows a faster analysis which leads to the observation, at a glance, of a spatial distribution of stress along a line. Three samples of lead tungstate crystals have been observed using this technique, and the obtained results are compared with the conoscopic observation. The samples have been tested both in unloaded condition and in a loaded configuration induced by means of a four points bending device, which allows to induce a known stress distribution in the crystal. The obtained results confirm, in a reliable manner, the sensitivity of the methodology to the crystal structure and stress.

  20. Preparation of high magneto-optical performance and crystalline quality Ce{sub 1}Gd{sub 2}Fe{sub 5−x}Ga{sub x}O{sub 12} films on CLNGG substrate crystal

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Qiu-ping; Zheng, Ze-yuan; Lin, Nan-xi; Liu, Xiao-feng; Hong, Can-huang; Hu, Xiao-lin, E-mail: linamethyst@fzu.edu.cn; Zhuang, Nai-feng; Chen, Jian-zhong, E-mail: j.z.chen@fzu.edu.cn

    2016-11-01

    Thin films of Ce{sub 1}Gd{sub 2}Fe{sub 5−x}Ga{sub x}O{sub 12} (Ce,Ga:GIG) were prepared on Gd{sub 3}Ga{sub 5}O{sub 12} (GGG) and Ca{sub 2.90}Li{sub 0.30}Nb{sub 1.93}Ga{sub 2.76}O{sub 12} (CLNGG) substrates by using radio frequency magnetron sputtering technique. The phase, grain orientation, surface morphology, transmittance, magnetism and magnetic circular dichroism (MCD) properties of films were analyzed. And the effects of lattice mismatch and non-magnetic Ga{sup 3+}-doping were discussed. The results show that the films with higher crystallized quality and lower stress can be obtained by growing on CLNGG than on GGG. Moreover, the coercive force, magnetization, magneto-optical effect intensity and orientation of film can be effectively regulated by adjusting Ga{sup 3+}-doped concentration. - Highlights: • With excellent magneto-optical performance, Ce,Ga:GIG film has a good application prospect. • Ce,Ga:GIG film with high quality were prepared on CLNGG by RF magnetron sputtering. • Crystalline quality and morphology of films are intently related to the substrate. • Ga{sup 3+} doping obviously affect on magnetism and magneto-optical property of Ce:GIG film.