Contact Kinetics in Fractal Macromolecules.

PubMed

Dolgushev, Maxim; Guérin, Thomas; Blumen, Alexander; Bénichou, Olivier; Voituriez, Raphaël

2015-11-13

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the mean first contact time for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the nonequilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the mean first contact time between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.

Retention of 14C-labeled multiwall carbon nanotubes by humic acid and polymers: Roles of macromolecule properties

PubMed Central

Zhao, Qing; Petersen, Elijah J.; Cornelis, Geert; Wang, Xilong; Guo, Xiaoying; Tao, Shu; Xing, Baoshan

2016-01-01

Developing methods to measure interactions of carbon nanotubes (CNTs) with soils and sediments and understanding the impact of soil and sediment properties on CNT deposition are essential for assessing CNT environmental risks. In this study, we utilized functionalized carbon-14 labeled nanotubes to systematically investigate retention of multiwall CNTs (MWCNTs) by 3 humic acids, 3 natural biopolymers, and 10 model solid-phase polymers, collectively termed macromolecules. Surface properties, rather than bulk properties of macromolecules, greatly influenced MWCNT retention. As shown via multiple linear regression analysis and path analysis, aromaticity and surface polarity were the two most positive factors for retention, suggesting retention was regulated by π-π stacking and hydrogen bonding interactions. Moreover, MWCNT deposition was irreversible. These observations may explain the high retention of MWCNT in natural soils. Moreover, our findings on the relative contribution of each macromolecule property on CNT retention provide information on macromolecule selection for removal of MWCNTs from wastewater and provide a method for measuring CNT interactions with organic macromolecules. PMID:27458320

Hollow Fiber Membrane Modification with Functional Zwitterionic Macromolecules for Improved Thromboresistance in Artificial Lungs

PubMed Central

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.

2015-01-01

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. PMID:25669307

Enhancement of Cell Membrane Invaginations, Vesiculation and Uptake of Macromolecules by Protonation of the Cell Surface

PubMed Central

Ben-Dov, Nadav; Korenstein, Rafi

2012-01-01

The different pathways of endocytosis share an initial step involving local inward curvature of the cell’s lipid bilayer. It has been shown that to generate membrane curvature, proteins or lipids enforce transversal asymmetry of the plasma membrane. Thus it emerges as a general phenomenon that transversal membrane asymmetry is the common required element for the formation of membrane curvature. The present study demonstrates that elevating proton concentration at the cell surface stimulates the formation of membrane invaginations and vesiculation accompanied by efficient uptake of macromolecules (Dextran-FITC, 70 kD), relative to the constitutive one. The insensitivity of proton induced uptake to inhibiting treatments and agents of the known endocytic pathways suggests the entry of macromolecules to proceeds via a yet undefined route. This is in line with the fact that neither ATP depletion, nor the lowering of temperature, abolishes the uptake process. In addition, fusion mechanism such as associated with low pH uptake of toxins and viral proteins can be disregarded by employing the polysaccharide dextran as the uptake molecule. The proton induced uptake increases linearly in the extracellular pH range of 6.5 to 4.5, and possesses a steep increase at the range of 4> pH>3, reaching a plateau at pH≤3. The kinetics of the uptake implies that the induced vesicles release their content to the cytosol and undergo rapid recycling to the plasma membrane. We suggest that protonation of the cell’s surface induces local charge asymmetries across the cell membrane bilayer, inducing inward curvature of the cell membrane and consequent vesiculation and uptake. PMID:22558127

Carbohydrates, proteins, cell surfaces, and the biochemistry of pathogenesis

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

Albersheim, P.; Anderson-Prouty, A.J.

1975-01-01

General plant resistance to pathogenic attack by a myriad of microorganisms, viruses, nematodes, and insects are reviewed. Specifically discussed are: The role of the cell wall and wall-degrading enzymes in infective processes; an hypothesis to account for varietal specificity in gene-for-gene host-pathogen systems; examples which demonstrate that cell surface recognition phenomena are mediated through the interaction of carbohydrate-containing macromolecules and proteins; elicitors of phytoalexin production; and further consideration of the hypothesis and how the gene-for-gene relationship may have evolved. (JWP)

INFLUENCE OF MACROMOLECULES ON CHEMICAL TRANSPORT

EPA Science Inventory

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 ...

Charging and Release Mechanisms of Flexible Macromolecules in Droplets

NASA Astrophysics Data System (ADS)

Oh, Myong In; Consta, Styliani

2017-08-01

We study systematically the charging and release mechanisms of a flexible macromolecule, modeled by poly(ethylene glycol) (PEG), in a droplet by using molecular dynamics simulations. We compare how PEG is solvated and charged by sodium Na+ ions in a droplet of water (H2O), acetonitrile (MeCN), and their mixtures. Initially, we examine the location and the conformation of the macromolecule in a droplet bearing no net charge. It is revealed that the presence of charge carriers do not affect the location of PEG in aqueous and MeCN droplets compared with that in the neutral droplets, but the location of the macromolecule and the droplet size do affect the PEG conformation. PEG is charged on the surface of a sodiated aqueous droplet that is found close to the Rayleigh limit. Its charging is coupled to the extrusion mechanism, where PEG segments leave the droplet once they coordinate a Na+ ion or in a correlated motion with Na+ ions. In contrast, as PEG resides in the interior of a MeCN droplet, it is sodiated inside the droplet. The compact macro-ion transitions through partially unwound states to an extended conformation, a process occurring during the final stage of desolvation and in the presence of only a handful of MeCN molecules. For charged H2O/MeCN droplets, the sodiation of PEG is determined by the H2O component, reflecting its slower evaporation and preference over MeCN for solvating Na+ ions. We use the simulation data to construct an analytical model that suggests that the droplet surface electric field may play a role in the macro-ion-droplet interactions that lead to the extrusion of the macro-ion. This study provides the first evidence of the effect of the surface electric field by using atomistic simulations. [Figure not available: see fulltext.

The Relationship Between Surface Curvature and Abdominal Aortic Aneurysm Wall Stress.

PubMed

de Galarreta, Sergio Ruiz; Cazón, Aitor; Antón, Raúl; Finol, Ender A

2017-08-01

The maximum diameter (MD) criterion is the most important factor when predicting risk of rupture of abdominal aortic aneurysms (AAAs). An elevated wall stress has also been linked to a high risk of aneurysm rupture, yet is an uncommon clinical practice to compute AAA wall stress. The purpose of this study is to assess whether other characteristics of the AAA geometry are statistically correlated with wall stress. Using in-house segmentation and meshing algorithms, 30 patient-specific AAA models were generated for finite element analysis (FEA). These models were subsequently used to estimate wall stress and maximum diameter and to evaluate the spatial distributions of wall thickness, cross-sectional diameter, mean curvature, and Gaussian curvature. Data analysis consisted of statistical correlations of the aforementioned geometry metrics with wall stress for the 30 AAA inner and outer wall surfaces. In addition, a linear regression analysis was performed with all the AAA wall surfaces to quantify the relationship of the geometric indices with wall stress. These analyses indicated that while all the geometry metrics have statistically significant correlations with wall stress, the local mean curvature (LMC) exhibits the highest average Pearson's correlation coefficient for both inner and outer wall surfaces. The linear regression analysis revealed coefficients of determination for the outer and inner wall surfaces of 0.712 and 0.516, respectively, with LMC having the largest effect on the linear regression equation with wall stress. This work underscores the importance of evaluating AAA mean wall curvature as a potential surrogate for wall stress.

Macromolecules Inquiry: Transformation of a Standard Biochemistry Lab

ERIC Educational Resources Information Center

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…

[Study on Hollow Brick Wall's Surface Temperature with Infrared Thermal Imaging Method].

PubMed

Tang, Ming-fang; Yin, Yi-hua

2015-05-01

To address the characteristic of uneven surface temperature of hollow brick wall, the present research adopts soft wares of both ThermaCAM P20 and ThermaCAM Reporter to test the application of infrared thermal image technique in measuring surface temperature of hollow brick wall, and further analyzes the thermal characteristics of hollow brick wall, and building material's impact on surface temperature distribution including hollow brick, masonry mortar, and so on. The research selects the construction site of a three-story-high residential, carries out the heat transfer experiment, and further examines the exterior wall constructed by 3 different hollow bricks including sintering shale hollow brick, masonry mortar and brick masonry. Infrared thermal image maps are collected, including 3 kinds of sintering shale hollow brick walls under indoor heating in winter; and temperature data of wall surface, and uniformity and frequency distribution are also collected for comparative analysis between 2 hollow bricks and 2 kinds of mortar masonry. The results show that improving heat preservation of hollow brick aid masonry mortar can effectively improve inner wall surface temperature and indoor thermal environment; non-uniformity of surface temperature decreases from 0. 6 to 0. 4 °C , and surface temperature frequency distribution changes from the asymmetric distribution into a normal distribution under the condition that energy-saving sintering shale hollow brick wall is constructed by thermal mortar replacing cement mortar masonry; frequency of average temperature increases as uniformity of surface temperature increases. This research provides a certain basis for promotion and optimization of hollow brick wall's thermal function.

Measuring the shapes of macromolecules – and why it matters

PubMed Central

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. PMID:24688748

Macromolecule diffusion and confinement in prokaryotic cells.

PubMed

Mika, Jacek T; Poolman, Bert

2011-02-01

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 extremely high macromolecule crowding of prokaryotes is used to rationalize the reported lower diffusion coefficients as compared to eukaryotes, and we speculate on the nature of the barriers for diffusion observed for proteins (and mRNAs) in vivo. Building on in vitro experiments and modeling studies, we evaluate the size dependence of diffusion coefficients for macromolecules in vivo, in case of both water-soluble and integral membrane proteins. We comment on the possibilities of anomalous diffusion and provide examples where the macromolecule mobility may be limiting biological processes. Copyright © 2010 Elsevier Ltd. All rights reserved.

MACROMOLECULES FACILITATE THE TRANSPORT OF TRACE ORGANICS

EPA Science Inventory

Macromolecules in the pore fluid of a soil may influence the mobility of hydrophobic compounds by their partitioning to the macromolecule, which moves with, or even faster than, the water. The mobility is described mathematically by a chemical transport model. The significance of...

13. THE SAME NORTH TRAINING WALL TOP SURFACE, LOOKING EAST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

13. THE SAME NORTH TRAINING WALL TOP SURFACE, LOOKING EAST FROM ATOP ADJACENT RIPRAP. THE TRAINING WALL IS TO THE RIGHT OF THE JUMBLED, LIGHT TONED RIPRAP. - Oakland Harbor Training Walls, Mouth of Federal Channel to Inner Harbor, Oakland, Alameda County, CA

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

PubMed

Zhang, Baofeng; Kilburg, Denise; Eastman, Peter; Pande, Vijay S; Gallicchio, Emilio

2017-04-15

We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion-exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii. The many-body nature of the model makes a port to GPU devices challenging. To our knowledge, this is the first reported full implementation of this model on GPU hardware. To accomplish this, we have used recursive strategies to construct the tree of overlaps and to accumulate volumes and their gradients on the tree data structures so as to minimize memory contention. The algorithm is used in the formulation of a surface area-based non-polar implicit solvent model implemented as an open source plug-in (named GaussVol) for the popular OpenMM library for molecular mechanics modeling. GaussVol is 50 to 100 times faster than our best optimized implementation for the CPUs, achieving speeds in excess of 100 ns/day with 1 fs time-step for protein-sized systems on commodity GPUs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Micropore surface area of alkali-soluble plant macromolecules (humic acids) drives their decomposition rates in soil.

PubMed

Papa, Gabriella; Spagnol, Manuela; Tambone, Fulvia; Pilu, Roberto; Scaglia, Barbara; Adani, Fabrizio

2010-02-01

Previous studies suggested that micropore surface area (MSA) of alkali-soluble bio-macromolecules of aerial plant residues of maize constitutes an important factor that explains their humification in soil, that is, preservation against biological degradation. On the other hand, root plant residue contributes to the soil humus balance, as well. Following the experimental design used in a previous paper published in this journal, this study shows that the biochemical recalcitrance of the alkali-soluble acid-insoluble fraction of the root plant material, contributed to the root maize humification of both Wild-type maize plants and its corresponding mutant brown midrib (bm3), this latter characterized by reduced lignin content. Humic acids (HAs) existed in root (root-HAs) were less degraded in soil than corresponding HAs existed in shoot (shoot-HAs): shoot-HAs bm3 (48%)>shoot-HAs Wild-type (37%)>root-HAs Wild-type (33%)>root-HAs bm3 (22%) (degradability shown in parenthesis). These differences were related to the MSA of HAs, that is, root-HAs having a higher MSA than shoot-HAs: shoot-HAs bm3 (41.43+/-1.2m(2)g(-1))macromolecules recalcitrance in soil.

Molecular Imprinting of Macromolecules for Sensor Applications.

PubMed

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.

Molecular Imprinting of Macromolecules for Sensor Applications

PubMed Central

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

2017-01-01

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. PMID:28422082

Investigation of Wall Shear Stress Behavior for Rough Surfaces with Blowing

NASA Astrophysics Data System (ADS)

Helvey, Jacob; Borchetta, Colby; Miller, Mark; Martin, Alexandre; Bailey, Sean

2014-11-01

We present an experimental study conducted in a turbulent channel flow wind tunnel to determine the modifications made to the turbulent flow over rough surfaces with flow injection through the surfaces. Hot-wire profile results from a quasi-two-dimensional, sinusoidally-rough surface indicate that the effects of roughness are enhanced by momentum injection through the surface. In particular, the wall shear stress was found to show behavior consistent with increased roughness height when surface blowing was increased. This observed behavior contradicts previously reported results for regular three-dimensional roughness which show a decrease in wall shear stress with additional blowing. It is unclear whether this discrepancy is due to differences in the roughness geometry under consideration or the use of the Clauser fit to estimate wall shear stress. Additional PIV experiments are being conducted for a three-dimensional fibrous surface to obtain Reynolds shear stress profiles. These results provide an additional method for estimation of wall-shear stress and thus allow verification of the use of the Clauser chart approach for flows with momentum injection through the surface. This research is supported by NASA Kentucky EPSCoR Award NNX10AV39A, and NASA RA Award NNX13AN04A.

Standard surface grinder for precision machining of thin-wall tubing

NASA Technical Reports Server (NTRS)

Jones, A.; Kotora, J., Jr.; Rein, J.; Smith, S. V.; Strack, D.; Stuckey, D.

1967-01-01

Standard surface grinder performs precision machining of thin-wall stainless steel tubing by electrical discharge grinding. A related adaptation, a traveling wire electrode fixture, is used for machining slots in thin-walled tubing.

Using a water-confined carbon nanotube to probe the electricity of sequential charged segments of macromolecules

NASA Astrophysics Data System (ADS)

Wang, Yu; Zhao, Yan-Jiao; Huang, Ji-Ping

2012-07-01

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 timescale 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.

Flexible Charged Macromolecules on Mixed Fluid Lipid Membranes: Theory and Monte Carlo Simulations

PubMed Central

Tzlil, Shelly; Ben-Shaul, Avinoam

2005-01-01

Fluid membranes containing charged lipids enhance binding of oppositely charged proteins by mobilizing these lipids into the interaction zone, overcoming the concomitant entropic losses due to lipid segregation and lower conformational freedom upon macromolecule adsorption. We study this energetic-entropic interplay using Monte Carlo simulations and theory. Our model system consists of a flexible cationic polyelectrolyte, interacting, via Debye-Hückel and short-ranged repulsive potentials, with membranes containing neutral lipids, 1% tetravalent, and 10% (or 1%) monovalent anionic lipids. Adsorption onto a fluid membrane is invariably stronger than to an equally charged frozen or uniform membrane. Although monovalent lipids may suffice for binding rigid macromolecules, polyvalent counter-lipids (e.g., phosphatidylinositol 4,5 bisphosphate), whose entropy loss upon localization is negligible, are crucial for binding flexible macromolecules, which lose conformational entropy upon adsorption. Extending Rosenbluth's Monte Carlo scheme we directly simulate polymer adsorption on fluid membranes. Yet, we argue that similar information could be derived from a biased superposition of quenched membrane simulations. Using a simple cell model we account for surface concentration effects, and show that the average adsorption probabilities on annealed and quenched membranes coincide at vanishing surface concentrations. We discuss the relevance of our model to the electrostatic-switch mechanism of, e.g., the myristoylated alanine-rich C kinase substrate protein. PMID:16126828

14. A CLOSER VIEW OF THE NORTH WALL TOP SURFACE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

14. A CLOSER VIEW OF THE NORTH WALL TOP SURFACE MASONRY, LOOKING EAST FROM A POINT NEAR THE PREVIOUS VIEW. - Oakland Harbor Training Walls, Mouth of Federal Channel to Inner Harbor, Oakland, Alameda County, CA

Effect of Inhibition of Deoxyribonucleic Acid and Protein Synthesis on the Direction of Cell Wall Growth in Streptococcus faecalis

PubMed Central

Higgins, M. L.; Daneo-Moore, L.; Boothby, D.; Shockman, G. D.

1974-01-01

Selective inhibition of protein synthesis in Streptococcus faecalis (ATCC 9790) was accompanied by a rapid and severe inhibition of cell division and a reduction of enlargement of cellular surface area. Continued synthesis of cell wall polymers resulted in rapid thickening of the wall to an extent not seen in exponential-phase populations. Thus, the normal direction of wall growth was changed from a preferential feeding out of new wall surface to that of thickening existing cell surfaces. However, the overall manner in which the wall thickened, from nascent septa toward polar regions, was the same in both exponential-phase and inhibited populations. In contrast, selective inhibition of deoxyribonucleic acid (DNA) synthesis using mitomycin C was accompanied by an increase in cellular surface area and by division of about 80% of the cells in random populations. Little or no wall thickening was observed until the synthesis of macromolecules other than DNA was impaired and further cell division ceased. Concomitant inhibition of both DNA and protein synthesis inhibited cell division but permitted an increase in average cell volume. In such doubly inhibited cells, walls thickened less than in cells inhibited for protein synthesis only. On the basis of the results obtained, a model for cell surface enlargement and cell division is presented. The model proposes that: (i) each wall enlargement site is influenced by an individual chromosome replication cycle; (ii) during chromosome replication peripheral surface enlargement would be favored over thickening (or septation); (iii) a signal associated with chromosome termination would favor thickening (and septation) at the expense of surface enlargement; and (iv) a factor or signal related to protein synthesis would be required for one or more of the near terminal stages of cell division or cell separation, or both. Images PMID:4133352

Iontophoretic transport of charged macromolecules across human sclera.

PubMed

Chopra, Poonam; Hao, Jinsong; Li, S Kevin

2010-03-30

The mechanisms of transscleral iontophoresis have been investigated previously with small molecules in rabbit sclera. The objective of the present study was to examine transscleral iontophoretic transport of charged macromolecules across excised human sclera. Passive and 2mA iontophoretic transport experiments were conducted in side-by-side diffusion cells with human sclera. The effects of iontophoresis upon transscleral transport of model permeants bovine serum albumin (BSA) and polystyrene sulfonic acid (PSS) as well as a model drug bevacizumab (BEV) were determined. Passive and iontophoretic transport experiments of tetraethylammonium (TEA) and salicylic acid (SA) and passive transport experiments of the macromolecules served as the controls. The results of iontophoresis enhanced transport of TEA and SA across human sclera were consistent with those in a previous rabbit sclera study. For the iontophoretic transport of macromolecules BSA and BEV, higher iontophoretic fluxes were observed in anodal iontophoresis as compared to passive and cathodal iontophoresis. This suggests the importance of electroosmosis. For the polyelectrolyte PSS, higher iontophoretic flux was observed in cathodal iontophoresis compared to anodal iontophoresis. Both electroosmosis and electrophoresis affected iontophoretic fluxes of the macromolecules; the relative contributions of electroosmosis and electrophoresis were a function of molecular size and charge of the macromolecules. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Manipulation of near-wall turbulence by surface slip and permeability

NASA Astrophysics Data System (ADS)

Gómez-de-Segura, G.; Fairhall, C. T.; MacDonald, M.; Chung, D.; García-Mayoral, R.

2018-04-01

We study the effect on near-wall turbulence of tangential slip and wall-normal transpiration, typically produced by textured surfaces and other surface manipulations. For this, we conduct direct numerical simulations (DNSs) with different virtual origins for the different velocity components. The different origins result in a relative wall-normal displacement of the near-wall, quasi-streamwise vortices with respect to the mean flow, which in turn produces a change in drag. The objective of this work is to extend the existing understanding on how these virtual origins affect the flow. In the literature, the virtual origins for the tangential velocities are typically characterised by slip boundary conditions, while the wall-normal velocity is assumed to be zero at the boundary plane. Here we explore different techniques to define and implement the three virtual origins, with special emphasis on the wall-normal one. We investigate impedance conditions relating the wall-normal velocity to the pressure, and linear relations between the velocity components and their wall-normal gradients, as is typically done to impose slip conditions. These models are first tested to represent a smooth wall below the boundary plane, with all virtual origins equal, and later for different tangential and wall-normal origins. Our results confirm that the change in drag is determined by the offset between the origins perceived by mean flow and the quasi-streamwise vortices or, more generally, the near-wall turbulent cycle. The origin for the latter, however, is not set by the spanwise virtual origin alone, as previously proposed, but by a combination of the spanwise and wall-normal origins, and mainly determined by the shallowest of the two. These observations allow us to extend the existing expression to predict the change in drag, accounting for the wall-normal effect when the transpiration is not negligible.

Colliding wall-jets on a cylindrical surface

NASA Astrophysics Data System (ADS)

Tesař, Václav; Peszynski, Kazimierz

2015-05-01

Paper discusses aerodynamics and potential engineering applications of an unusual and in literature practically unknown fluid flow configuration, with two wall-jets attached to a cylindrical surface so that they collide head-on and by mutual conjunction generate a single jet directed away from the wall. Applications are envisaged in pneumatic sensors, particularly those operating at low Reynolds numbers. Performed experimental investigation, combined with numerical flowfield computations, revealed several interesting aspects. The most interesting among them is the discovery of symmetry-breaking existence of three different stable flow regimes. This opens a possibility for fluidic tristable amplifiers and systems operating with ternary logic.

Navier-Stokes Computations With One-Equation Turbulence Model for Flows Along Concave Wall Surfaces

NASA Technical Reports Server (NTRS)

Wang, Chi R.

2005-01-01

This report presents the use of a time-marching three-dimensional compressible Navier-Stokes equation numerical solver with a one-equation turbulence model to simulate the flow fields developed along concave wall surfaces without and with a downstream extension flat wall surface. The 3-D Navier- Stokes numerical solver came from the NASA Glenn-HT code. The one-equation turbulence model was derived from the Spalart and Allmaras model. The computational approach was first calibrated with the computations of the velocity and Reynolds shear stress profiles of a steady flat plate boundary layer flow. The computational approach was then used to simulate developing boundary layer flows along concave wall surfaces without and with a downstream extension wall. The author investigated the computational results of surface friction factors, near surface velocity components, near wall temperatures, and a turbulent shear stress component in terms of turbulence modeling, computational mesh configurations, inlet turbulence level, and time iteration step. The computational results were compared with existing measurements of skin friction factors, velocity components, and shear stresses of the developing boundary layer flows. With a fine computational mesh and a one-equation model, the computational approach could predict accurately the skin friction factors, near surface velocity and temperature, and shear stress within the flows. The computed velocity components and shear stresses also showed the vortices effect on the velocity variations over a concave wall. The computed eddy viscosities at the near wall locations were also compared with the results from a two equation turbulence modeling technique. The inlet turbulence length scale was found to have little effect on the eddy viscosities at locations near the concave wall surface. The eddy viscosities, from the one-equation and two-equation modeling, were comparable at most stream-wise stations. The present one

Noise reduction methods for nucleic acid and macromolecule sequencing

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

Schuller, Ivan K.; Di Ventra, Massimiliano; Balatsky, Alexander

Methods, systems, and devices are disclosed for processing macromolecule sequencing data with substantial noise reduction. In one aspect, a method for reducing noise in a sequential measurement of a macromolecule comprising serial subunits includes cross-correlating multiple measured signals of a physical property of subunits of interest of the macromolecule, the multiple measured signals including the time data associated with the measurement of the signal, to remove or at least reduce signal noise that is not in the same frequency and in phase with the systematic signal contribution of the measured signals.

Diffusion of macromolecules in self-assembled cellulose/hemicellulose hydrogels.

PubMed

Lopez-Sanchez, Patricia; Schuster, Erich; Wang, Dongjie; Gidley, Michael J; Strom, Anna

2015-05-28

Cellulose hydrogels are extensively applied in many biotechnological fields and are also used as models for plant cell walls. We synthesised model cellulosic hydrogels containing hemicelluloses, as a biomimetic of plant cell walls, in order to study the role of hemicelluloses on their mass transport properties. Microbial cellulose is able to self-assemble into composites when hemicelluloses, such as xyloglucan and arabinoxylan, are present in the incubation media, leading to hydrogels with different nano and microstructures. We investigated the diffusivities of a series of fluorescently labelled dextrans, of different molecular weight, and proteins, including a plant pectin methyl esterase (PME), using fluorescence recovery after photobleaching (FRAP). The presence of xyloglucan, known to be able to crosslink cellulose fibres, confirmed by scanning electron microscopy (SEM) and (13)C NMR, reduced mobility of macromolecules of molecular weight higher than 10 kDa, reflected in lower diffusion coefficients. Furthermore PME diffusion was reduced in composites containing xyloglucan, despite the lack of a particular binding motif in PME for this polysaccharide, suggesting possible non-specific interactions between PME and this hemicellulose. In contrast, hydrogels containing arabinoxylan coating cellulose fibres showed enhanced diffusivity of the molecules studied. The different diffusivities were related to the architectural features found in the composites as a function of polysaccharide composition. Our results show the effect of model hemicelluloses in the mass transport properties of cellulose networks in highly hydrated environments relevant to understanding the role of hemicelluloses in the permeability of plant cell walls and aiding design of plant based materials with tailored properties.

Quantifying the importance of galactofuranose in Aspergillus nidulans hyphal wall surface organization by atomic force microscopy.

PubMed

Paul, Biplab C; El-Ganiny, Amira M; Abbas, Mariam; Kaminskyj, Susan G W; Dahms, Tanya E S

2011-05-01

The fungal wall mediates cell-environment interactions. Galactofuranose (Galf), the five-member ring form of galactose, has a relatively low abundance in Aspergillus walls yet is important for fungal growth and fitness. Aspergillus nidulans strains deleted for Galf biosynthesis enzymes UgeA (UDP-glucose-4-epimerase) and UgmA (UDP-galactopyranose mutase) lacked immunolocalizable Galf, had growth and sporulation defects, and had abnormal wall architecture. We used atomic force microscopy and force spectroscopy to image and quantify cell wall viscoelasticity and surface adhesion of ugeAΔ and ugmAΔ strains. We compared the results for ugeAΔ and ugmAΔ strains with the results for a wild-type strain (AAE1) and the ugeB deletion strain, which has wild-type growth and sporulation. Our results suggest that UgeA and UgmA are important for cell wall surface subunit organization and wall viscoelasticity. The ugeAΔ and ugmAΔ strains had significantly larger surface subunits and lower cell wall viscoelastic moduli than those of AAE1 or ugeBΔ hyphae. Double deletion strains (ugeAΔ ugeBΔ and ugeAΔ ugmAΔ) had more-disorganized surface subunits than single deletion strains. Changes in wall surface structure correlated with changes in its viscoelastic modulus for both fixed and living hyphae. Wild-type walls had the largest viscoelastic modulus, while the walls of the double deletion strains had the smallest. The ugmAΔ strain and particularly the ugeAΔ ugmAΔ double deletion strain were more adhesive to hydrophilic surfaces than the wild type, consistent with changes in wall viscoelasticity and surface organization. We propose that Galf is necessary for full maturation of A. nidulans walls during hyphal extension.

A Course on Macromolecules.

ERIC Educational Resources Information Center

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)

Antimicrobial resistance challenged with metal-based antimicrobial macromolecules.

PubMed

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.

Dermal and transdermal delivery of pharmaceutically relevant macromolecules.

PubMed

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.

PlaMoM: a comprehensive database compiles plant mobile macromolecules

PubMed Central

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

PlaMoM: a comprehensive database compiles plant mobile macromolecules.

PubMed

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.

Identifiability, reducibility, and adaptability in allosteric macromolecules.

PubMed

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.

Identifiability, reducibility, and adaptability in allosteric macromolecules

PubMed Central

Bohner, Gergő

2017-01-01

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 Ca2+-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. PMID:28416647

Flocculation of colloidal clay by bacterial polysaccharides: effect of macromolecule charge and structure.

PubMed

Labille, J; Thomas, F; Milas, M; Vanhaverbeke, C

2005-04-01

The molecular mechanism of montmorillonite flocculation by bacterial polysaccharides was investigated, with special emphasis on the effect of carboxylic charges in the macromolecules on the mechanisms of interaction with the clay surface. An indirect way to quantify the energy of interaction was used, by comparing the flocculation ability of variously acidic polysaccharides. Data on tensile strength of aggregates in diluted suspension were collected by timed size measurements in the domain 0.1-600 microm, using laser diffraction. The flow behavior of settled aggregates was studied by rheology measurements. Flocculation of colloidal clay suspension by polysaccharides requires cancelling of the electrostatic repulsions by salts, which allows approach of clay surfaces close enough to be bridged by adsorbing macromolecules. The amount of acidic charges of the polysaccharides, and especially their location in the molecular structure, governs the bridging mechanism and the resulting tensile strength of the aggregates. The exposure of carboxylate groups located on side chains strongly promotes flocculation. In turn, charges located on the backbone of the polysaccharide are less accessible to interaction, and the flocculation ability of such polysaccharides is lowered. Measurements at different pH indicate that adsorption of acidic polysaccharides occurs via electrostatic interactions on the amphoteric edge surface of clay platelets, whereas neutral polysaccharides rather adsorb via weak interactions. Increased tensile strength in diluted aggregates due to strong surface interactions results in proportionally increased viscosity of the concentrated aggregates.

Surface Proteins of Gram-Positive Bacteria and Mechanisms of Their Targeting to the Cell Wall Envelope

PubMed Central

Navarre, William Wiley; Schneewind, Olaf

1999-01-01

The cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialized binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections. In this review we describe the mechanisms for both sorting and targeting of proteins to the envelope of gram-positive bacteria and review the functions of known surface proteins. PMID:10066836

Do plant cell walls have a code?

PubMed

Tavares, Eveline Q P; Buckeridge, Marcos S

2015-12-01

A code is a set of rules that establish correspondence between two worlds, signs (consisting of encrypted information) and meaning (of the decrypted message). A third element, the adaptor, connects both worlds, assigning meaning to a code. We propose that a Glycomic Code exists in plant cell walls where signs are represented by monosaccharides and phenylpropanoids and meaning is cell wall architecture with its highly complex association of polymers. Cell wall biosynthetic mechanisms, structure, architecture and properties are addressed according to Code Biology perspective, focusing on how they oppose to cell wall deconstruction. Cell wall hydrolysis is mainly focused as a mechanism of decryption of the Glycomic Code. Evidence for encoded information in cell wall polymers fine structure is highlighted and the implications of the existence of the Glycomic Code are discussed. Aspects related to fine structure are responsible for polysaccharide packing and polymer-polymer interactions, affecting the final cell wall architecture. The question whether polymers assembly within a wall display similar properties as other biological macromolecules (i.e. proteins, DNA, histones) is addressed, i.e. do they display a code? Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Perfect mixing of immiscible macromolecules at fluid interfaces

NASA Astrophysics Data System (ADS)

Sheiko, Sergei; Matyjaszewski, Krzysztof; Tsukruk, Vladimir; Carrillo, Jan-Michael; Rubinstein, Michael; Dobrynin, Andrey; Zhou, Jing

2014-03-01

Macromolecules typically phase separate unless their shapes and chemical compositions are tailored to explicitly drive mixing. But now our research has shown that physical constraints can drive spontaneous mixing of chemically different species. We have obtained long-range 2D arrays of perfectly mixed macromolecules having a variety of molecular architectures and chemistries, including linear chains, block-copolymer stars, and bottlebrush copolymers with hydrophobic, hydrophilic, and lipophobic chemical compositions. This is achieved by entropy-driven enhancement of steric repulsion between macromolecules anchored on a substrate. By monitoring the kinetics of mixing, we have proved that molecular intercalation is an equilibrium state. The array spacing is controlled by the length of the brush side chains. This entropic templating strategy opens new ways for generating patterns on sub-100 nm length scales with potential application in lithography, directed self-assembly, and biomedical assays. Financial support from the National Science Foundation DMR-0906985, DMR-1004576, DMR-1122483, and DMR-0907515.

Experimental Investigation of Compliant Wall Surface Deformation in Turbulent Boundary Layer

NASA Astrophysics Data System (ADS)

Wang, Jin; Agarwal, Karuna; Katz, Joseph

2017-11-01

On-going research integrates Tomographic PIV (TPIV) with Mach-Zehnder Interferometry (MZI) to measure the correlations between deformation of a compliant wall and a turbulent channel flow or a boundary layer. Aiming to extend the scope to two-way coupling, in the present experiment the wall properties have been designed, based on a theoretical analysis, to increase the amplitude of deformation to several μm, achieving the same order of magnitude as the boundary layer wall unit (5-10 μm). It requires higher speeds and a softer surface that has a Young's modulus of 0.1MPa (vs. 1Mpa before), as well as proper thickness (5 mm) that maximize the wall response to excitation at scales that fall within the temporal and spatial resolution of the instruments. The experiments are performed in a water tunnel extension to the JHU refractive index matched facility. The transparent compliant surface is made of PDMS molded on the tunnel window, and measurements are performed at friction velocity Reynolds numbers in the 1000-7000 range. MZI measures the 2D surface deformation as several magnifications. The time-resolved 3D pressure distribution is determined by calculating to spatial distribution of material acceleration from the TPIV data and integrating it using a GPU-based, parallel-line, omni-directional integration method. ONR.

Implementation of a diffusion convection surface evolution model in WallDYN

NASA Astrophysics Data System (ADS)

Schmid, K.

2013-07-01

In thermonuclear fusion experiments with multiple plasma facing materials the formation of mixed materials is inevitable. The formation of these mixed material layers is a dynamic process driven the tight interaction between transport in the plasma scrape off layer and erosion/(re-) deposition at the surface. To track this global material erosion/deposition balance and the resulting formation of mixed material layers the WallDYN code has been developed which couples surface processes and plasma transport. The current surface model in WallDYN cannot fully handle the growth of layers nor does it include diffusion. However at elevated temperatures diffusion is a key process in the formation of mixed materials. To remedy this shortcoming a new surface model has been developed which, for the first time, describes both layer growth/recession and diffusion in a single continuous diffusion/convection equation. The paper will detail the derivation of the new surface model and compare it to TRIDYN calculations.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption-Desorption Transition.

PubMed

Grebíková, Lucie; Whittington, Stuart G; Vancso, Julius G

2018-05-23

The adsorption-desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption-desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption-desorption transitions.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption–Desorption Transition

PubMed Central

2018-01-01

The adsorption–desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption–desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption–desorption transitions. PMID:29712430

The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

PubMed Central

Gilliland, Gary L.; Tung, Michael; Ladner, Jane

1996-01-01

The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

Phase Domain Walls in Weakly Nonlinear Deep Water Surface Gravity Waves.

PubMed

Tsitoura, F; Gietz, U; Chabchoub, A; Hoffmann, N

2018-06-01

We report a theoretical derivation, an experimental observation and a numerical validation of nonlinear phase domain walls in weakly nonlinear deep water surface gravity waves. The domain walls presented are connecting homogeneous zones of weakly nonlinear plane Stokes waves of identical amplitude and wave vector but differences in phase. By exploiting symmetry transformations within the framework of the nonlinear Schrödinger equation we demonstrate the existence of exact analytical solutions representing such domain walls in the weakly nonlinear limit. The walls are in general oblique to the direction of the wave vector and stationary in moving reference frames. Experimental and numerical studies confirm and visualize the findings. Our present results demonstrate that nonlinear domain walls do exist in the weakly nonlinear regime of general systems exhibiting dispersive waves.

Phase Domain Walls in Weakly Nonlinear Deep Water Surface Gravity Waves

NASA Astrophysics Data System (ADS)

Tsitoura, F.; Gietz, U.; Chabchoub, A.; Hoffmann, N.

2018-06-01

We report a theoretical derivation, an experimental observation and a numerical validation of nonlinear phase domain walls in weakly nonlinear deep water surface gravity waves. The domain walls presented are connecting homogeneous zones of weakly nonlinear plane Stokes waves of identical amplitude and wave vector but differences in phase. By exploiting symmetry transformations within the framework of the nonlinear Schrödinger equation we demonstrate the existence of exact analytical solutions representing such domain walls in the weakly nonlinear limit. The walls are in general oblique to the direction of the wave vector and stationary in moving reference frames. Experimental and numerical studies confirm and visualize the findings. Our present results demonstrate that nonlinear domain walls do exist in the weakly nonlinear regime of general systems exhibiting dispersive waves.

Induced superhydrophobic and antimicrobial character of zinc metal modified ceramic wall tile surfaces

NASA Astrophysics Data System (ADS)

Özcan, Selçuk; Açıkbaş, Gökhan; Çalış Açıkbaş, Nurcan

2018-04-01

Hydrophobic surfaces are also known to have antimicrobial effect by restricting the adherence of microorganisms. However, ceramic products are produced by high temperature processes resulting in a hydrophilic surface. In this study, an industrial ceramic wall tile glaze composition was modified by the inclusion of metallic zinc powder in the glaze suspension applied on the pre-sintered wall tile bodies by spraying. The glazed tiles were gloss fired at industrially applicable peak temperatures ranging from 980 °C to 1100 °C. The fired tile surfaces were coated with a commercial fluoropolymer avoiding water absorption. The surfaces were characterized with SEM, EDS, XRD techniques, roughness, sessile water drop contact angle, surface energy measurements, and standard antimicrobial tests. The surface hydrophobicity and the antimicrobial activity results were compared with that of unmodified, uncoated gloss fired wall tiles. A superhydrophobic contact angle of 150° was achieved at 1000 °C peak temperature due to the formation of micro-structured nanocrystalline zinc oxide granules providing a specific surface topography. At higher peak temperatures the hydrophobicity was lost as the specific granular surface topography deteriorated with the conversion of zinc oxide granules to the ubiquitous willemite crystals embedded in the glassy matrix. The antimicrobial efficacy also correlated with the hydrophobic character.

Coupled Segmentation of Nuclear and Membrane-bound Macromolecules through Voting and Multiphase Level Set

PubMed Central

Wen, Quan

2014-01-01

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. PMID:25530633

Self-assembly in densely grafted macromolecules with amphiphilic monomer units: diagram of states.

PubMed

Lazutin, A A; Vasilevskaya, V V; Khokhlov, A R

2017-11-22

By means of computer modelling, the self-organization of dense planar brushes of macromolecules with amphiphilic monomer units was addressed and their state diagram was constructed. The diagram of states includes the following regions: disordered position of monomer units with respect to each other, strands composed of a few polymer chains and lamellae with different domain spacing. The transformation of lamellae structures with different domain spacing occurred within the intermediate region and could proceed through the formation of so-called parking garage structures. The parking garage structure joins the lamellae with large (on the top of the brushes) and small (close to the grafted surface) domain spacing, which appears like a system of inclined locally parallel layers connected with each other by bridges. The parking garage structures were observed for incompatible A and B groups in selective solvents, which result in aggregation of the side B groups and dense packing of amphiphilic macromolecules in the restricted volume of the planar brushes.

Chemically active colloids near osmotic-responsive walls with surface-chemistry gradients

NASA Astrophysics Data System (ADS)

Popescu, M. N.; Uspal, W. E.; Dietrich, S.

2017-04-01

Chemically active colloids move by creating gradients in the composition of the surrounding solution and by exploiting the differences in their interactions with the various molecular species in solution. If such particles move near boundaries, e.g. the walls of the container confining the suspension, gradients in the composition of the solution are also created along the wall. This give rise to chemi-osmosis (via the interactions of the wall with the molecular species forming the solution), which drives flows coupling back to the colloid and thus influences its motility. Employing an approximate ‘point-particle’ analysis, we show analytically that—owing to this kind of induced active response (chemi-osmosis) of the wall—such chemically active colloids can align with, and follow, gradients in the surface chemistry of the wall. In this sense, these artificial ‘swimmers’ exhibit a primitive form of thigmotaxis with the meaning of sensing the proximity of a (not necessarily discontinuous) physical change in the environment. We show that the alignment with the surface-chemistry gradient is generic for chemically active colloids as long as they exhibit motility in an unbounded fluid, i.e. this phenomenon does not depend on the exact details of the propulsion mechanism. The results are discussed in the context of simple models of chemical activity, corresponding to Janus particles with ‘source’ chemical reactions on one half of the surface and either ‘inert’ or ‘sink’ reactions over the other half.

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

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

Glagolev, Mikhail K.; Vasilevskaya, Valentina V., E-mail: vvvas@polly.phys.msu.ru; Khokhlov, Alexei R.

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 singlemore » 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.« less

Surface complexation modeling of proton and Cd adsorption onto an algal cell wall.

PubMed

Kaulbach, Emily S; Szymanowski, Jennifer E S; Fein, Jeremy B

2005-06-01

This study quantifies Cd adsorption onto the cell wall of the algal species Pseudokirchneriella subcapitata by applying a surface complexation approach to model the observed adsorption behavior. We use potentiometric titrations to determine deprotonation constants and site concentrations for the functional groups on the algal cell wall. Adsorption and desorption kinetics experiments illustrate that adsorption of Cd onto the cell wall is rapid and reversible, except under low pH conditions. Adsorption experiments conducted as a function of pH and total Cd concentration yield the stoichiometry and site-specific stability constants for the important Cd-algal surface complexes. We model the acid/base properties of the algal cell wall by invoking four discrete surface functional group types, with pKa values of 3.9 +/- 0.3, 5.4 +/- 0.1, 7.6 +/- 0.3, and 9.6 +/- 0.4. The results of the Cd adsorption experiments indicate that the first, third, and fourth sites contribute to Cd adsorption under the experimental conditions, with calculated log stability constant values of 4.1 +/- 0.5, 5.4 +/- 0.5, and 6.1 +/- 0.4, respectively. Our results suggest that the stabilities of the Cd-surface complexes are high enough for algal adsorption to affect the fate and transport of Cd under some conditions and that on a per gram basis, algae and bacteria exhibit broadly similar extents of Cd adsorption.

Critical surface roughness for wall bounded flow of viscous fluids in an electric submersible pump

NASA Astrophysics Data System (ADS)

Deshmukh, Dhairyasheel; Siddique, Md Hamid; Kenyery, Frank; Samad, Abdus

2017-11-01

Surface roughness plays a vital role in the performance of an electric submersible pump (ESP). A 3-D numerical analysis has been carried out to find the roughness effect on ESP. The performance of pump for steady wall bounded turbulent flows is evaluated at different roughness values and compared with smooth surface considering a non-dimensional roughness factor K. The k- ω SST turbulence model with fine mesh at near wall region captures the rough wall effects accurately. Computational results are validated with experimental results of water (1 cP), at a design speed (3000 RPM). Maximum head is observed for a hydraulically smooth surface (K=0). When roughness factor is increased, the head decreases till critical roughness factor (K=0.1) due to frictional loss. Further increase in roughness factor (K>0.1) increases the head due to near wall turbulence. The performance of ESP is analyzed for turbulent kinetic energy and eddy viscosity at different roughness values. The wall disturbance over the rough surface affects the pressure distribution and velocity field. The roughness effect is predominant for high viscosity oil (43cP) as compared to water. Moreover, the study at off-design conditions showed that Reynolds number influences the overall roughness effect.

The anchorless adhesin Eap (extracellular adherence protein) from Staphylococcus aureus selectively recognizes extracellular matrix aggregates but binds promiscuously to monomeric matrix macromolecules.

PubMed

Hansen, Uwe; Hussain, Muzaffar; Villone, Daniela; Herrmann, Mathias; Robenek, Horst; Peters, Georg; Sinha, Bhanu; Bruckner, Peter

2006-05-01

Besides a number of cell wall-anchored adhesins, the majority of Staphylococcus aureus strains produce anchorless, cell wall-associated proteins, such as Eap (extracellular adherence protein). Eap contains four to six tandem repeat (EAP)-domains. Eap mediates diverse biological functions, including adherence and immunomodulation, thus contributing to S. aureus pathogenesis. Eap binding to host macromolecules is unusually promiscuous and includes matrix or matricellular proteins as well as plasma proteins. The structural basis of this promiscuity is poorly understood. Here, we show that in spite of the preferential location of the binding epitopes within triple helical regions in some collagens there is a striking specificity of Eap binding to different collagen types. Collagen I, but not collagen II, is a binding substrate in monomolecular form. However, collagen I is virtually unrecognized by Eap when incorporated into banded fibrils. By contrast, microfibrils containing collagen VI as well as basement membrane-associated networks containing collagen IV, or aggregates containing fibronectin bound Eap as effectively as the monomeric proteins. Therefore, Eap-binding to extracellular matrix ligands is promiscuous at the molecular level but not indiscriminate with respect to supramolecular structures containing the same macromolecules. In addition, Eap bound to banded fibrils after their partial disintegration by matrix-degrading proteinases, including matrix metalloproteinase 1. Therefore, adherence to matrix suprastructures by S. aureus can be supported by inflammatory reactions.

Impacts of Organic Macromolecules, Chlorophyll and Soot on Arctic Sea Ice

NASA Astrophysics Data System (ADS)

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.

An Overview of Biological Macromolecule Crystallization

PubMed Central

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

Surface-subsurface turbulent interaction at the interface of a permeable bed: influence of the wall permeability

NASA Astrophysics Data System (ADS)

Kim, T.; Blois, G.; Best, J.; Christensen, K. T.

2017-12-01

Coarse-gravel river beds possess a high degree of permeability. Flow interactions between surface and subsurface flow across the bed interface is key to a number of natural processes occurring in the hyporheic zone. In fact, it is increasingly recognized that these interactions drive mass, momentum and energy transport across the interface, and consequently control biochemical processes as well as stability of sediments. The current study explores the role of the wall permeability in surface and subsurface flow interaction under controlled experimental conditions on a physical model of a gravel bed. The present wall model was constructed by five layers of cubically arranged spheres (d=25.4mm, where d is a diameter) providing 48% of porosity. Surface topography was removed by cutting half of a diameter on the top layer of spheres to render the flow surface smooth and highlight the impact of the permeability on the overlying flow. An impermeable smooth wall was also considered as a baseline of comparison for the permeable wall flow. To obtain basic flow statistics, low-frame-rate high-resolution PIV measurements were performed first in the streamwise-wall-normal (x-y) plane and refractive-index matching was employed to optically access the flow within the permeable wall. Time-resolved PIV experiments in the same facility were followed to investigate the flow interaction across the wall interface in sptaio-temporal domain. In this paper, a detailed analysis of the first and second order velocity statistics as well as the amplitude modulation for the flow overlying the permeable smooth wall will be presented.

Interaction of flexible surface hairs with near-wall turbulence.

PubMed

Brücker, Ch

2011-05-11

The interaction of near-wall turbulence with hairy surfaces is investigated in a turbulent boundary layer flow along a flat plate in an oil channel at Re = 1.2 × 10⁶. The plate is covered locally with a dense carpet of elastomeric micro-hairs (length L = 1 mm, length in viscous units L( + ) = 30) which are arranged in a regular grid (60 × 30 hairs with a streamwise spacing Δx( + )≈15 and a spanwise spacing Δy( + )≈30). Instead of the micro-structures used in previous studies for sensory applications, the surface hairs are considerably larger and much more densely distributed with a spacing of S/D < 5 such that they interact with each other by flow coupling. The non-fluctuating mean part of the flow forces a substantial pre-bending in the streamwise direction (reconfiguration). As a consequence, the hairs align with the streamwise direction, thus imposing anisotropic damping characteristics with regard to flow fluctuations in streamwise and spanwise or wall-normal directions. Near-wall high-frequency disturbances excited by the passage of turbulent sweeps are dampened over their course along the carpet. The cooperative action of the hairs leads to an energy transfer from small-scale motion to larger scales, thus increasing the coherence of the motion pattern in streamwise and spanwise directions. As a consequence of the specific arrangement of the micro-hairs in streamwise columns a reduced spanwise meandering and stabilization of the streamwise velocity streaks is achieved by promoting varicose waves and inhibiting sinusoidal waves. Streak stabilization is known to be a major contributor to turbulent drag reduction. Thus it is concluded that hairy surfaces may be of benefit for turbulent drag reduction as hypothesized by Bartenwerfer and Bechert (1991 Z. Flugwiss. Weltraumforsch. 15 19-26).

Modification of the large-scale features of high Reynolds number wall turbulence by passive surface obtrusions

NASA Astrophysics Data System (ADS)

Monty, J. P.; Allen, J. J.; Lien, K.; Chong, M. S.

2011-12-01

A high Reynolds number boundary-layer wind-tunnel facility at New Mexico State University was fitted with a regularly distributed braille surface. The surface was such that braille dots were closely packed in the streamwise direction and sparsely spaced in the spanwise direction. This novel surface had an unexpected influence on the flow: the energy of the very large-scale features of wall turbulence (approximately six-times the boundary-layer thickness in length) became significantly attenuated, even into the logarithmic region. To the author's knowledge, this is the first experimental study to report a modification of `superstructures' in a rough-wall turbulent boundary layer. The result gives rise to the possibility that flow control through very small, passive surface roughness may be possible at high Reynolds numbers, without the prohibitive drag penalty anticipated heretofore. Evidence was also found for the uninhibited existence of the near-wall cycle, well known to smooth-wall-turbulence researchers, in the spanwise space between roughness elements.

Cross-tie walls and magnetic singularities on the surface of permalloy films (abstract)

NASA Astrophysics Data System (ADS)

Lee, Y.; Kueny, A.; Koymen, A. R.

1997-04-01

An understanding of the surface magnetic microstructure of thin polycrystalline permalloy films is important for the development of improved magnetoresistive sensors. Scanning electron microscopy with polarization analysis (SEMPA) was used to image the surface magnetic domain structure of permalloy films in ultrahigh vacuum. The SEMPA system uses a compact Mott electron spin polarimeter with a Th foil (operating at 25 keV) that has been attached to the back of a hemispherical energy analyzer. Two orthogonal in-plane components of the electron spin polarization were measured to obtain magnetic domain images with excellent contrast. 350 Å Ni83Fe17 films, deposited by Honeywell-Micro Switch using dc magnetron sputtering, were studied. The samples were demagnetized along the easy axis by an ac magnetic field with decreasing amplitude. Using SEMPA, zigzag domain walls separating two large approximately head-on domains were observed. Cross-tie walls were observed with a periodic vortex structure along the straight edges of the zigzag domain walls. The cross-tie walls occur at the points where the magnetization is reversed by 180° across the straight edges of the wall. At high magnification, the elliptical and hyperbolic singularities at the cross-tie walls were clearly observed. In addition, the Néel part and the Bloch part of the cross-tie were distinguished This is a detailed study of cross-tie walls on sputter deposited thin permalloy films using SEMPA and our results are in good agreement with theoretical calculations.

Effects of thickness, insulation, and surface color on the net heat loss through an adobe wall

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

Herman, R.W.

1980-01-01

A finite difference computer program was written and run to study the net thermal losses through a large variety of adobe walls. Fifty-four different combinations of surface color, wall thickness, and insulation position and R value were modeled over a typical two week winter period for locations similar to Albuquerque, New Mexico. A transient analysis of the heat loss from the room to the interior wall surface was compared to both conventional U value and steady-state calculations.

Bacterial Cell Enlargement Requires Control of Cell Wall Stiffness Mediated by Peptidoglycan Hydrolases.

PubMed

Wheeler, Richard; Turner, Robert D; Bailey, Richard G; Salamaga, Bartłomiej; Mesnage, Stéphane; Mohamad, Sharifah A S; Hayhurst, Emma J; Horsburgh, Malcolm; Hobbs, Jamie K; Foster, Simon J

2015-07-28

Most bacterial cells are enclosed in a single macromolecule of the cell wall polymer, peptidoglycan, which is required for shape determination and maintenance of viability, while peptidoglycan biosynthesis is an important antibiotic target. It is hypothesized that cellular enlargement requires regional expansion of the cell wall through coordinated insertion and hydrolysis of peptidoglycan. Here, a group of (apparent glucosaminidase) peptidoglycan hydrolases are identified that are together required for cell enlargement and correct cellular morphology of Staphylococcus aureus, demonstrating the overall importance of this enzyme activity. These are Atl, SagA, ScaH, and SagB. The major advance here is the explanation of the observed morphological defects in terms of the mechanical and biochemical properties of peptidoglycan. It was shown that cells lacking groups of these hydrolases have increased surface stiffness and, in the absence of SagB, substantially increased glycan chain length. This indicates that, beyond their established roles (for example in cell separation), some hydrolases enable cellular enlargement by making peptidoglycan easier to stretch, providing the first direct evidence demonstrating that cellular enlargement occurs via modulation of the mechanical properties of peptidoglycan. Understanding bacterial growth and division is a fundamental problem, and knowledge in this area underlies the treatment of many infectious diseases. Almost all bacteria are surrounded by a macromolecule of peptidoglycan that encloses the cell and maintains shape, and bacterial cells must increase the size of this molecule in order to enlarge themselves. This requires not only the insertion of new peptidoglycan monomers, a process targeted by antibiotics, including penicillin, but also breakage of existing bonds, a potentially hazardous activity for the cell. Using Staphylococcus aureus, we have identified a set of enzymes that are critical for cellular enlargement. We

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

PubMed

Beard, D A; Schlick, T

2001-01-01

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels. Copyright 2000 John Wiley & Sons, Inc.

High and low thermal conductivity of amorphous macromolecules

NASA Astrophysics Data System (ADS)

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.

Photocatalytic surface reactions on indoor wall paint.

PubMed

Salthammer, T; Fuhrmann, F

2007-09-15

The reduction of indoor air pollutants by air cleaning systems has received considerable interest, and a number of techniques are now available. So far, the method of photocatalysis was mainly applied by use of titanium dioxide (TiO2) in flow reactors under UV light of high intensity. Nowadays, indoor wall paints are equipped with modified TiO2 to work as a catalyst under indoor daylight or artificial light. In chamber experiments carried out under indoor related conditions itwas shown thatthe method works for nitrogen dioxide with air exchange and for formaldehyde without air exchange at high concentrations. In further experiments with volatile organic compounds (VOCs), a small effect was found for terpenoids with high kOH rate constants. For other VOCs and carbon monoxide there was no degradation at all or the surface acted as a reversible sink. Secondary emissions from the reaction of paint constituents were observed on exposure to light. From the results it is concluded that recipes of photocatalytic wall paints need to be optimized for better efficiency under indoor conditions.

Wall shear stress measurement in blade end-wall corner region

NASA Technical Reports Server (NTRS)

Bhargava, R.; Raj, R.; Boldman, D. R.

1987-01-01

The magnitude and the direction of wall shear stress and surface pressure in the blade end-wall corner region were investigated. The measurements were obtained on a specially designed Preston tube, the tip of which could be concentrically rotated about its axis of rotation at the measurement location. The magnitude of wall shear stress in the vicinity of the corner was observed to increase significantly (170 percent) compared to its far-upstream value; the increase was consistently higher on the blade surface compared to the value on the plate surface of the blade end-wall corner. On both surfaces in the blade end-wall corner, the variation of the wall shear stress direction was found to be more predominant in the vicinity of the blade leading-edge location. The trend of the measured wall shear stress direction showed good agreement with the limiting streamline directions obtained from the flow visualization studies.

Development for equipment of the milk macromolecules content detection

NASA Astrophysics Data System (ADS)

Ding, Guochao; Li, Weimin; Shang, Tingyi; Xi, Yang; Gao, Yunli; Zhou, Zhen

Developed an experimental device for rapid and accurate detection of milk macromolecular content. This device developed based on laser scattered through principle, the principle use of the ingredients of the scattered light and transmitted light ratio characterization of macromolecules. Peristaltic pump to achieve automatic input and output of the milk samples, designing weak signal detection amplifier circuit for detecting the ratio with ICL7650. Real-time operating system μC / OS-II is the core design of the software part of the whole system. The experimental data prove that the device can achieve a fast real-time measurement of milk macromolecules.

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

PubMed Central

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

2015-01-01

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. PMID:26269573

High throughput screening of ligand binding to macromolecules using high resolution powder diffraction

DOEpatents

Von Dreele, Robert B.; D'Amico, Kevin

2006-10-31

A process is provided for the high throughput screening of binding of ligands to macromolecules using high resolution powder diffraction data including producing a first sample slurry of a selected polycrystalline macromolecule material and a solvent, producing a second sample slurry of a selected polycrystalline macromolecule material, one or more ligands and the solvent, obtaining a high resolution powder diffraction pattern on each of said first sample slurry and the second sample slurry, and, comparing the high resolution powder diffraction pattern of the first sample slurry and the high resolution powder diffraction pattern of the second sample slurry whereby a difference in the high resolution powder diffraction patterns of the first sample slurry and the second sample slurry provides a positive indication for the formation of a complex between the selected polycrystalline macromolecule material and at least one of the one or more ligands.

Visualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow.

PubMed

Ghim, Mean; Alpresa, Paola; Yang, Sung-Wook; Braakman, Sietse T; Gray, Stephen G; Sherwin, Spencer J; van Reeuwijk, Maarten; Weinberg, Peter D

2017-11-01

Transport of macromolecules across vascular endothelium and its modification by fluid mechanical forces are important for normal tissue function and in the development of atherosclerosis. However, the routes by which macromolecules cross endothelium, the hemodynamic stresses that maintain endothelial physiology or trigger disease, and the dependence of transendothelial transport on hemodynamic stresses are controversial. We visualized pathways for macromolecule transport and determined the effect on these pathways of different types of flow. Endothelial monolayers were cultured under static conditions or on an orbital shaker producing different flow profiles in different parts of the wells. Fluorescent tracers that bound to the substrate after crossing the endothelium were used to identify transport pathways. Maps of tracer distribution were compared with numerical simulations of flow to determine effects of different shear stress metrics on permeability. Albumin-sized tracers dominantly crossed the cultured endothelium via junctions between neighboring cells, high-density lipoprotein-sized tracers crossed at tricellular junctions, and low-density lipoprotein-sized tracers crossed through cells. Cells aligned close to the angle that minimized shear stresses across their long axis. The rate of paracellular transport under flow correlated with the magnitude of these minimized transverse stresses, whereas transport across cells was uniformly reduced by all types of flow. These results contradict the long-standing two-pore theory of solute transport across microvessel walls and the consensus view that endothelial cells align with the mean shear vector. They suggest that endothelial cells minimize transverse shear, supporting its postulated proatherogenic role. Preliminary data show that similar tracer techniques are practicable in vivo. NEW & NOTEWORTHY Solutes of increasing size crossed cultured endothelium through intercellular junctions, through tricellular

Surface Chemical Properties of Purified Root Cell Walls from Two Tobacco Genotypes Exhibiting Different Tolerance to Manganese Toxicity 1

PubMed Central

Wang, Jian; Evangelou, Bill P.; Nielsen, Mark T.

1992-01-01

Surface chemical characteristics of root cell walls extracted from two tobacco genotypes exhibiting differential tolerance to Mn toxicity were studied using potentiometric pH titration and Fourier transform infrared spectroscopy. The Mn-sensitive genotype KY 14 showed a stronger interaction of its cell wall surface with metal ions than did the Mn-tolerant genotype Tobacco Introduction (T.I.) 1112. This observation may be attributed to the relatively higher ratio of COO− to COOH in KY 14 cell walls than that found in the cell walls of T.I. 1112 in the pH range of 4 to 10. For both genotypes, the strength of binding between metal ions and cell wall surface was in the order of Cu > Ca > Mn > Mg > Na. However, a slightly higher preference of Ca over Mn was observed with the T.I. 1112 cell wall. This may explain the high accumulation of Mn in the leaves of Mn-tolerant genotype T.I. 1112 rather than the high accumulation of Mn in roots, as occurred in Mn-sensitive KY 14. It is concluded that surface chemical characteristics of cell walls may play an important role in plant metal ion uptake and tolerance. PMID:16652989

High Reynolds number rough wall turbulent boundary layer experiments using Braille surfaces

NASA Astrophysics Data System (ADS)

Harris, Michael; Monty, Jason; Nova, Todd; Allen, James; Chong, Min

2007-11-01

This paper details smooth, transitional and fully rough turbulent boundary layer experiments in the New Mexico State high Reynolds number rough wall wind tunnel. The initial surface tested was generated with a Braille printer and consisted of an uniform array of Braille points. The average point height being 0.5mm, the spacing between the points in the span was 0.5mm and the surface consisted of span wise rows separated by 4mm. The wavelength to peak ratio was 8:1. The boundary layer thickness at the measurement location was 190mm giving a large separation of roughness height to layer thickness. The maximum friction velocity was uτ=1.5m/s at Rex=3.8 x10^7. Results for the skin friction co-efficient show that this surface follows a Nikuradse type inflectional curve and that Townsends outer layer similarity hypothesis is valid for rough wall flows with a large separation of scales. Mean flow and turbulence statistics will be presented.

Construction of Hydrophobic Wood Surface and Mechanical Property of Wood Cell Wall on Nanoscale Modified by Dimethyldichlorosilane

NASA Astrophysics Data System (ADS)

Yang, Rui; Wang, Siqun; Zhou, Dingguo; Zhang, Jie; Lan, Ping; Jia, Chong

2018-01-01

Dimethyldichlorosilane was used to improve the hydrophobicity of wood surface. The water contact angle of the treated wood surface increased from 85° to 143°, which indicated increased hydrophobicity. The nanomechanical properties of the wood cell wall were evaluated using a nanoindentation test to analyse the hydrophobic mechanism on the nano scale. The elastic modulus of the cell wall was significantly affected by the concentration but the influence of treatment time is insignificant. The hardness of the cell wall for treated samples was significantly affected by both treatment time and concentration. The interaction between treatment time and concentration was extremely significant for the elastic modulus of the wood cell wall.

Macromolecule mapping of the brain using ultrashort-TE acquisition and reference-based metabolite removal.

PubMed

Lam, Fan; Li, Yudu; Clifford, Bryan; Liang, Zhi-Pei

2018-05-01

To develop a practical method for mapping macromolecule distribution in the brain using ultrashort-TE MRSI data. An FID-based chemical shift imaging acquisition without metabolite-nulling pulses was used to acquire ultrashort-TE MRSI data that capture the macromolecule signals with high signal-to-noise-ratio (SNR) efficiency. To remove the metabolite signals from the ultrashort-TE data, single voxel spectroscopy data were obtained to determine a set of high-quality metabolite reference spectra. These spectra were then incorporated into a generalized series (GS) model to represent general metabolite spatiospectral distributions. A time-segmented algorithm was developed to back-extrapolate the GS model-based metabolite distribution from truncated FIDs and remove it from the MRSI data. Numerical simulations and in vivo experiments have been performed to evaluate the proposed method. Simulation results demonstrate accurate metabolite signal extrapolation by the proposed method given a high-quality reference. For in vivo experiments, the proposed method is able to produce spatiospectral distributions of macromolecules in the brain with high SNR from data acquired in about 10 minutes. We further demonstrate that the high-dimensional macromolecule spatiospectral distribution resides in a low-dimensional subspace. This finding provides a new opportunity to use subspace models for quantification and accelerated macromolecule mapping. Robustness of the proposed method is also demonstrated using multiple data sets from the same and different subjects. The proposed method is able to obtain macromolecule distributions in the brain from ultrashort-TE acquisitions. It can also be used for acquiring training data to determine a low-dimensional subspace to represent the macromolecule signals for subspace-based MRSI. Magn Reson Med 79:2460-2469, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate.

PubMed

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.

Bacterial Cell Enlargement Requires Control of Cell Wall Stiffness Mediated by Peptidoglycan Hydrolases

PubMed Central

Wheeler, Richard; Turner, Robert D.; Bailey, Richard G.; Salamaga, Bartłomiej; Mesnage, Stéphane; Mohamad, Sharifah A. S.; Hayhurst, Emma J.; Horsburgh, Malcolm; Hobbs, Jamie K.

2015-01-01

ABSTRACT Most bacterial cells are enclosed in a single macromolecule of the cell wall polymer, peptidoglycan, which is required for shape determination and maintenance of viability, while peptidoglycan biosynthesis is an important antibiotic target. It is hypothesized that cellular enlargement requires regional expansion of the cell wall through coordinated insertion and hydrolysis of peptidoglycan. Here, a group of (apparent glucosaminidase) peptidoglycan hydrolases are identified that are together required for cell enlargement and correct cellular morphology of Staphylococcus aureus, demonstrating the overall importance of this enzyme activity. These are Atl, SagA, ScaH, and SagB. The major advance here is the explanation of the observed morphological defects in terms of the mechanical and biochemical properties of peptidoglycan. It was shown that cells lacking groups of these hydrolases have increased surface stiffness and, in the absence of SagB, substantially increased glycan chain length. This indicates that, beyond their established roles (for example in cell separation), some hydrolases enable cellular enlargement by making peptidoglycan easier to stretch, providing the first direct evidence demonstrating that cellular enlargement occurs via modulation of the mechanical properties of peptidoglycan. PMID:26220963

Optimization of Surface Roughness and Wall Thickness in Dieless Incremental Forming Of Aluminum Sheet Using Taguchi

NASA Astrophysics Data System (ADS)

Hamedon, Zamzuri; Kuang, Shea Cheng; Jaafar, Hasnulhadi; Azhari, Azmir

2018-03-01

Incremental sheet forming is a versatile sheet metal forming process where a sheet metal is formed into its final shape by a series of localized deformation without a specialised die. However, it still has many shortcomings that need to be overcome such as geometric accuracy, surface roughness, formability, forming speed, and so on. This project focus on minimising the surface roughness of aluminium sheet and improving its thickness uniformity in incremental sheet forming via optimisation of wall angle, feed rate, and step size. Besides, the effect of wall angle, feed rate, and step size to the surface roughness and thickness uniformity of aluminium sheet was investigated in this project. From the results, it was observed that surface roughness and thickness uniformity were inversely varied due to the formation of surface waviness. Increase in feed rate and decrease in step size will produce a lower surface roughness, while uniform thickness reduction was obtained by reducing the wall angle and step size. By using Taguchi analysis, the optimum parameters for minimum surface roughness and uniform thickness reduction of aluminium sheet were determined. The finding of this project helps to reduce the time in optimising the surface roughness and thickness uniformity in incremental sheet forming.

A Generalized Wall Function

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Povinelli, Louis A.; Liu, Nan-Suey; Potapczuk, Mark G.; Lumley, J. L.

1999-01-01

The asymptotic solutions, described by Tennekes and Lumley (1972), for surface flows in a channel, pipe or boundary layer at large Reynolds numbers are revisited. These solutions can be extended to more complex flows such as the flows with various pressure gradients, zero wall stress and rough surfaces, etc. In computational fluid dynamics (CFD), these solutions can be used as the boundary conditions to bridge the near-wall region of turbulent flows so that there is no need to have the fine grids near the wall unless the near-wall flow structures are required to resolve. These solutions are referred to as the wall functions. Furthermore, a generalized and unified law of the wall which is valid for whole surface layer (including viscous sublayer, buffer layer and inertial sublayer) is analytically constructed. The generalized law of the wall shows that the effect of both adverse and favorable pressure gradients on the surface flow is very significant. Such as unified wall function will be useful not only in deriving analytic expressions for surface flow properties but also bringing a great convenience for CFD methods to place accurate boundary conditions at any location away from the wall. The extended wall functions introduced in this paper can be used for complex flows with acceleration, deceleration, separation, recirculation and rough surfaces.

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

PubMed

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.

A rapid and practical technique for real-time monitoring of biomolecular interactions using mechanical responses of macromolecules

NASA Astrophysics Data System (ADS)

Tarhan, Mehmet C.; Lafitte, Nicolas; Tauran, Yannick; Jalabert, Laurent; Kumemura, Momoko; Perret, Grégoire; Kim, Beomjoon; Coleman, Anthony W.; Fujita, Hiroyuki; Collard, Dominique

2016-06-01

Monitoring biological reactions using the mechanical response of macromolecules is an alternative approach to immunoassays for providing real-time information about the underlying molecular mechanisms. Although force spectroscopy techniques, e.g. AFM and optical tweezers, perform precise molecular measurements at the single molecule level, sophisticated operation prevent their intensive use for systematic biosensing. Exploiting the biomechanical assay concept, we used micro-electro mechanical systems (MEMS) to develop a rapid platform for monitoring bio/chemical interactions of bio macromolecules, e.g. DNA, using their mechanical properties. The MEMS device provided real-time monitoring of reaction dynamics without any surface or molecular modifications. A microfluidic device with a side opening was fabricated for the optimal performance of the MEMS device to operate at the air-liquid interface for performing bioassays in liquid while actuating/sensing in air. The minimal immersion of the MEMS device in the channel provided long-term measurement stability (>10 h). Importantly, the method allowed monitoring effects of multiple solutions on the same macromolecule bundle (demonstrated with DNA bundles) without compromising the reproducibility. We monitored two different types of effects on the mechanical responses of DNA bundles (stiffness and viscous losses) exposed to pH changes (2.1 to 4.8) and different Ag+ concentrations (1 μM to 0.1 M).

Fabrication of a novel biosensor for macromolecules detection through molecular imprinting technique

NASA Astrophysics Data System (ADS)

Yu, Yingjie

There is an increasing need for precise molecular detection as a diagnostic tool for early identification of diseases, pathogens, and abnormal protein levels in the body. Typical chemical analytical methods are generally costly, unstable, and time-consuming. Molecular imprinting (MI) technique, based on the "lock and key model", could be a simple method to overcome those shortcomings. In this study, a self-assembled monolayer (SAM) was employed as a platform to fabricate MI biosensor for detection of macromolecules. I demonstrated that, when the monolayer was formed on a rough surface, this method was in fact templating molecules in three dimensions, and hence was not limited by the height of the monolayer, but rather by the height of the roughness. This hypothesis was tested on biomolecules of multiple length scales. The SAM is assembled on the walls of the niche, forming a 3D pattern of the analyte uniquely molded to its contour. The surfaces with multi-scale roughness were prepared by evaporation of gold onto electropolished (smooth) and unpolished (rough) Si wafers, where the native roughness was found to have a normal distribution centered around 5 and 90 nm respectively. Our studies, using molecules, such as proteins, i.e., hemoglobin, ranging from a few nanometers, to viruses (i.e. polio, adenovirus), ranging from several tens of nanometers, and protein complexes ranging from several hundred nanometers, showed that when the size of the analyte matched the roughness of the gold surface, this method was very effective and could detect even small changes in the configuration, such as those induced by changes in the pH of the system. The detection method was further quantified by applying it to the detection of CEA in pancreatic cyst fluid obtained from 18 patients under IRB 95867-6. The results of the MI biosensor were directly compared with those obtained using ELISA in the hospital pathology laboratory with excellent agreement, except that the MI biosensor

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

DTIC Science & Technology

2016-04-12

AFRL-AFOSR-CL-TR-2016-0012 Intramolecular Charge Transfer of Conjugated Liquid Crystal Ferrocene Macromolecules Ronald Ziolo CIQA Final Report 07/07...3. DATES COVERED (From - To)  15 Aug 2014 to 14 Jan 2016 4. TITLE AND SUBTITLE Intramolecular Charge Transfer of Conjugated Liquid Crystal Ferrocene...characterization of a new series of conjugated macromolecules bearing ferrocene as a highly efficient electron donor material coupled to 2,5-di(alcoxy) benzene

[Diffusion and diffusion-osmosis models of the charged macromolecule transfer in barriers of biosystems].

PubMed

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.

Sensitivity of WallDYN material migration modeling to uncertainties in mixed-material surface binding energies

DOE PAGES

Nichols, J. H.; Jaworski, M. A.; Schmid, K.

2017-03-09

The WallDYN package has recently been applied to a number of tokamaks to self-consistently model the evolution of mixed-material plasma facing surfaces. A key component of the WallDYN model is the concentration-dependent surface sputtering rate, calculated using SDTRIM.SP. This modeled sputtering rate is strongly influenced by the surface binding energies (SBEs) of the constituent materials, which are well known for pure elements but often are poorly constrained for mixed-materials. This work examines the sensitivity of WallDYN surface evolution calculations to different models for mixed-material SBEs, focusing on the carbon/lithium/oxygen/deuterium system present in NSTX. A realistic plasma background is reconstructed frommore » a high density, H-mode NSTX discharge, featuring an attached outer strike point with local density and temperature of 4 × 10 20 m -3 and 4 eV, respectively. It is found that various mixed-material SBE models lead to significant qualitative and quantitative changes in the surface evolution profile at the outer divertor, with the highest leverage parameter being the C-Li binding model. Uncertainties of order 50%, appearing on time scales relevant to tokamak experiments, highlight the importance of choosing an appropriate mixed-material sputtering representation when modeling the surface evolution of plasma facing components. Lastly, these results are generalized to other fusion-relevant materials with different ranges of SBEs.« less

Sensitivity of WallDYN material migration modeling to uncertainties in mixed-material surface binding energies

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

Nichols, J. H.; Jaworski, M. A.; Schmid, K.

The WallDYN package has recently been applied to a number of tokamaks to self-consistently model the evolution of mixed-material plasma facing surfaces. A key component of the WallDYN model is the concentration-dependent surface sputtering rate, calculated using SDTRIM.SP. This modeled sputtering rate is strongly influenced by the surface binding energies (SBEs) of the constituent materials, which are well known for pure elements but often are poorly constrained for mixed-materials. This work examines the sensitivity of WallDYN surface evolution calculations to different models for mixed-material SBEs, focusing on the carbon/lithium/oxygen/deuterium system present in NSTX. A realistic plasma background is reconstructed frommore » a high density, H-mode NSTX discharge, featuring an attached outer strike point with local density and temperature of 4 × 10 20 m -3 and 4 eV, respectively. It is found that various mixed-material SBE models lead to significant qualitative and quantitative changes in the surface evolution profile at the outer divertor, with the highest leverage parameter being the C-Li binding model. Uncertainties of order 50%, appearing on time scales relevant to tokamak experiments, highlight the importance of choosing an appropriate mixed-material sputtering representation when modeling the surface evolution of plasma facing components. Lastly, these results are generalized to other fusion-relevant materials with different ranges of SBEs.« less

Ice nucleation rates of single protein complexes and single macromolecules

NASA Astrophysics Data System (ADS)

Stratmann, F.; Wex, H.; Niedermeier, D.; Hartmann, S.; Augustin, S.; Clauss, T.; Voigtlaender, J.; Pummer, B.; Grothe, H.

2012-12-01

With our flow-tube LACIS (Leipzig Aerosol cloud Interaction Simulator), we measured immersion freezing of droplets containing biological ice nucleating (IN) agents. From our measurements, we were able to deduce ice nucleation rates for single IN protein complexes (for Snomax) and for IN macromolecules (in the case of Birch pollen). For the measurements, aerosol particles were produced from solutions/suspensions of either Snomax (deadened and partly fractionalized pseudomonas syringae bacteria) or of Birch pollen washing water (BW in the following). All particles were dried and size selected before entering LACIS. In LACIS, particles were activated to droplets, and we measured the fraction of all droplets that froze (F(ice)) as function of temperature. For Snomax, a strong increase in F(ice) was observed around -7 to -10°C, for BW around -19 to -25°C, respectively. After this initial steep increase, F(ice) stayed constant for both examined substances down to -35°C. We found that the values of F(ice) in the plateau region depended on the dry particle size. The initial solution used to generate the particles contained parts of bacteria with ice active protein complexes on them in the case of Snomax, or IN macromolecules in the case of BW (Pummer et al., 2011). We show that the distribution of the IN proteins or IN molecules in the aerosol particles follows the Poisson distribution. With this knowledge, derivation of the ice nucleation rates for single IN protein complexes or for single IN macromolecules is possible. Combining the Poisson distribution with a stochastic model and using the derived nucleation rates, we can reproduce not only our measurements for both examined substances, but also past measurements done for Snomax and even pseudomonas syringae bacteria. As an additional peculiarity, we seem to observe two different macromolecules being ice active for Birch trees growing in Central Europe or Northern Europe, with the latter initiating freezing at

18. INTERIOR SURFACE OF THE SHORT SOUTH WALL OF AR9, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

18. INTERIOR SURFACE OF THE SHORT SOUTH WALL OF AR-9, WITH THE MORE RECENT CONCRETE BLOCK CONTROL ROOM AT THE LEFT AND ASSOCIATED CONCRETE PAVING IN THE FOREGROUND. - Edwards Air Force Base, South Base, Rammed Earth Aircraft Dispersal Revetments, Western Shore of Rogers Dry Lake, Boron, Kern County, CA

Isothermal titration calorimetry for measuring macromolecule-ligand affinity.

PubMed

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

2011-09-07

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.

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

NASA Astrophysics Data System (ADS)

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.

The Electric Potential of a Macromolecule in a Solvent: A Fundamental Approach

NASA Astrophysics Data System (ADS)

Juffer, André H.; Botta, Eugen F. F.; van Keulen, Bert A. M.; van der Ploeg, Auke; Berendsen, Herman J. C.

1991-11-01

A general numerical method is presented to compute the electric potential for a macromolecule of arbitrary shape in a solvent with nonzero ionic strength. The model is based on a continuum description of the dielectric and screening properties of the system, which consists of a bounded internal region with discrete charges and an infinite external region. The potential obeys the Poisson equation in the internal region and the linearized Poisson-Boltzmann equation in the external region, coupled through appropriate boundary conditions. It is shown how this three-dimensional problem can be presented as a pair of coupled integral equations for the potential and the normal component of the electric field at the dielectric interface. These equations can be solved by a straightforward application of boundary element techniques. The solution involves the decomposition of a matrix that depends only on the geometry of the surface and not on the positions of the charges. With this approach the number of unknowns is reduced by an order of magnitude with respect to the usual finite difference methods. Special attention is given to the numerical inaccuracies resulting from charges which are located close to the interface; an adapted formulation is given for that case. The method is tested both for a spherical geometry, for which an exact solution is available, and for a realistic problem, for which a finite difference solution and experimental verification is available. The latter concerns the shift in acid strength (pK-values) of histidines in the copper-containing protein azurin on oxidation of the copper, for various values of the ionic strength. A general method is given to triangulate a macromolecular surface. The possibility is discussed to use the method presented here for a correct treatment of long-range electrostatic interactions in simulations of solvated macromolecules, which form an essential part of correct potentials of mean force.

Surface-enhanced resonant Raman spectroscopy (SERRS) of single-walled carbon nanotubes absorbed on the Ag-coated anodic aluminum oxide (AAO) surface

NASA Astrophysics Data System (ADS)

Dou, X. Y.; Zhou, Z. P.; Tan, P. H.; Song, L.; Liu, L. F.; Zhao, X. W.; Luo, S. D.; Yan, X. Q.; Liu, D. F.; Wang, J. X.; Gao, Y.; Zhang, Z. X.; Yuan, H. J.; Zhou, W. Y.; Xie, S. S.

2005-05-01

In this paper, we developed a new kind of substrate, the silver-coated anodic aluminum oxide (AAO), to investigate the characters of surface-enhanced resonant Raman scattering (SERRS) of the dilute single-walled carbon nanotubes. Homogeneous Ag-coated AAO substrate was obtained by decomposing the AgNO 3 on the surface of AAO. single-walled carbon nanotubes (SWNTs) were directly grown onto this substrate through floating catalyst chemical vapor deposition method (CVD). SERRS of SWNTs was carried out using several different wavelength lasers. The bands coming from metallic SWNTs were significantly enhanced. The two SERRS mechanisms, the “electromagnetic” and “chemical” mechanism, were mainly responsible for the experiment results.

Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity

PubMed Central

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

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

NASA Astrophysics Data System (ADS)

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

Surface enhanced Raman scattering analyses of individual silver nanoaggregates on living single yeast cell wall

NASA Astrophysics Data System (ADS)

Sujith, Athiyanathil; Itoh, Tamitake; Abe, Hiroko; Anas, Abdul Aziz; Yoshida, Kenichi; Biju, Vasudevanpillai; Ishikawa, Mitsuru

2008-03-01

We labeled the living yeast cell surface (Saccharomyces cerevisiae strain W303-1A) by silver nanoparticles which can form nanoaggregates and found to show surface enhanced Raman scattering (SERS) activity. Blinking of SERS and its polarization dependence reveal that SERS signals are from amplified electromagnetic field at nanometric Ag nanoparticles gaps with single or a few molecules sensitivity. We tentatively assigned SERS spectra from a yeast cell wall to mannoproteins. Nanoaggregate-by-nanoaggregate variations and temporal fluctuations of SERS spectra are discussed in terms of inhomogeneous mannoprotein distribution on a cell wall and possible ways of Ag nanoaggregate adsorption, respectively.

Surface density of accumulated electrons on walls in contact with a plasma

NASA Technical Reports Server (NTRS)

De, B. R.

1975-01-01

It is shown that the surface density of accumulated electrons on a wall in contact with a plasma can be expressed as a simple function of the Debye shielding distance in the plasma. The result may have applications to problems involving objects immersed in a space plasma.

Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate

PubMed Central

Lebedeva, Natalia V.; Nese, Alper; Sun, Frank C.; Matyjaszewski, Krzysztof; Sheiko, Sergei S.

2012-01-01

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 (kBT) 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 = V0(1 - e-βx)2 - fx, we determined the depth and width of the potential to be V0 = 141 ± 19 kJ/mol and β-1 = 0.18 ± 0.03 Å, respectively. Whereas the V0 value is in reasonable agreement with the activation energy Ea = 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 De = 350 kJ/mol. Moreover, the force constant Kx = 2β2V0 = 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 Kl = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains. PMID:22645366

The effects of recirculation flows on mass transfer from the arterial wall to flowing blood.

PubMed

Zhang, Zhiguo; Deng, Xiaoyan; Fan, Yubo; Guidoin, Robert

2008-01-01

Using a sudden tubular expansion as a model of an arterial stenosis, the effect of disturbed flow on mass transfer from the arterial wall to flowing blood was studied theoretically and tested experimentally by measuring the dissolution rate of benzoic acid disks forming the outer tube of a sudden tubular expansion. The study revealed that mass transfer from vessel wall to flowing fluid in regions of disturbed flow is independent of wall shear rates. The rate of mass transfer is significantly higher in regions of disturbed flow with a local maximum around the reattachment point where the wall shear rate is zero. The experimental study also revealed that the rate of mass transfer from the vessel wall to a flowing fluid is much higher in the presence of microspheres (as models of blood cells) in the flowing fluid and under the condition of pulsatile flow than in steady flow. These results imply that flow disturbance may enhance the transport of biochemicals and macromolecules, such as plasma proteins and lipoproteins synthesized within the blood vessel wall, from the blood vessel wall to flowing blood.

Imaging domain walls between nematic quantum Hall phases on the surface of bismuth

NASA Astrophysics Data System (ADS)

Ding, Hao; Randeria, Mallika T.; Feldman, Benjamin E.; Ji, Huiwen; Cava, Robert J.; Yazdani, Ali

The sensitivity of nematic electronic phases to disorder results in short range ordering and the formation of domains. Local probes are required to investigate the character of these domains and the boundaries between them, which remain hidden in global measurements that average over microscopic configurations. In this talk, I will describe measurements performed with a scanning tunneling microscope to study local nematic order on the surface of bismuth at high magnetic field. By imaging individual anisotropic cyclotron orbit wavefunctions that are pinned to atomic-scale surface defects, we directly resolve local nematic behavior and study the evolution of nematic states across a domain wall. Through spectroscopic mapping, we explore how the broken-symmetry Landau levels disperse across the domain wall, the influence of exchange interactions at such a boundary, and the formation of one-dimensional edge states.

Higher dimensional curved domain walls on Kähler surfaces

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

Akbar, Fiki T., E-mail: ftakbar@fi.itb.ac.id; Gunara, Bobby E., E-mail: bobby@fi.itb.ac.id; Radjabaycolle, Flinn C.

In this paper we study some aspects of curved BPS-like domain walls in higher dimensional gravity theory coupled to scalars where the scalars span a complex Kähler surface with scalar potential turned on. Assuming that a fake superpotential has a special form which depends on Kähler potential and a holomorphic function, we prove that BPS-like equations have a local unique solution. Then, we analyze the vacuum structure of the theory including their stability using dynamical system and their existence in ultraviolet-infrared regions using renormalization group flow.

Specificity of marine microbial surface interactions.

PubMed Central

Imam, S H; Bard, R F; Tosteson, T R

1984-01-01

The macromolecular surface components involved in intraspecific cell surface interactions of the green microalga Chlorella vulgaris and closely associated bacteria were investigated. The specific surface attachment between this alga and its associated bacteria is mediated by lectin-like macromolecules associated with the surfaces of these cells. The binding activity of these surface polymers was inhibited by specific simple sugars; this suggests the involvement of specific receptor-ligand binding sites on the interactive surfaces. Epifluorescent microscopic evaluation of bacteria-alga interactions in the presence and absence of the macromolecules that mediate these interactions showed that the glycoproteins active in these processes were specific to the microbial sources from which they were obtained. The demonstration and definition of the specificity of these interactions in mixed microbial populations may play an important role in our understanding of the dynamics of marine microbial populations in the sea. PMID:6508293

Single molecule optical measurements of orientation and rotations of biological macromolecules

PubMed Central

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

2016-01-01

The 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 measuring 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, we review the relevant types of probes and labeling techniques, and we highlight the advantages and disadvantages of these technologies for addressing specific inquiries. PMID:28192292

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

PubMed

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

2016-11-22

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.

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

NASA Astrophysics Data System (ADS)

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.

A density functional theory for association of fluid molecules with a functionalized surface: fluid-wall single and double bonding.

PubMed

Haghmoradi, Amin; Wang, Le; Chapman, Walter G

2017-02-01

In this manuscript we extend Wertheim's two-density formalism beyond its first order to model a system of fluid molecules with a single association site close to a planar hard wall with association sites on its surface in a density functional theory framework. The association sites of the fluid molecules are small enough that they can form only one bond, while the wall association sites are large enough to bond with more than one fluid molecule. The effects of temperature and of bulk fluid and wall site densities on the fluid density profile, extent of association, and competition between single and double bonding of fluid segments at the wall sites versus distance from the wall are presented. The theory predictions are compared with new Monte Carlo simulation results and they are in good agreement. The theory captures the surface coverage over wide ranges of temperature and bulk density by introducing the effect of steric hindrance in fluid association at a wall site.

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

PubMed

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.

Route of steroid-activated macromolecules through nuclear pores imaged with atomic force microscopy.

PubMed

Oberleithner, H; Schäfer, C; Shahin, V; Albermann, L

2003-02-01

In eukaryotic cells, two concentric membranes, the nuclear envelope (NE), separate the nucleus from the cytoplasm. The NE is punctured by nuclear pore complexes (NPCs; molecular mass 120 MDa) that serve as regulated pathways for macromolecules entering and leaving the nuclear compartment. Transport across NPCs occurs through central channels. Such import and export of macromolecules through individual NPCs can be elicited in the Xenopus laevis oocyte by injecting the mineralocorticoid aldosterone and can be visualized with atomic force microscopy. The electrical NE resistance in intact cell nuclei can be measured in parallel. Resistance increases when macromolecules are engaged with the NPC. This article describe six observations made from these experiments and the conclusions that can be drawn from them. (i) A homogeneous population of macromolecules (approx. 100 kDa) attaches to the cytoplasmic face of the NPC 2 min after aldosterone injection. They are most likely to be aldosterone receptors. After a few minutes, they have disappeared. (ii) Large plugs (approx. molecular mass 1 MDa) appear in the central channels 20 min after hormone injection. They are most likely to be ribonucleoproteins exiting the nucleus. (iii) Electrical resistance measurements in isolated nuclei reveal transient electrical NE resistance peaks: an early (2 min) peak and a late (20 min) peak. Electrical peaks reflect macromolecule interaction with the NPC. (iv) Spironolactone blocks both the early and late peaks. This indicates that classic aldosterone receptors are involved in the pregenomic (early) and post-genomic (late) responses. (v) Actinomycin D and, independently, RNase A block the late electrical peak, confirming that plugs are genomic in nature. (vi) Intracellular calcium chelation blocks both early and late electrical peaks. Thus, the release of calcium from internal stores, which is known to be the first intracellular signal in response to aldosterone, is a prerequisite for the

Cell wall structure suitable for surface display of proteins in Saccharomyces cerevisiae.

PubMed

Matsuoka, Hiroyuki; Hashimoto, Kazuya; Saijo, Aki; Takada, Yuki; Kondo, Akihiko; Ueda, Mitsuyoshi; Ooshima, Hiroshi; Tachibana, Taro; Azuma, Masayuki

2014-02-01

A display system for adding new protein functions to the cell surfaces of microorganisms has been developed, and applications of the system to various fields have been proposed. With the aim of constructing a cell surface environment suitable for protein display in Saccharomyces cerevisiae, the cell surface structures of cell wall mutants were investigated. Four cell wall mutant strains were selected by analyses using a GFP display system via a GPI anchor. β-Glucosidase and endoglucanase II were displayed on the cell surface in the four mutants, and their activities were evaluated. mnn2 deletion strain exhibited the highest activity for both the enzymes. In particular, endoglucanase II activity using carboxymethylcellulose as a substrate in the mutant strain was 1.9-fold higher than that of the wild-type strain. In addition, the activity of endoglucanase II released from the mnn2 deletion strain by Zymolyase 20T treatment was higher than that from the wild-type strain. The results of green fluorescent protein (GFP) and endoglucanase displays suggest that the amounts of enzyme displayed on the cell surface were increased by the mnn2 deletion. The enzyme activity of the mnn2 deletion strain was compared with that of the wild-type strain. The relative value (mnn2 deletion mutant/wild-type strain) of endoglucanase II activity using carboxymethylcellulose as a substrate was higher than that of β-glucosidase activity using p-nitrophenyl-β-glucopyranoside as a substrate, suggesting that the cell surface environment of the mnn2 deletion strain facilitates the binding of high-molecular-weight substrates to the active sites of the displayed enzymes. Copyright © 2014 John Wiley & Sons, Ltd.

Bioactive surface modifications on inner walls of poly-tetra-fluoro-ethylene tubes using dielectric barrier discharge

NASA Astrophysics Data System (ADS)

Cho, Yong Ki; Park, Daewon; Kim, Hoonbae; Lee, Hyerim; Park, Heonyong; Kim, Hong Ja; Jung, Donggeun

2014-03-01

Bioactive surface modification can be used in a variety of medical polymeric materials in the fields of biochips and biosensors, artificial membranes, and vascular grafts. In this study, the surface modification of the inner walls of poly-tetra-fluoro-ethylene (PTFE) tubing was carried out to improve vascular grafts, which are made of biocompatible material for the human body in the medical field. Focus was centered on the cell attachment of the inner wall of the PTFE by sequential processes of hydrogen plasma treatment, hydrocarbon deposition, and reactive plasma treatment on the PFTE surface using micro plasma discharge. Micro plasma was generated by a medium-frequency alternating current high-voltage generator. The preliminary modification of PTFE was conducted by a plasma of hydrogen and argon gases. The hydrocarbon thin film was deposited on modified PTFE with a mixture of acetylene and argon gases. The reactive plasma treatment using oxygen plasma was done to give biocompatible functionality to the inner wall surface. The hydrophobic surface of bare PTFE is made hydrophilic by the reactive plasma treatment due to the formation of carbonyl groups on the surface. The reactive treatment could lead to improved attachment of smooth muscle cells (SMCs) on the modified PTFE tubing. Fourier transform infrared absorption spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, and water contact angle measurement were used for the analysis of the surface modification. The SMC-attached PTFE tube developed will be applicable to in vitro human vasculature-mimetic model systems, and to medical vascular grafts.

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

PubMed Central

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

2017-01-01

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. DOI: http://dx.doi.org/10.7554/eLife.25932.001 PMID:28498105

Effect of nano-scale morphology on micro-channel wall surface and electrical characterization in lead silicate glass micro-channel plate

NASA Astrophysics Data System (ADS)

Cai, Hua; Li, Fangjun; Xu, Yanglei; Bo, Tiezhu; Zhou, Dongzhan; Lian, Jiao; Li, Qing; Cao, Zhenbo; Xu, Tao; Wang, Caili; Liu, Hui; Li, Guoen; Jia, Jinsheng

2017-10-01

Micro-channel plate (MCP) is a two dimensional arrays of microscopic channel charge particle multiplier. Silicate composition and hydrogen reduction are keys to determine surface morphology of micro-channel wall in MCP. In this paper, lead silicate glass micro-channel plates in two different cesium contents (0at%, 0.5at%) and two different hydrogen reduction temperatures (400°C,450°C) were present. The nano-scale morphology, elements content and chemical states of microporous wall surface treated under different alkaline compositions and reduction conditions was investigated by Atomic Force Microscopy (AFM) and X-ray Photoelectron Spectroscopy (XPS), respectively. Meanwhile, the electrical characterizations of MCP, including the bulk resistance, electron gain and the density of dark current, were measured in a Vacuum Photoelectron Imaging Test Facility (VPIT).The results indicated that the granular phase occurred on the surface of microporous wall and diffuses in bulk glass is an aggregate of Pb atom derived from the reduction of Pb2+. In micro-channel plate, the electron gain and bulk resistance were mainly correlated to particle size and distribution, the density of dark current (DDC) went up with the increasing root-mean-square roughness (RMS) on the microporous wall surface. Adding cesiums improved the size of Pb atomic aggregation, lowered the relative concentration of [Pb] reduced from Pb2+ and decreased the total roughness of micro-channel wall surface, leading a higher bulk resistance, a lower electron gain and a less dark current. Increasing hydrogen reduction temperature also improved the size of Pb atomic aggregation, but enhanced the relative concentration of [Pb] and enlarged the total roughness of micro-channel wall surface, leading a higher bulk resistance, a lower electron gain and a larger dark current. The reasons for the difference of electrical characteristics were discussed.

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

ERIC Educational Resources Information Center

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)

Ocular delivery of macromolecules

PubMed Central

Kim, Yoo-Chun; Chiang, Bryce; Wu, Xianggen; Prausnitz, Mark R.

2014-01-01

Biopharmaceuticals are making increasing impact on medicine, including treatment of indications in the eye. Macromolecular drugs are typically given by physician-administered invasive delivery methods, because non--invasive ocular delivery methods, such as eye drops, and systemic delivery, have low bioavailability and/or poor ocular targeting. There is a need to improve delivery of biopharmaceuticals to enable less-invasive delivery routes, less-frequent dosing through controlled-release drug delivery and improved drug targeting within the eye to increase efficacy and reduce side effects. This review discusses the barriers to drug delivery via various ophthalmic routes of administration in the context of macromolecule delivery and discusses efforts to develop controlled-release systems for delivery of biopharmaceuticals to the eye. The growing number of macromolecular therapies in the eye needs improved drug delivery methods that increase drug efficacy, safety and patient compliance. PMID:24998941

Identification of Characteristic Macromolecules of Escherichia coli Genotypes by Atomic Force Microscope Nanoscale Mechanical Mapping

NASA Astrophysics Data System (ADS)

Chang, Alice Chinghsuan; Liu, Bernard Haochih

2018-02-01

The categorization of microbial strains is conventionally based on the molecular method, and seldom are the morphological characteristics in the bacterial strains studied. In this research, we revealed the macromolecular structures of the bacterial surface via AFM mechanical mapping, whose resolution was not only determined by the nanoscale tip size but also the mechanical properties of the specimen. This technique enabled the nanoscale study of membranous structures of microbial strains with simple specimen preparation and flexible working environments, which overcame the multiple restrictions in electron microscopy and label-enable biochemical analytical methods. The characteristic macromolecules located among cellular surface were considered as surface layer proteins and were found to be specific to the Escherichia coli genotypes, from which the averaged molecular sizes were characterized with diameters ranging from 38 to 66 nm, and the molecular shapes were kidney-like or round. In conclusion, the surface macromolecular structures have unique characteristics that link to the E. coli genotype, which suggests that the genomic effects on cellular morphologies can be rapidly identified using AFM mechanical mapping. [Figure not available: see fulltext.

The Role of Law-of-the-Wall and Roughness Scale in the Surface Stress Model for LES of the Rough-wall Boundary Layer

NASA Astrophysics Data System (ADS)

Brasseur, James; Paes, Paulo; Chamecki, Marcelo

2017-11-01

Large-eddy simulation (LES) of the high Reynolds number rough-wall boundary layer requires both a subfilter-scale model for the unresolved inertial term and a ``surface stress model'' (SSM) for space-time local surface momentum flux. Standard SSMs assume proportionality between the local surface shear stress vector and the local resolved-scale velocity vector at the first grid level. Because the proportionality coefficient incorporates a surface roughness scale z0 within a functional form taken from law-of-the-wall (LOTW), it is commonly stated that LOTW is ``assumed,'' and therefore ``forced'' on the LES. We show that this is not the case; the LOTW form is the ``drag law'' used to relate friction velocity to mean resolved velocity at the first grid level consistent with z0 as the height where mean velocity vanishes. Whereas standard SSMs do not force LOTW on the prediction, we show that parameterized roughness does not match ``true'' z0 when LOTW is not predicted, or does not exist. By extrapolating mean velocity, we show a serious mismatch between true z0 and parameterized z0 in the presence of a spurious ``overshoot'' in normalized mean velocity gradient. We shall discuss the source of the problem and its potential resolution.

An experimental study of near wall flow parameters in the blade end-wall corner region

NASA Technical Reports Server (NTRS)

Bhargava, Rakesh K.; Raj, Rishi S.

1989-01-01

The near wall flow parameters in the blade end-wall corner region is investigated. The blade end-wall corner region was simulated by mounting an airfoil section (NACA 65-015 base profile) symmetric blades on both sides of the flat plate with semi-circular leading edge. The initial 7 cm from the leading edge of the flat plate was roughened by gluing No. 4 floor sanding paper to artificially increase the boundary layer thickness on the flat plate. The initial flow conditions of the boundary layer upstream of the corner region are expected to dictate the behavior of flow inside the corner region. Therefore, an experimental investigation was extended to study the combined effect of initial roughness and increased level of free stream turbulence on the development of a 2-D turbulent boundary layer in the absence of the blade. The measurement techniques employed in the present investigation included, the conventional pitot and pitot-static probes, wall taps, the Preston tube, piezoresistive transducer and the normal sensor hot-wire probe. The pitot and pitot-static probes were used to obtain mean velocity profile measurements within the boundary layer. The measurements of mean surface static pressure were obtained with the surface static tube and the conventional wall tap method. The wall shear vector measurements were made with a specially constructed Preston tube. The flush mounted piezoresistive type pressure transducer were employed to measure the wall pressure fluctuation field. The velocity fluctuation measurements, used in obtaining the wall pressure-velocity correlation data, were made with normal single sensor hot-wire probe. At different streamwise stations, in the blade end-wall corner region, the mean values of surface static pressure varied more on the end-wall surface in the corner region were mainly caused by the changes in the curvature of the streamlines. The magnitude of the wall shear stress in the blade end-wall corner region increased significantly

Delta L: An Apparatus for Measuring Macromolecule Crystal Growth Rates in Microgravity

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Strongly diffracting high quality macromolecule crystals of suitable volume are keenly sought for X-ray diffraction analysis so that high-resolution molecular structure data can be obtained. Such data is of tremendous value to medical research, agriculture and commercial biotechnology. In previous studies by many investigators microgravity has been reported in some instances to improve biological macromolecule X-ray crystal quality while little or no improvement was observed in other cases. A better understanding of processes effecting crystal quality improvement in microgravity will therefore be of great benefit in optimizing crystallization success in microgravity. In ground based research with the protein lysozyme we have previously shown that a population of crystals grown under the same solution conditions, exhibit a variation in X-ray diffraction properties (Judge et al., 1999). We have also observed that under the same solution conditions, individual crystals will grow at slightly different growth rates. This phenomenon is called growth rate dispersion. For small molecule materials growth rate dispersion has been directly related to crystal quality (Cunningham et al., 1991; Ristic et al., 1991). We therefore postulate that microgravity may act to improve crystal quality by reducing growth rate dispersion. If this is the case then as different, Materials exhibit different degrees of growth rate dispersion on the ground then growth rate dispersion could be used to screen which materials may benefit the most from microgravity crystallization. In order to assess this theory the Delta L hardware is being developed so that macromolecule crystal growth rates can be measured in microgravity. Crystal growth rate is defined as the change or delta in crystal size (defined as a characteristic length, L) over time; hence the name of the hardware. Delta L will consist of an optics, a fluids, and a data acquisition sub-assemblies. The optics assembly will consist of a

Some properties of the walls of metaxylem vessels of maize roots, including tests of the wettability of their lumenal wall surfaces

PubMed Central

McCully, Margaret; Canny, Martin; Baker, Adam; Miller, Celia

2014-01-01

Background and Aims Since the proposal of the cohesion theory there has been a paradox that the lumenal surface of vessels is rich in hydrophobic lignin, while tension in the rising sap requires adhesion to a hydrophilic surface. This study sought to characterize the strength of that adhesion in maize (Zea mays), the wettability of the vessel surface, and to reconcile this with its histochemical and physical nature. Methods Wettability was assessed by emptying the maize root vessels of sap, perfusing them with either water or oil, and examining the adhesion (as revealed by contact angles) of the two liquids to vessel walls by cryo-scanning electron microscopy. The phobicity of the lumenal surface was also assessed histochemically with hydrophilic and hydrophobic probes. Key Results Pit borders in the lumen-facing vessel wall surface were wetted by both sap/water and oil. The attraction for oil was weaker: water could replace oil but not vice versa. Pit apertures repelled oil and were strongly stained by hydrophilic probes. Pit chambers were probably hydrophilic. Oil never entered the pits. When vessels were emptied and cryo-fixed immediately, pit chambers facing away from the vessels were always sap-filled. Pit chambers facing vessel lumens were either sap- or gas-filled. Sap from adjoining tracheary elements entering empty vessels accumulated on the lumenal surface in hemispherical drops, which spread out with decreasing contact angles to fill the lumen. Conclusions The vessel lumenal surface has a dual nature, namely a mosaic of hydrophilic and hydrophobic patches at the micrometre scale, with hydrophilic predominating. A key role is shown, for the first time, of overarching borders of pits in determining the dual nature of the surface. In gas-filled (embolized) vessels they are hydrophobic. When wetted by sap (vessels refilling or full) they are hydrophilic. A hypothesis is proposed to explain the switch between the two states. PMID:24709790

Influence of hesperidin on renal cell surface glycoprotein content, nucleic acids, lysosomal enzymes and macromolecules against 7, 12-dimethylbenz [a] anthracene induced experimental breast carcinoma.

PubMed

Nandakumar, Natarajan; Jayaprakash, Ramachandran; Balasubramanian, Maruthaiveeran Periyasamy

2012-01-01

Therapeutic substances may reduce the risk of developing cancer by modulating the factors responsible for carcinogenesis. To evaluate these hypotheses, the present study was designed to investigate the modulatory effect of bioflavonoid "Hesperidin" against DMBA induced experimental breast cancer with reference to renal cell surface glycoproteins, nucleic acids, protein content, lipid profile and lysosomal enzymes. The female sprague-dawley rats were orally administered with single dose of 7, 12-DMBA to induce breast cancer and were treated with hesperidin [30 mg/kg/body weight] for a consecutive 45 days. The results revealed that there was a significant elevation in the levels of glycoproteins, nucleic acids, lysosomal enzymes and also significant alterations in macromolecules in renal tissues of cancer bearing animals. Interestingly, the altered levels of these parameters were remarkably reverted back to near normal in hesperidin treatment. The histopathological analysis of liver and kidney tissues were well supported the biochemical alterations and inevitably proves the protective role of hesperidin. It is proposed that, the effect of hesperidin during DMBA induced breast cancer could be due to the intervention strategies of hesperidin in the protein, nucleic acid biosynthesis, membrane stabilizing potentials on lysosomal compartment and inhibitory effect on cell surface glycoproteins and bio-fuel such as lipids.

Motion of single wandering diblock-macromolecules directed by a PTFE nano-fence: real time SFM observations.

PubMed

Gallyamov, Marat O; Qin, Shuhui; Matyjaszewski, Krzysztof; Khokhlov, Alexei; Möller, Martin

2009-07-21

Using SFM we have observed a peculiar twisting motion of diblock macromolecules pre-collapsed in ethanol vapour during their subsequent spreading in water vapour. The intrinsic asymmetry of the diblock macromolecules has been considered to be the reason for such twisting. Further, friction-deposited PTFE nano-stripes have been employed as nano-trails with the purpose of inducing lateral directed motion of the asymmetric diblock macromolecules under cyclic impact from the changing vapour surroundings. Indeed, some of the macromolecules have demonstrated a certain tendency to orient along the PTFE stripes, and some of the oriented ones have moved occasionally in a directed manner along the trail. However, it has been difficult to reliably record such directed motion at the single molecule level due to some mobility of the PTFE nano-trails themselves in the changing vapour environment. In vapours, the PTFE stripes have demonstrated a distinct tendency towards conjunction. This tendency has manifested itself in efficient expelling of groups of the mobile brush-like molecules from the areas between two PTFE stripes joining in a zip-fastener manner. This different kind of vapour-induced cooperative macromolecular motion has been reliably observed as being directed. The PTFE nano-frame experiences some deformation when constraining the spreading macromolecules. We have estimated the possible force causing such deformation of the PTFE fence. The force has been found to be a few pN as calculated by a partial contribution from every single molecule of the constrained group.

Basal-body-associated macromolecules: a continuing debate.

PubMed

Pierre Mignot, J; Brugerolle, G; Didier, P; Bornens, M

1993-07-01

Controversy over the possibility that centrioles/basal bodies contain nucleic acids has overshadowed results demonstrating other macromolecules in the lumen of these organelles. Glycogen particles, which are known to be present within the lumen of the centriole/basal body of sperm cells, have now been found in basal bodies of protists belonging to three different groups. Here, we extend the debate on a role for RNA in basal body/centriole function and speculate on the origin and the function of centriolar glycogen.

Experimental investigation of compliant wall surface deformation in a turbulent channel flow

NASA Astrophysics Data System (ADS)

Zhang, Cao; Wang, Jin; Katz, Joseph

2016-11-01

The dynamic response of a compliant wall under a turbulent channel flow is investigated by simultaneously measuring the time-resolved, 3D flow field (using tomographic PIV) and the 2D surface deformation (using interferometry). The pressure distributions are calculated by spatially integrating the material acceleration field. The Reynolds number is Reτ = 2300, and the centerline velocity (U0) is 15% of the material shear speed. The wavenumber-frequency spectra of the wall deformation contain a non-advected low-frequency component and advected modes, some traveling downstream at U0 and others at 0.72U0. Trends in the wall dynamics are elucidated by correlating the deformation with flow variables. The spatial pressure-deformation correlations peak at y/ h 0.12 (h is half channel height), the elevation of Reynolds shear stress maximum in the log-layer. Streamwise lagging of the deformation behind the pressure is caused in part by phase-lag of the pressure with decreasing distance from the wall, and in part by material damping. Positive deformations (bumps) are preferentially associated with ejections, which involve spanwise vortices located downstream and quasi-streamwise vortices with spanwise offset, consistent with hairpin-like structures. The negative deformations (dents) are preferentially associated with pressure maxima at the transition between an upstream sweep to a downstream ejection. Sponsored by ONR.

Turbine airfoil with outer wall thickness indicators

DOEpatents

Marra, John J; James, Allister W; Merrill, Gary B

2013-08-06

A turbine airfoil usable in a turbine engine and including a depth indicator for determining outer wall blade thickness. The airfoil may include an outer wall having a plurality of grooves in the outer surface of the outer wall. The grooves may have a depth that represents a desired outer surface and wall thickness of the outer wall. The material forming an outer surface of the outer wall may be removed to be flush with an innermost point in each groove, thereby reducing the wall thickness and increasing efficiency. The plurality of grooves may be positioned in a radially outer region of the airfoil proximate to the tip.

Attachment of Salmonella strains to a plant cell wall model is modulated by surface characteristics and not by specific carbohydrate interactions.

PubMed

Tan, Michelle Sze-Fan; Moore, Sean C; Tabor, Rico F; Fegan, Narelle; Rahman, Sadequr; Dykes, Gary A

2016-09-15

Processing of fresh produce exposes cut surfaces of plant cell walls that then become vulnerable to human foodborne pathogen attachment and contamination, particularly by Salmonella enterica. Plant cell walls are mainly composed of the polysaccharides cellulose, pectin and hemicelluloses (predominantly xyloglucan). Our previous work used bacterial cellulose-based plant cell wall models to study the interaction between Salmonella and the various plant cell wall components. We demonstrated that Salmonella attachment was favoured in the presence of pectin while xyloglucan had no effect on its attachment. Xyloglucan significantly increased the attachment of Salmonella cells to the plant cell wall model only when it was in association with pectin. In this study, we investigate whether the plant cell wall polysaccharides mediate Salmonella attachment to the bacterial cellulose-based plant cell wall models through specific carbohydrate interactions or through the effects of carbohydrates on the physical characteristics of the attachment surface. We found that none of the monosaccharides that make up the plant cell wall polysaccharides specifically inhibit Salmonella attachment to the bacterial cellulose-based plant cell wall models. Confocal laser scanning microscopy showed that Salmonella cells can penetrate and attach within the tightly arranged bacterial cellulose network. Analysis of images obtained from atomic force microscopy revealed that the bacterial cellulose-pectin-xyloglucan composite with 0.3 % (w/v) xyloglucan, previously shown to have the highest number of Salmonella cells attached to it, had significantly thicker cellulose fibrils compared to other composites. Scanning electron microscopy images also showed that the bacterial cellulose and bacterial cellulose-xyloglucan composites were more porous when compared to the other composites containing pectin. Our study found that the attachment of Salmonella cells to cut plant cell walls was not mediated by

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

NASA Astrophysics Data System (ADS)

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.

Self-assembly of an amphiphilic macromolecule under spherical confinement: An efficient route to generate hollow nanospheres

NASA Astrophysics Data System (ADS)

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.

Lactobacillus plantarum 299v surface-bound GAPDH: a new insight into enzyme cell walls location.

PubMed

Saad, N; Urdaci, M; Vignoles, C; Chaignepain, S; Tallon, R; Schmitter, J M; Bressollier, P

2009-12-01

The aim of this study was to provide new insight into the mechanism whereby the housekeeping enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) locates to cell walls of Lactobacillus plantarum 299v. After purification, cytosolic and cell wall GAPDH (cw-GAPDH) forms were characterized and shown to be identical homotetrameric active enzymes. GAPDH concentration on cell walls was growth-time dependent. Free GAPDH was not observed on the culture supernatant at any time during growth, and provoked cell lysis was not concomitant with any reassociation of GAPDH onto the cell surface. Hence, with the possibility of cw-GAPDH resulting from autolysis being unlikely, entrapment of intracellular GAPDH on the cell wall after a passive efflux through altered plasma membrane was investigated. Flow cytometry was used to assess L. plantarum 299v membrane permeabilization after labeling with propidium iodide (PI). By combining PI uptake and cw-GAPDH activity measurements, we demonstrate here that the increase in cw-GAPDH concentration from the early exponential phase to the late stationary phase is closely related to an increase in plasma membrane permeability during growth. Moreover, we observed that increases in both plasma membrane permeability and cw-GAPDH activity were delayed when glucose was added during L. plantarum 299v growth. Using a double labeling of L. plantarum 299v cells with anti-GAPDH antibodies and propidium iodide, we established unambiguously that cells with impaired membrane manifest five times more cw-GAPDH than unaltered cells. Our results show that plasma membrane permeability appears to be closely related to the efflux of GAPDH on the bacterial cell surface, offering new insight into the understanding of the cell wall location of this enzyme.

Ordered mesoporous polymer-silica hybrid nanoparticles as vehicles for the intracellular controlled release of macromolecules.

PubMed

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.

Calculation of wall effects of flow on a perforated wall with a code of surface singularities

NASA Astrophysics Data System (ADS)

Piat, J. F.

1994-07-01

Simplifying assumptions are inherent in the analytic method previously used for the determination of wall interferences on a model in a wind tunnel. To eliminate these assumptions, a new code based on the vortex lattice method was developed. It is suitable for processing any shape of test sections with limited areas of porous wall, the characteristic of which can be nonlinear. Calculation of wall effects in S3MA wind tunnel, whose test section is rectangular 0.78 m x 0.56 m, and fitted with two or four perforated walls, have been performed. Wall porosity factors have been adjusted to obtain the best fit between measured and computed pressure distributions on the test section walls. The code was checked by measuring nearly equal drag coefficients for a model tested in S3MA wind tunnel (after wall corrections) and in S2MA wind tunnel whose test section is seven times larger (negligible wall corrections).

Macromolecule Crystal Quality Improvement in Microgravity: The Role of Impurities

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, Edward H.; Pusey, Marc L.; Sportiello, Michael G.; Todd, Paul; Bellamy, Henry; Borgstahl, Gloria E.; Pokros, Matt; Cassanto, John M.

2000-01-01

While macromolecule impurities may affect crystal size and morphology the over-riding question is; "How do macromolecule impurities effect crystal X-ray quality and diffraction resolution?" In the case of chicken egg white lysozyme, crystals can be grown in the presence of a number of impurities without affecting diffraction resolution. One impurity however, the lysozyme dimer, does negatively impact the X-ray crystal properties. Crystal quality improvement as a result of better partitioning of this impurity during crystallization in microgravity has been reported'. In our recent experimental work dimer partitioning was found to be not significantly different between the two environments. Mosaicity analysis of pure crystals showed a reduced mosaicity and increased signal to noise for the microgravity grown crystals. Dimer incorporation however, did greatly reduce the resolution limit in both ground and microgravity grown crystals. These results indicate that impurity effects in microgravity are complex and may rely on the conditions or techniques employed.

JAIL: a structure-based interface library for macromolecules.

PubMed

Günther, Stefan; von Eichborn, Joachim; May, Patrick; Preissner, Robert

2009-01-01

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular interfaces, those between interacting protein domains, interfaces of different protein chains and interfaces between proteins and nucleic acids. This results in a total number of about 184,000 database entries. All the interfaces can easily be identified by a detailed search form or by a hierarchical tree that describes the protein domain architectures classified by the SCOP database. Visual inspection of the interfaces is possible via an interactive protein viewer. Furthermore, large scale analyses are supported by an implemented sequential and by a structural clustering. Similar interfaces as well as non-redundant interfaces can be easily picked out. Additionally, the sequential conservation of binding sites was also included in the database and is retrievable via Jmol. A comprehensive download section allows the composition of representative data sets with user defined parameters. The huge data set in combination with various search options allow a comprehensive view on all interfaces between macromolecules included in the Protein Data Bank (PDB). The download of the data sets supports numerous further investigations in macromolecular recognition. JAIL is publicly available at http://bioinformatics.charite.de/jail.

Learning-based automated segmentation of the carotid artery vessel wall in dual-sequence MRI using subdivision surface fitting.

PubMed

Gao, Shan; van 't Klooster, Ronald; Kitslaar, Pieter H; Coolen, Bram F; van den Berg, Alexandra M; Smits, Loek P; Shahzad, Rahil; Shamonin, Denis P; de Koning, Patrick J H; Nederveen, Aart J; van der Geest, Rob J

2017-10-01

The quantification of vessel wall morphology and plaque burden requires vessel segmentation, which is generally performed by manual delineations. The purpose of our work is to develop and evaluate a new 3D model-based approach for carotid artery wall segmentation from dual-sequence MRI. The proposed method segments the lumen and outer wall surfaces including the bifurcation region by fitting a subdivision surface constructed hierarchical-tree model to the image data. In particular, a hybrid segmentation which combines deformable model fitting with boundary classification was applied to extract the lumen surface. The 3D model ensures the correct shape and topology of the carotid artery, while the boundary classification uses combined image information of 3D TOF-MRA and 3D BB-MRI to promote accurate delineation of the lumen boundaries. The proposed algorithm was validated on 25 subjects (48 arteries) including both healthy volunteers and atherosclerotic patients with 30% to 70% carotid stenosis. For both lumen and outer wall border detection, our result shows good agreement between manually and automatically determined contours, with contour-to-contour distance less than 1 pixel as well as Dice overlap greater than 0.87 at all different carotid artery sections. The presented 3D segmentation technique has demonstrated the capability of providing vessel wall delineation for 3D carotid MRI data with high accuracy and limited user interaction. This brings benefits to large-scale patient studies for assessing the effect of pharmacological treatment of atherosclerosis by reducing image analysis time and bias between human observers. © 2017 American Association of Physicists in Medicine.

Loss of Urinary Macromolecules in Mice Causes Interstitial and Intratubular Renal Calcification Dependent on the Underlying Conditions

NASA Astrophysics Data System (ADS)

Wu, Xue-Ru; Lieske, John C.; Evan, Andrew P.; Sommer, Andre J.; Liaw, Lucy; Mo, Lan

2008-09-01

Urinary protein macromolecules have long been thought to play a role in influencing the various phases of urolithiasis including nucleation, growth, aggregation of mineral crystals and their subsequent adhesion to the renal epithelial cells. However, compelling evidence regarding their precise role was lacking, due partly to the fact that most prior studies were done in vitro and results were highly variable depending on the experimental conditions. The advent of genetic engineering technology has made it possible to study urinary protein macromolecules within an in vivo biological system. Indeed, recent studies have begun to shed light on the net effects of loss of one or more macromolecules on the earliest steps of urolithiasis. This paper focuses on the in vivo consequences of inactivating Tamm-Horsfall protein and/or osteopontin, two major urinary glycoproteins, using the knockout approach. The renal phenotypes of both single and double knockout mice under spontaneous or hyperoxaluric conditions will be described. The functional significance of the urinary macromolecules as critical defense factors against renal calcification will also be discussed.

Solid State Nuclear Magnetic Resonance Studies of the Murchison Organic Macromolecule

NASA Technical Reports Server (NTRS)

Cody, G. D., III; Alexander, C. M. OD.; Tera, F.

2001-01-01

We have used high speed H-1 (DEPTH) and C-13 (VACP MAS-slow spinning) solid state NMR to determine the contributions of protonated vs non-protonated carbon in the Murchison Macromolecule. Additional information is contained in the original extended abstract.

Arachidonic acid with taurine enhances pulmonary absorption of macromolecules without any serious histopathological damages.

PubMed

Miyake, Masateru; Minami, Takanori; Yamazaki, Hiroyuki; Emoto, Chie; Mukai, Tadashi; Toguchi, Hajime

2017-05-01

Therapeutic peptides and protein are being used in several indications; however, their poor permeability still remains to be solved. This study focused on the pulmonary route of macromolecules. First, the effects of arachidonic acid (AA) as an absorption enhancer on drug serum concentration, after intratracheal administration, were investigated in rats. Second, the safety of AA was assessed in rats in an acute toxicity study for 7days. AA enhanced the exposure of both interferon-α (IFN-α) and fluorescein isothiocyanate 4000 (FD-4). In addition, the histopathological analysis indicated that AA caused alveolitis and bronchitis in rats. In combination with Taurine (Tau), these lung injuries were prevented through the histopathological analysis. The combined use of Tau with AA did not show any changes in the pharmacokinetics of FD-4. From these results, we suggest the combined use of AA with Tau as a novel formulation on the pulmonary route of macromolecule drugs. This formulation could improve the bioavailability of macromolecule drugs without any serious local damage to the lungs. Copyright © 2017 Elsevier B.V. All rights reserved.

Newly developed surface coil for endoluminal MRI, depiction of pig gastric wall layers and vascular architecture in ex vivo study.

PubMed

Morita, Yoshinori; Kutsumi, Hiromu; Yoshinaka, Hayato; Matsuoka, Yuichiro; Kuroda, Kagayaki; Gotanda, Masakazu; Sekino, Naomi; Kumamoto, Etsuko; Yoshida, Masaru; Inokuchi, Hideto; Azuma, Takeshi

2009-01-01

The purpose of this study was to visualize the gastric wall layers and to depict the vascular architecture in vitro by using resected porcine stomachs studied with high-spatial resolution magnetic resonance (MR) imaging. Normal dissected porcine stomach samples (n = 4) were examined with a 3 Tesla MR system using a newly developed surface coil. MR images were obtained by the surface coil as receiver and a head coil as transmitter. High-spatial-resolution spin-echo MR images were obtained with a field of view of 8 x 8 cm, a matrix of 256 x 128 and slice thicknesses of 3 and 5 mm. T1 and T2-weighted MR images clearly depicted the normal porcine gastric walls as consisting of four distinct layers. In addition, vascular architectures in proper muscle layers were also visualized, which were confirmed by histological examinations to correspond to blood vessels. High-spatial-resolution MR imaging using a surface coil placed closely to the gastric wall enabled the differentiation of porcine gastric wall layers and the depiction of the blood vessels in proper muscle layer in this experimental study.

The Effect of Hypertension on the Transport of LDL Across the Deformable Arterial Wall

NASA Astrophysics Data System (ADS)

Dabagh, Mahsa; Jalali, Payman

2010-05-01

The influences of increased endothelial cell turnover and deformation of the intima on the transport of low-density lipoprotein (LDL) under hypertension are investigated by applying a multilayered model of aortic wall. The thickness and properties of the endothelium, intima, internal elastic lamina (IEL), and media are affected by the transmural pressure. Navier-Stokes and Brinkman equations are applied for the transport of the transmural flow and the convective-diffusion equation is solved for LDL transport. LDL macromolecules enter the intima through leaky junctions, and then pass through the media layer where they permeate over the surface of smooth muscle cells (SMC). Uptake of LDL by cells is modeled through a uniform reaction evenly distributed in the macroscopically homogeneous media layer. The results show that transmural pressure significantly affects the LDL fluxes across the leaky junction, the intima, fenestral pores in the IEL, and the media layer. Many realistic predictions including the proper magnitudes for the permeability of endothelium and intimal layers, and the hydraulic conductivity of all layers as well as their trends with pressure are predicted by the present model.

Computational Study of Surface Tension and Wall Adhesion Effects on an Oil Film Flow Underneath an Air Boundary Layer

NASA Technical Reports Server (NTRS)

Celic, Alan; Zilliac, Gregory G.

1998-01-01

The fringe-imaging skin friction (FISF) technique, which was originally developed by D. J. Monson and G. G. Mateer at Ames Research Center and recently extended to 3-D flows, is the most accurate skin friction measurement technique currently available. The principle of this technique is that the skin friction at a point on an aerodynamic surface can be determined by measuring the time-rate-of-change of the thickness of an oil drop placed on the surface under the influence of the external air boundary layer. Lubrication theory is used to relate the oil-patch thickness variation to shear stress. The uncertainty of FISF measurements is estimated to be as low as 4 percent, yet little is known about the effects of surface tension and wall adhesion forces on the measured results. A modified version of the free-surface Navier-Stokes solver RIPPLE, developed at Los Alamos National Laboratories, was used to compute the time development of an oil drop on a surface under a simulated air boundary layer. RIPPLE uses the volume of fluid method to track the surface and the continuum surface force approach to model surface tension and wall adhesion effects. The development of an oil drop, over a time period of approximately 4 seconds, was studied. Under the influence of shear imposed by an air boundary layer, the computed profile of the drop rapidly changes from its initial circular-arc shape to a wedge-like shape. Comparison of the time-varying oil-thickness distributions computed using RIPPLE and also computed using a greatly simplified numerical model of an oil drop equation which does not include surface tension and wall adhesion effects) was used to evaluate the effects of surface tension on FISF measurement results. The effects of surface tension were found to be small but not necessarily negligible in some cases.

Mitochondrial transit peptide exhibits cell penetration ability and efficiently delivers macromolecules to mitochondria.

PubMed

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.

Electrochemical synthesis of gold nanoparticles on the surface of multi-walled carbon nanotubes with glassy carbon electrode and their application

NASA Astrophysics Data System (ADS)

Song, Y. Z.; Li, X.; Song, Y.; Cheng, Z. P.; Zhong, H.; Xu, J. M.; Lu, J. S.; Wei, C. G.; Zhu, A. F.; Wu, F. Y.; Xu, J.

2013-01-01

Gold nanoparticles on the surface of multi-walled carbon nanotubes with glassy carbon electrode were prepared using electrochemical synthesis method. The thin films of gold Nanoparticles/multi-walled carbon nanotubes were characterized by scanning electron microscopy, powder X-ray diffraction, and cyclic voltammetry. Electrochemical behavior of adrenaline hydrochloride at gold nanoparticles/multi-walled carbon nanotube modified glassy carbon electrode was investigated. A simple, sensitive, and inexpensive method for determination of adrenaline hydrochloride was proposed.

Direct Observation of Domain-Wall Surface Tension by Deflating or Inflating a Magnetic Bubble

NASA Astrophysics Data System (ADS)

Zhang, Xueying; Vernier, Nicolas; Zhao, Weisheng; Yu, Haiming; Vila, Laurent; Zhang, Yue; Ravelosona, Dafiné

2018-02-01

The surface energy of a magnetic domain wall (DW) strongly affects its static and dynamic behaviors. However, this effect is seldom directly observed, and some of the related phenomena are not well understood. Moreover, a reliable method to quantify the DW surface energy is still absent. Here, we report a series of experiments in which the DW surface energy becomes a dominant parameter. We observe that a semicircular magnetic domain bubble can spontaneously collapse under the Laplace pressure induced by DW surface energy. We further demonstrate that the surface energy can lead to a geometrically induced pinning when the DW propagates in a Hall cross or from a nanowire into a nucleation pad. Based on these observations, we develop two methods to quantify the DW surface energy, which can be very helpful in the estimation of intrinsic parameters such as Dzyaloshinskii-Moriya interactions or exchange stiffness in magnetic ultrathin films.

Development of wall climbing robot

NASA Astrophysics Data System (ADS)

Kojima, Hisao; Toyama, Ryousei; Kobayashi, Kengo

1992-03-01

A configuration design is presented for a wall-climbing robot with high payload which is capable of moving on diversified surfaces of walls including the wall surface to ceilings in every direction. A developed quadruped wall climbing robot, NINJYA-1, is introduced. NINJYA-1 is composed of legs based on a 3D parallel link mechanism and a VM (Valve-regulated Multiple) sucker which will be able to suck even if there are grooves and a small difference in level. A wall climbing robot which supports rescue operation at a high building using a VM sucker is also introduced. Finally, a wall climbing robot named Disk Rover with a disk-type magnetic wheel is shown. The wheel shape is calculated by FEM. The disk-type magnetic wheel has a force three times more powerful than the one heretofore in use.

A film-based wall shear stress sensor for wall-bounded turbulent flows

NASA Astrophysics Data System (ADS)

Amili, Omid; Soria, Julio

2011-07-01

In wall-bounded turbulent flows, determination of wall shear stress is an important task. The main objective of the present work is to develop a sensor which is capable of measuring surface shear stress over an extended region applicable to wall-bounded turbulent flows. This sensor, as a direct method for measuring wall shear stress, consists of mounting a thin flexible film on the solid surface. The sensor is made of a homogeneous, isotropic, and incompressible material. The geometry and mechanical properties of the film are measured, and particles with the nominal size of 11 μm in diameter are embedded on the film's surface to act as markers. An optical technique is used to measure the film deformation caused by the flow. The film has typically deflection of less than 2% of the material thickness under maximum loading. The sensor sensitivity can be adjusted by changing the thickness of the layer or the shear modulus of the film's material. The paper reports the sensor fabrication, static and dynamic calibration procedure, and its application to a fully developed turbulent channel flow at Reynolds numbers in the range of 90,000-130,000 based on the bulk velocity and channel full height. The results are compared to alternative wall shear stress measurement methods.

The Impact of Sonication on the Surface Quality of Single-Walled Carbon Nanotubes.

PubMed

Koh, Byumseok; Cheng, Wei

2015-08-01

Sonication process is regularly adopted for dispersing single-walled carbon nanotubes (SWCNTs) in an aqueous medium. This can be achieved by either covalent functionalization of SWCNTs with strong acid or by noncovalent functionalization using dispersants that adsorb onto the surface of SWCNTs during dispersion. Because the dispersion process is usually performed using sonication, unintentional free radical formation during sonication process may induce covalent modification of SWCNT surface. Herein, we have systematically investigated the status of SWCNT surface modification under various sonication conditions using Raman spectroscopy. Comparing ID /IG (Raman intensities between D and G bands) ratio of SWCNTs under various sonication conditions suggests that typical sonication conditions (1-6 h bath sonication with sonication power between 3 and 80 W) in aqueous media do not induce covalent modification of SWCNT surface. In addition, we confirm that SWCNT dispersion with single-stranded DNA (ssDNA) involves noncovalent adsorption of ssDNA onto the surface of SWCNTs, but not covalent linkage between ssDNA and SWCNT surface. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Smooth deuterated cellulose films for the visualisation of adsorbed bio-macromolecules

PubMed Central

Su, Jielong; Raghuwanshi, Vikram S.; Raverty, Warwick; Garvey, Christopher J.; Holden, Peter J.; Gillon, Marie; Holt, Stephen A.; Tabor, Rico; Batchelor, Warren; Garnier, Gil

2016-01-01

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. PMID:27796332

Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition.

PubMed

Rivera-Sánchez, María Del C; García-Arriaga, Marilyn; Hobley, Gerard; Morales-de-Echegaray, Ana V; Rivera, José M

2017-10-31

Most drugs are small molecules because of their attractive pharmacokinetics, manageable development and manufacturing, and effective binding into the concave crevices of bio-macromolecules. Despite these features, they often fall short when it comes to effectively recognizing the surfaces of bio-macromolecules. One way to overcome the challenge of biomolecular surface recognition is to develop small molecules that become self-assembled ligands (SALs) prior to binding. Herein, we report SALs made from 8-aryl-2'-deoxyguanosine derivatives forming precise hydrophilic supramolecular G-quadruplexes (SGQs) with excellent size, shape, and charge complementarity to G-quadruplex DNA (QDNA). We show that only those compounds forming SGQs act as SALs, which in turn differentially stabilize QDNAs from selected oncogene promoters and the human telomeric regions. Fluorescence resonance energy-transfer melting assays are consistent with spectroscopic, calorimetric, and light scattering studies, showing the formation of a "sandwichlike" complex QDNA·SGQ·QDNA. These results open the door for the advent of SALs that recognize QDNAs and potentially the surfaces of other bio-macromolecules such as proteins.

β-(1,3)-Glucan Unmasking in Some Candida albicans Mutants Correlates with Increases in Cell Wall Surface Roughness and Decreases in Cell Wall Elasticity

DOE PAGES

Hasim, Sahar; Allison, David P.; Retterer, Scott T.; ...

2016-11-14

Candida albicans is among the most common human fungal pathogens, causing a broad range of infections, including life-threatening systemic infections. The cell wall of C. albicans is the interface between the fungus and the innate immune system. The cell wall is composed of an outer layer enriched in mannosylated glycoproteins (mannan) and an inner layer enriched in β-(1,3)-glucan and chitin. Detection of C. albicans by Dectin-1, a C-type signaling lectin specific for β-(1,3)-glucan, is important for the innate immune system to recognize systemic fungal infections. Increased exposure of β-(1,3)-glucan to the immune system occurs when the mannan layer is alteredmore » or removed in a process called unmasking. Nanoscale changes to the cell wall during unmasking were explored in this paper in live cells with atomic force microscopy (AFM). Two mutants, the cho1Δ/Δ and kre5Δ/Δ mutants, were selected as representatives that exhibit modest and strong unmasking, respectively. Comparisons of the cho1Δ/Δ and kre5Δ/Δ mutants to the wild type reveal morphological changes in their cell walls that correlate with decreases in cell wall elasticity. In addition, AFM tips functionalized with Dectin-1 revealed that the forces of binding of Dectin-1 to all of the strains were similar, but the frequency of binding was highest for the kre5Δ/Δ mutant, decreased for the cho1Δ/Δ mutant, and rare for the wild type. These data show that nanoscale changes in surface topology are correlated with increased Dectin-1 adhesion and decreased cell wall elasticity. Finally, AFM, using tips functionalized with immunologically relevant molecules, can map epitopes of the cell wall and increase our understanding of pathogen recognition by the immune system.« less

β-(1,3)-Glucan Unmasking in Some Candida albicans Mutants Correlates with Increases in Cell Wall Surface Roughness and Decreases in Cell Wall Elasticity

PubMed Central

Hasim, Sahar; Allison, David P.; Retterer, Scott T.; Hopke, Alex; Wheeler, Robert T.; Doktycz, Mitchel J.

2016-01-01

ABSTRACT Candida albicans is among the most common human fungal pathogens, causing a broad range of infections, including life-threatening systemic infections. The cell wall of C. albicans is the interface between the fungus and the innate immune system. The cell wall is composed of an outer layer enriched in mannosylated glycoproteins (mannan) and an inner layer enriched in β-(1,3)-glucan and chitin. Detection of C. albicans by Dectin-1, a C-type signaling lectin specific for β-(1,3)-glucan, is important for the innate immune system to recognize systemic fungal infections. Increased exposure of β-(1,3)-glucan to the immune system occurs when the mannan layer is altered or removed in a process called unmasking. Nanoscale changes to the cell wall during unmasking were explored in live cells with atomic force microscopy (AFM). Two mutants, the cho1Δ/Δ and kre5Δ/Δ mutants, were selected as representatives that exhibit modest and strong unmasking, respectively. Comparisons of the cho1Δ/Δ and kre5Δ/Δ mutants to the wild type reveal morphological changes in their cell walls that correlate with decreases in cell wall elasticity. In addition, AFM tips functionalized with Dectin-1 revealed that the forces of binding of Dectin-1 to all of the strains were similar, but the frequency of binding was highest for the kre5Δ/Δ mutant, decreased for the cho1Δ/Δ mutant, and rare for the wild type. These data show that nanoscale changes in surface topology are correlated with increased Dectin-1 adhesion and decreased cell wall elasticity. AFM, using tips functionalized with immunologically relevant molecules, can map epitopes of the cell wall and increase our understanding of pathogen recognition by the immune system. PMID:27849179

β-(1,3)-Glucan Unmasking in Some Candida albicans Mutants Correlates with Increases in Cell Wall Surface Roughness and Decreases in Cell Wall Elasticity

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

Hasim, Sahar; Allison, David P.; Retterer, Scott T.

Candida albicans is among the most common human fungal pathogens, causing a broad range of infections, including life-threatening systemic infections. The cell wall of C. albicans is the interface between the fungus and the innate immune system. The cell wall is composed of an outer layer enriched in mannosylated glycoproteins (mannan) and an inner layer enriched in β-(1,3)-glucan and chitin. Detection of C. albicans by Dectin-1, a C-type signaling lectin specific for β-(1,3)-glucan, is important for the innate immune system to recognize systemic fungal infections. Increased exposure of β-(1,3)-glucan to the immune system occurs when the mannan layer is alteredmore » or removed in a process called unmasking. Nanoscale changes to the cell wall during unmasking were explored in this paper in live cells with atomic force microscopy (AFM). Two mutants, the cho1Δ/Δ and kre5Δ/Δ mutants, were selected as representatives that exhibit modest and strong unmasking, respectively. Comparisons of the cho1Δ/Δ and kre5Δ/Δ mutants to the wild type reveal morphological changes in their cell walls that correlate with decreases in cell wall elasticity. In addition, AFM tips functionalized with Dectin-1 revealed that the forces of binding of Dectin-1 to all of the strains were similar, but the frequency of binding was highest for the kre5Δ/Δ mutant, decreased for the cho1Δ/Δ mutant, and rare for the wild type. These data show that nanoscale changes in surface topology are correlated with increased Dectin-1 adhesion and decreased cell wall elasticity. Finally, AFM, using tips functionalized with immunologically relevant molecules, can map epitopes of the cell wall and increase our understanding of pathogen recognition by the immune system.« less

Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering.

PubMed

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.

Evanescent wave cavity ring-down spectroscopy (EW-CRDS) as a probe of macromolecule adsorption kinetics at functionalized interfaces.

PubMed

O'Connell, Michael A; de Cuendias, Anne; Gayet, Florence; Shirley, Ian M; Mackenzie, Stuart R; Haddleton, David M; Unwin, Patrick R

2012-05-01

Evanescent wave cavity ring-down spectroscopy (EW-CRDS) has been employed to study the interfacial adsorption kinetics of coumarin-tagged macromolecules onto a range of functionalized planar surfaces. Such studies are valuable in designing polymers for complex systems where the degree of interaction between the polymer and surface needs to be tailored. Three tagged synthetic polymers with different functionalities are examined: poly(acrylic acid) (PAA), poly(3-sulfopropyl methacrylate, potassium salt) (PSPMA), and a mannose-modified glycopolymer. Adsorption transients at the silica/water interface are found to be characteristic for each polymer, and kinetics are deduced from the initial rates. The chemistry of the adsorption interfaces has been varied by, first, manipulation of silica surface chemistry via the bulk pH, followed by surfaces modified by poly(L-glutamic acid) (PGA) and cellulose, giving five chemically different surfaces. Complementary atomic force microscopy (AFM) imaging has been used for additional surface characterization of adsorbed layers and functionalized interfaces to allow adsorption rates to be interpreted more fully. Adsorption rates for PSPMA and the glycopolymer are seen to be highly surface sensitive, with significantly higher rates on cellulose-modified surfaces, whereas PAA shows a much smaller rate dependence on the nature of the adsorption surface.

Microwave background distortions from domain walls

NASA Technical Reports Server (NTRS)

Goetz, Guenter; Noetzold, Dirk

1990-01-01

Domain walls arising in a cosmic phase transition after decoupling were recently proposed as seeds for the formation of large scale structure. The distortion induced in the microwave background radiation is calculated in dependence of the wall thickness, surface density, scalar field potential, cosmic redshift and the velocity of the wall. It was found that the maximal redshift distortion for both spherical and planar walls is of the order pi G sigma H(sup -1)(sub 0), where sigma is the surface energy density and H(sup -1)(sub 0) the Hubble parameter. It was also found that, for a wall thickness smaller than the horizon, walls can be treated as infinitely thin, i.e., the redshift distortion is independent of the wall thickness and the specific form of the scalar potential. For planar walls moving with a Lorentz-factor gamma the redshift distortion is enhanced by gamma cubed.

Screening for Glycosylphosphatidylinositol-Modified Cell Wall Proteins in Pichia pastoris and Their Recombinant Expression on the Cell Surface

PubMed Central

Zhang, Li; Liang, Shuli; Zhou, Xinying; Jin, Zi; Jiang, Fengchun; Han, Shuangyan; Zheng, Suiping

2013-01-01

Glycosylphosphatidylinositol (GPI)-anchored glycoproteins have various intrinsic functions in yeasts and different uses in vitro. In the present study, the genome of Pichia pastoris GS115 was screened for potential GPI-modified cell wall proteins. Fifty putative GPI-anchored proteins were selected on the basis of (i) the presence of a C-terminal GPI attachment signal sequence, (ii) the presence of an N-terminal signal sequence for secretion, and (iii) the absence of transmembrane domains in mature protein. The predicted GPI-anchored proteins were fused to an alpha-factor secretion signal as a substitute for their own N-terminal signal peptides and tagged with the chimeric reporters FLAG tag and mature Candida antarctica lipase B (CALB). The expression of fusion proteins on the cell surface of P. pastoris GS115 was determined by whole-cell flow cytometry and immunoblotting analysis of the cell wall extracts obtained by β-1,3-glucanase digestion. CALB displayed on the cell surface of P. pastoris GS115 with the predicted GPI-anchored proteins was examined on the basis of potential hydrolysis of p-nitrophenyl butyrate. Finally, 13 proteins were confirmed to be GPI-modified cell wall proteins in P. pastoris GS115, which can be used to display heterologous proteins on the yeast cell surface. PMID:23835174

Combined effects of suction/injection and wall surface curvature on natural convection flow in a vertical micro-porous annulus

NASA Astrophysics Data System (ADS)

Jha, B. K.; Aina, B.; Muhammad, S. A.

2015-03-01

This study investigates analytically the hydrodynamic and thermal behaviour of a fully developed natural convection flow in a vertical micro-porous-annulus (MPA) taking into account the velocity slip and temperature jump at the outer surface of inner porous cylinder and inner surface of outer porous cylinder. A closed — form solution is presented for velocity, temperature, volume flow rate, skin friction and rate of heat transfer expressed as a Nusselt number. The influence of each governing parameter on hydrodynamic and thermal behaviour is discussed with the aid of graphs. During the course of investigation, it is found that as suction/injection on the cylinder walls increases, the fluid velocity and temperature is enhanced. In addition, it is observed that wall surface curvature has a significant effect on flow and thermal characteristics.

Effect of Osmolytes on the Conformational Behavior of a Macromolecule in a Cytoplasm-like Crowded Environment: A Femtosecond Mid-IR Pump-Probe Spectroscopy Study.

PubMed

Kundu, Achintya; Verma, Pramod Kumar; Cho, Minhaeng

2018-02-15

Osmolytes found endogenously in almost all living beings play an important role in regulating cell volume under harsh environment. Here, to address the longstanding questions about the underlying mechanism of osmolyte effects, we use femtosecond mid-IR pump-probe spectroscopy with two different IR probes that are the OD stretching mode of HDO and the azido stretching mode of azido-derivatized poly(ethylene glycol) dimethyl ether (PEGDME). Our experimental results show that protecting osmolytes bind strongly with water molecules and dehydrate polymer surface, which results in promoting intramolecular interactions of the polymer. By contrast, urea behaves like water molecules without significantly disrupting water H-bonding network and favors extended and random-coil segments of the polymer chain by directly participating in solvation of the polymer. Our findings highlight the importance of direct interaction between urea and macromolecule, while protecting osmolytes indirectly affect the macromolecule through enhancing the water-osmolyte interaction in a crowded environment, which is the case that is often encountered in real biological systems.

Multimodal optical measurement in vitro of surface deformations and wall thickness of the pressurized aortic arch

NASA Astrophysics Data System (ADS)

Genovese, Katia; Humphrey, Jay D.

2015-04-01

Computational modeling of arterial mechanics continues to progress, even to the point of allowing the study of complex regions such as the aortic arch. Nevertheless, most prior studies assign homogeneous and isotropic material properties and constant wall thickness even when implementing patient-specific luminal geometries obtained from medical imaging. These assumptions are not due to computational limitations, but rather to the lack of spatially dense sets of experimental data that describe regional variations in mechanical properties and wall thickness in such complex arterial regions. In this work, we addressed technical challenges associated with in vitro measurement of overall geometry, full-field surface deformations, and regional wall thickness of the porcine aortic arch in its native anatomical configuration. Specifically, we combined two digital image correlation-based approaches, standard and panoramic, to track surface geometry and finite deformations during pressurization, with a 360-deg fringe projection system to contour the outer and inner geometry. The latter provided, for the first time, information on heterogeneous distributions of wall thickness of the arch and associated branches in the unloaded state. Results showed that mechanical responses vary significantly with orientation and location (e.g., less extensible in the circumferential direction and with increasing distance from the heart) and that the arch exhibits a nearly linear increase in pressure-induced strain up to 40%, consistent with other findings on proximal porcine aortas. Thickness measurements revealed strong regional differences, thus emphasizing the need to include nonuniform thicknesses in theoretical and computational studies of complex arterial geometries.

Controlled method of reducing electrophoretic mobility of macromolecules, particles, or cells

NASA Technical Reports Server (NTRS)

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.

Plant cell wall extensibility: connecting plant cell growth with cell wall structure, mechanics, and the action of wall-modifying enzymes

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

Cosgrove, Daniel J.

The advent of user-friendly instruments for measuring force/deflection curves of plant surfaces at high spatial resolution has resulted in a recent outpouring of reports of the ‘Young's modulus’ of plant cell walls. The stimulus for these mechanical measurements comes from biomechanical models of morphogenesis of meristems and other tissues, as well as single cells, in which cell wall stress feeds back to regulate microtubule organization, auxin transport, cellulose deposition, and future growth directionality. In this article I review the differences between elastic modulus and wall extensibility in the context of cell growth. Some of the inherent complexities, assumptions, and potentialmore » pitfalls in the interpretation of indentation force/deflection curves are discussed. Reported values of elastic moduli from surface indentation measurements appear to be 10- to >1000-fold smaller than realistic tensile elastic moduli in the plane of plant cell walls. Potential reasons for this disparity are discussed, but further work is needed to make sense of the huge range in reported values. The significance of wall stress relaxation for growth is reviewed and connected to recent advances and remaining enigmas in our concepts of how cellulose, hemicellulose, and pectins are assembled to make an extensible cell wall. A comparison of the loosening action of α-expansin and Cel12A endoglucanase is used to illustrate two different ways in which cell walls may be made more extensible and the divergent effects on wall mechanics.« less

Stiffness Matrix of Thin-Walled Open Bar Subject to Bending, Bending Torsion and Shift of Cross Section Middle Surface

NASA Astrophysics Data System (ADS)

Panasenko, N. N.; Sinelschikov, A. V.

2017-11-01

One of the main stages in the analysis of complex 3D structures and engineering constructions made of thin-walled open bars using FEM is a stiffness matrix developing. Taking into account middle surface shear deformation caused by the work of tangential stresses in the formula to calculate a potential energy of thin-walled open bars, the authors obtain an important correction at calculation of the bar deformation and fundamental frequencies. The results of the analysis of the free end buckling of a cantilever H-bar under plane bending differ from exact solution by 0.53%. In the course of comparison of the obtained results with the cantilever bar buckling regardless the middle surface shear deformation, an increase made 16.6%. The stiffness matrix of a thin-walled open bar developed in the present work can be integrated into any software suite using FEM for the analysis of complex 3-D structures and engineering constructions with n-freedoms.

Formation and characterization of calcium orthophosphates in the presence of two different acidic macromolecules

NASA Astrophysics Data System (ADS)

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.

Quantification of in vivo short echo-time proton magnetic resonance spectra at 14.1 T using two different approaches of modelling the macromolecule spectrum

NASA Astrophysics Data System (ADS)

Cudalbu, C.; Mlynárik, V.; Xin, L.; Gruetter, Rolf

2009-10-01

Reliable quantification of the macromolecule signals in short echo-time 1H MRS spectra is particularly important at high magnetic fields for an accurate quantification of metabolite concentrations (the neurochemical profile) due to effectively increased spectral resolution of the macromolecule components. The purpose of the present study was to assess two approaches of quantification, which take the contribution of macromolecules into account in the quantification step. 1H spectra were acquired on a 14.1 T/26 cm horizontal scanner on five rats using the ultra-short echo-time SPECIAL (spin echo full intensity acquired localization) spectroscopy sequence. Metabolite concentrations were estimated using LCModel, combined with a simulated basis set of metabolites using published spectral parameters and either the spectrum of macromolecules measured in vivo, using an inversion recovery technique, or baseline simulated by the built-in spline function. The fitted spline function resulted in a smooth approximation of the in vivo macromolecules, but in accordance with previous studies using Subtract-QUEST could not reproduce completely all features of the in vivo spectrum of macromolecules at 14.1 T. As a consequence, the measured macromolecular 'baseline' led to a more accurate and reliable quantification at higher field strengths.

Solid-state NMR investigations of cellulose structure and interactions with matrix polysaccharides in plant primary cell walls.

PubMed

Wang, Tuo; Hong, Mei

2016-01-01

Until recently, the 3D architecture of plant cell walls was poorly understood due to the lack of high-resolution techniques for characterizing the molecular structure, dynamics, and intermolecular interactions of the wall polysaccharides in these insoluble biomolecular mixtures. We introduced multidimensional solid-state NMR (SSNMR) spectroscopy, coupled with (13)C labelling of whole plants, to determine the spatial arrangements of macromolecules in near-native plant cell walls. Here we review key evidence from 2D and 3D correlation NMR spectra that show relatively few cellulose-hemicellulose cross peaks but many cellulose-pectin cross peaks, indicating that cellulose microfibrils are not extensively coated by hemicellulose and all three major polysaccharides exist in a single network rather than two separate networks as previously proposed. The number of glucan chains in the primary-wall cellulose microfibrils has been under active debate recently. We show detailed analysis of quantitative (13)C SSNMR spectra of cellulose in various wild-type (WT) and mutant Arabidopsis and Brachypodium primary cell walls, which consistently indicate that primary-wall cellulose microfibrils contain at least 24 glucan chains. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

[Glycoproteins of mucus of gastric and duodenal wall surface during ulcerogenesis and the impact of fenugreek].

PubMed

Khil'ko, T D; Iakubtsova, I V; Preobrazhens'ka, T D; Ostapchenko, L I

2013-01-01

The comparative evaluation of qualitative and quantitative composition of glycoproteins of gastric and duodenal wall surface layer of protective mucus in the normal, at the modeling of ulcers in rats and at the introduction to animals with ulcerative lesions of fenugreek extract carried out. It was shown in control (normally) the general level of glycosylation of glycoproteins gastric mucus is 1.7 times more than the duodenum. Under acute stress model ulceration in the stomach mucus decrease in hexosamine (1.4 times), galactose (2.2 times), fucose (1.3-fold) and an increase in NANA (3.6 times) observed. Under cysteamine model ulceration in duodenal mucus increase galactose (2.7 times), NANA (2.4 times), fucose (1.8-fold) but significant decrease in the amount of hexosamines 3 times compared to the control occurred. It was proved the protective effect of fenugreek extract to the wall surface mucus of the stomach and duodenum mucosa under conditions modeling ulceration in rats.

Textural break foundation wall construction modules

DOEpatents

Phillips, Steven J.

1990-01-01

Below-grade, textural-break foundation wall structures are provided for inhibiting diffusion and advection of liquids and gases into and out from a surrounding hydrogeologic environment. The foundation wall structure includes a foundation wall having an interior and exterior surface and a porous medium disposed around a portion of the exterior surface. The structure further includes a modular barrier disposed around a portion of the porous medium. The modular barrier is substantially removable from the hydrogeologic environment.

The renal excretion and retention of macromolecules: The chemical structure effect.

PubMed

Rypácek, F; Drobník, J; Chmelar, V; Kálal, J

1982-01-01

Five derivatives of polyaspartamide were used as macromolecular models to study the effect of chemical structure of macromolecules on their renal excretion and retention. The parent polymer was formed solely by N(2-hydroxyethyl)aspartamide units (I) and in its derivatives about 20% of 2-hydroxyethyl groups were randomly replaced by either n-butyl- (II), 2(4-hydroxyphenyl)ethyl- (III, N- dimethylamino propyl- (IV) or the aspartamide unit was modified to free aspartic acid carboxyl (V). The rate of clearance from the serum, the deposition in the kidney tissue in comparison with the deposition in reticuloendothelial system organs-liver and spleen, as well as tissue and cellular localisation of deposits were studied on rabbits and mice taking advantage of fluorescence labelling. The clearance of macromolecular models from the serum compartment by the glomerular filtration is mainly molecular weight controlled, while the retention of macromolecules possessing the same molecular weight by the kidney tubular epithelium is strongly affected chemical modification. About thirty and hundred times higher retentions due to reabsorption in proximal tubule were found with macromolecular models II and III respectively.

Adsorption of Wine Constituents on Functionalized Surfaces.

PubMed

Mierczynska-Vasilev, Agnieszka; Smith, Paul A

2016-10-18

The adsorption of macromolecules on solid surfaces is of great importance in the field of nanotechnology, biomaterials, biotechnological, and food processes. In the field of oenology adsorption of wine macromolecules such as polyphenols, polysaccharides, and proteins is much less desirable on membrane materials because of fouling and reduced filtering performance. On the other hand, adsorption of these molecules on processing aids is very beneficial for achieving wine clarity and stability. In this article, the effect of surface chemical functionalities on the adsorption of white, rosé, and red wine constituents was evaluated. Allylamine, acrylic acid, and ethanol were selected as precursors for plasma polymerization in order to generate coatings rich in amine, carboxyl, and hydroxyl chemical groups, respectively. The surface chemical functionalities were characterized by X-ray photoelectron spectroscopy (XPS) and the ability of different surface chemical functionalities to adsorb wine constituents were characterized by quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy (AFM). The results demonstrated that the amine and carboxyl modified surfaces encourage adsorption of constituents from white wine. The hydroxyl modified surfaces have the ability to preferentially adsorb rosé wine constituents, whereas red wine adsorbed to the highest extent on acrylic acid surface.

Simple quantification of surface carboxylic acids on chemically oxidized multi-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Gong, Hyejin; Kim, Seong-Taek; Lee, Jong Doo; Yim, Sanggyu

2013-02-01

The surface of multi-walled carbon nanotube (MWCNT) was chemically oxidized using nitric acid and sulfuric-nitric acid mixtures. Thermogravimetric analysis, transmission electron microscopy and infrared spectroscopy revealed that the use of acid mixtures led to higher degree of oxidation. More quantitative identification of surface carboxylic acids was carried out using X-ray photoelectron spectroscopy (XPS) and acid-base titration. However, these techniques are costly and require very long analysis times to promptly respond to the extent of the reaction. We propose a much simpler method using pH measurements and pre-determined pKa value in order to estimate the concentration of carboxylic acids on the oxidized MWCNT surfaces. The results from this technique were consistent with those obtained from XPS and titration, and it is expected that this simple quantification method can provide a cheap and fast way to monitor and control the oxidation reaction of MWCNT.

Mechanics of the Adhesive Properties of Ivy Nanoparticles

DTIC Science & Technology

2013-11-21

macromolecule with multiple physiological functions in the growth of plants, such as signaling, cell wall plasticizer, guiding pollen tube growth, and many...others. The AGPs on the stigma surface were believed to act as an adhesive base for pollens , indicating the adhesion function that AGPs play in plants

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

EPA Science Inventory

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...

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

ERIC Educational Resources Information Center

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)

Penetrative Internal Oxidation from Alloy 690 Surfaces and Stress Corrosion Crack Walls during Exposure to PWR Primary Water

NASA Astrophysics Data System (ADS)

Olszta, Matthew J.; Schreiber, Daniel K.; Thomas, Larry E.; Bruemmer, Stephen M.

Analytical electron microscopy and three-dimensional atom probe tomography (ATP) examinations of surface and near-surface oxidation have been performed on Ni-30%Cr alloy 690 materials after exposure to high-temperature, simulated PWR primary water. The oxidation nanostructures have been characterized at crack walls after stress-corrosion crack growth tests and at polished surfaces of unstressed specimens for the same alloys. Localized oxidation was discovered for both crack walls and surfaces as continuous filaments (typically <10 nm in diameter) extending from the water interface into the alloy 690 matrix reaching depths of 500 nm. These filaments consisted of discrete, plate-shaped Cr2O3 particles surrounded by a distribution of nanocrystalline, rock-salt (Ni-Cr-Fe) oxide. The oxide-containing filament depth was found to increase with exposure time and, at longer times, the filaments became very dense at the surface leaving only isolated islands of metal. Individual dislocations were oxidized in non-deformed materials, while the oxidation path appeared to be along more complex dislocation substructures in heavily deformed materials. This paper will highlight the use of high resolution scanning and transmission electron microscopy in combination with APT to better elucidate the microstructure and microchemistry of the filamentary oxidation.

Membrane-active macromolecules kill antibiotic-tolerant bacteria and potentiate antibiotics towards Gram-negative bacteria

PubMed Central

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.

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. PMID:28837596

Multifunctional gadolinium-based dendritic macromolecules as liver targeting imaging probes.

PubMed

Luo, Kui; Liu, Gang; He, Bin; Wu, Yao; Gong, Qingyong; Song, Bin; Ai, Hua; Gu, Zhongwei

2011-04-01

The quest for highly efficient and safe contrast agents has become the key factor for successful application of magnetic resonance imaging (MRI). The gadolinium (Gd) based dendritic macromolecules, with precise and tunable nanoscopic sizes, are excellent candidates as multivalent MRI probes. In this paper, a novel series of Gd-based multifunctional peptide dendritic probes (generation 2, 3, and 4) possessing highly controlled structures and single molecular weight were designed and prepared as liver MRI probes. These macromolecular Gd-ligand agents exhibited up to 3-fold increase in T(1) relaxivity comparing to Gd-DTPA complexes. No obvious in vitro cytotoxicity was observed from the measured concentrations. These dendritic probes were further functionalized with multiple galactosyl moieties and led to much higher cell uptake in vitro as demonstrated in T(1)-weighted scans. During in vivo animal studies, the probes provided better signal intensity (SI) enhancement in mouse liver, especially at 60 min post-injection, with the most efficient enhancement from the galactosyl moiety decorated third generation dendrimer. The imaging results were verified with analysis of Gd content in liver tissues. The design strategy of multifunctional Gd-ligand peptide dendritic macromolecules in this study may be used for developing other sensitive MRI probes with targeting capability. Copyright © 2011 Elsevier Ltd. All rights reserved.

Plant cell wall extensibility: connecting plant cell growth with cell wall structure, mechanics, and the action of wall-modifying enzymes.

PubMed

Cosgrove, Daniel J

2016-01-01

The advent of user-friendly instruments for measuring force/deflection curves of plant surfaces at high spatial resolution has resulted in a recent outpouring of reports of the 'Young's modulus' of plant cell walls. The stimulus for these mechanical measurements comes from biomechanical models of morphogenesis of meristems and other tissues, as well as single cells, in which cell wall stress feeds back to regulate microtubule organization, auxin transport, cellulose deposition, and future growth directionality. In this article I review the differences between elastic modulus and wall extensibility in the context of cell growth. Some of the inherent complexities, assumptions, and potential pitfalls in the interpretation of indentation force/deflection curves are discussed. Reported values of elastic moduli from surface indentation measurements appear to be 10- to >1000-fold smaller than realistic tensile elastic moduli in the plane of plant cell walls. Potential reasons for this disparity are discussed, but further work is needed to make sense of the huge range in reported values. The significance of wall stress relaxation for growth is reviewed and connected to recent advances and remaining enigmas in our concepts of how cellulose, hemicellulose, and pectins are assembled to make an extensible cell wall. A comparison of the loosening action of α-expansin and Cel12A endoglucanase is used to illustrate two different ways in which cell walls may be made more extensible and the divergent effects on wall mechanics. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Improved data visualization techniques for analyzing macromolecule structural changes.

PubMed

Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

2012-10-01

The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. Copyright © 2012 The Protein Society.

Improved data visualization techniques for analyzing macromolecule structural changes

PubMed Central

Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

2012-01-01

The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. PMID:22898970

Explicit Solvent Simulations of Friction between Brush Layers of Charged and Neutral Bottle-Brush Macromolecules

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

Carrillo, Jan-Michael; Brown, W Michael; Dobrynin, Andrey

2012-01-01

We study friction between charged and neutral brush layers of bottle-brush macromolecules using molecular dynamics simulations. In our simulations the solvent molecules were treated explicitly. The deformation of the bottle-brush macromolecules under the shear were studied as a function of the substrate separation and shear stress. For charged bottle-brush layers we study effect of the added salt on the brush lubricating properties to elucidate factors responsible for energy dissipation in charged and neutral brush systems. Our simulations have shown that for both charged and neutral brush systems the main deformation mode of the bottle-brush macromolecule is associated with the backbonemore » deformation. This deformation mode manifests itself in the backbone deformation ratio, , and shear viscosity, , to be universal functions of the Weissenberg number W. The value of the friction coefficient, , and viscosity, , are larger for the charged bottle-brush coatings in comparison with those for neutral brushes at the same separation distance, D, between substrates. The additional energy dissipation generated by brush sliding in charged bottle-brush systems is due to electrostatic coupling between bottle-brush and counterion motion. This coupling weakens as salt concentration, cs, increases resulting in values of the viscosity, , and friction coefficient, , approaching corresponding values obtained for neutral brush systems.« less

Wave propagation in fluid-conveying viscoelastic single-walled carbon nanotubes with surface and nonlocal effects

NASA Astrophysics Data System (ADS)

Zhen, Ya-Xin

2017-02-01

In this paper, the transverse wave propagation in fluid-conveying viscoelastic single-walled carbon nanotubes is investigated based on nonlocal elasticity theory with consideration of surface effect. The governing equation is formulated utilizing nonlocal Euler-Bernoulli beam theory and Kelvin-Voigt model. Explicit wave dispersion relation is developed and wave phase velocities and frequencies are obtained. The effect of the fluid flow velocity, structural damping, surface effect, small scale effects and tube diameter on the wave propagation properties are discussed with different wave numbers. The wave frequency increases with the increase of fluid flow velocity, but decreases with the increases of tube diameter and wave number. The effect of surface elasticity and residual surface tension is more significant for small wave number and tube diameter. For larger values of wave number and nonlocal parameters, the real part of frequency ratio raises.

Surface tailored single walled carbon nanotubes as catalyst support for direct methanol fuel cell

NASA Astrophysics Data System (ADS)

Kireeti, Kota V. M. K.; Jha, Neetu

2017-10-01

A strategy for tuning the surface property of Single Walled Carbon Nanotubes (SWNTs) for enhanced methanol oxidation reaction (MOR) and oxygen reduction reaction (ORR) along with methanol tolerance is presented. The surface functionality is tailored using controlled acid and base treatment. Acid treatment leads to the attachment of carboxylic carbon (CC) fragments to SWNT making it hydrophilic (P3-SWNT). Base treatment of P3-SWNT with 0.05 M NaOH reduces the CCs and makes it hydrophobic (P33-SWNT). Pt catalyst supported on the P3-SWNT possesses enhanced MOR whereas that supported on P33-SWNT not only enhances ORR kinetics but also possess good tolerance towards methanol oxidation as verified by the electrochemical technique.

Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

PubMed

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.

Comparison of gold nanoparticle mediated photoporation: vapor nanobubbles outperform direct heating for delivering macromolecules in live cells.

PubMed

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.

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

NASA Astrophysics Data System (ADS)

Marazzi, Marco; Gattuso, Hugo; Monari, Antonio; Assfeld, Xavier

2018-04-01

Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes – often drugs or pollutants – that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/ molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.

Validating metal binding sites in macromolecule structures using the CheckMyMetal web server

PubMed Central

Zheng, Heping; Chordia, Mahendra D.; Cooper, David R.; Chruszcz, Maksymilian; Müller, Peter; Sheldrick, George M.

2015-01-01

Metals play vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules where metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal binding environments. The "CheckMyMetal" (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal binding sites in macromolecular structures in respect to 7350 metal binding sites observed in a benchmark dataset of 2304 high resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal binding sites and alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the anticipated results section. CMM was designed for a broad audience—biomedical researchers studying metal-containing proteins and nucleic acids—but is equally well suited for structural biologists to validate new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure modeled with a few hundred amino acids. PMID:24356774

Scale resolving computation of submerged wall jets on flat wall with different roughness heights

NASA Astrophysics Data System (ADS)

Paik, Joongcheol; Bombardelli, Fabian

2014-11-01

Scale-adaptive simulation is used to investigate the response of velocity and turbulence in submerged wall jets to abrupt changes from smooth to rough beds. The submerged wall jets were experimentally investigated by Dey and Sarkar [JFM, 556, 337, 2006] at the Reynolds number of 17500 the Froude number of 4.09 and the submergence ratio of 1.12 on different rough beds that were generated by uniform sediments of different median diameters The SAS is carried out by means of a second-order-accurate finite volume method in space and time and the effect of bottom roughness is treated by the approach of Cebeci (2004). The evolution of free surface is captured by employing the two-phase volume of fluid (VOF) technique. The numerical results obtained by the SAS approach, incorporated with the VOF and the rough wall treatment, are in good agreement with the experimental measurements. The computed turbulent boundary layer grows more quickly and the depression of the free surface is more increased on the rough wall than those on smooth wall. The size of the fully developed zone shrinks and the decay rate of maximum streamwise velocity and Reynolds stress components are faster with increase in the wall roughness. Supported by NSF and NRF of Korea.

Vapor Wall Deposition in Chambers: Theoretical Considerations

NASA Astrophysics Data System (ADS)

McVay, R.; Cappa, C. D.; Seinfeld, J.

2014-12-01

In order to constrain the effects of vapor wall deposition on measured secondary organic aerosol (SOA) yields in laboratory chambers, Zhang et al. (2014) varied the seed aerosol surface area in toluene oxidation and observed a clear increase in the SOA yield with increasing seed surface area. Using a coupled vapor-particle dynamics model, we examine the extent to which this increase is the result of vapor wall deposition versus kinetic limitations arising from imperfect accommodation of organic species into the particle phase. We show that a seed surface area dependence of the SOA yield is present only when condensation of vapors onto particles is kinetically limited. The existence of kinetic limitation can be predicted by comparing the characteristic timescales of gas-phase reaction, vapor wall deposition, and gas-particle equilibration. The gas-particle equilibration timescale depends on the gas-particle accommodation coefficient αp. Regardless of the extent of kinetic limitation, vapor wall deposition depresses the SOA yield from that in its absence since vapor molecules that might otherwise condense on particles deposit on the walls. To accurately extrapolate chamber-derived yields to atmospheric conditions, both vapor wall deposition and kinetic limitations must be taken into account.

Significance of wall structure, macromolecular composition, and surface polymers to the survival and transport of Cryptosporidium parvum Oocysts

USDA-ARS?s Scientific Manuscript database

The structure and composition of the oocyst wall are primary factors determining the survival of Cryptosporidium parvum oocysts outside the host. An external polymer matrix (glycocalyx) may mediate interactions with environmental surfaces and, thus, affect the transport of oocysts in water, soil, an...

Macromolecule exchange in Cuscuta-host plant interactions.

PubMed

Kim, Gunjune; Westwood, James H

2015-08-01

Cuscuta species (dodders) are parasitic plants that are able to grow on many different host plants and can be destructive to crops. The connections between Cuscuta and its hosts allow movement of not only water and small nutrients, but also macromolecules including mRNA, proteins and viruses. Recent studies show that RNAs move bidirectionally between hosts and parasites and involve a large number of different genes. Although the function of mobile mRNAs has not been demonstrated in this system, small RNAs are also transmitted and a silencing construct expressed in hosts is able to affect expression of the target gene in the parasite. High throughput sequencing of host-parasite associations has the potential to greatly accelerate understanding of this remarkable interaction. Copyright © 2015 Elsevier Ltd. All rights reserved.

A comparison RSM and ANN surface roughness models in thin-wall machining of Ti6Al4V using vegetable oils under MQL-condition

NASA Astrophysics Data System (ADS)

Mohruni, Amrifan Saladin; Yanis, Muhammad; Sharif, Safian; Yani, Irsyadi; Yuliwati, Erna; Ismail, Ahmad Fauzi; Shayfull, Zamree

2017-09-01

Thin-wall components as usually applied in the structural parts of aeronautical industry require significant challenges in machining. Unacceptable surface roughness can occur during machining of thin-wall. Titanium product such Ti6Al4V is mostly applied to get the appropriate surface texture in thin wall designed requirements. In this study, the comparison of the accuracy between Response Surface Methodology (RSM) and Artificial Neural Networks (ANN) in the prediction of surface roughness was conducted. Furthermore, the machining tests were carried out under Minimum Quantity Lubrication (MQL) using AlCrN-coated carbide tools. The use of Coconut oil as cutting fluids was also chosen in order to evaluate its performance when involved in end milling. This selection of cutting fluids is based on the better performance of oxidative stability than that of other vegetable based cutting fluids. The cutting speed, feed rate, radial and axial depth of cut were used as independent variables, while surface roughness is evaluated as the dependent variable or output. The results showed that the feed rate is the most significant factors in increasing the surface roughness value followed by the radial depth of cut and lastly the axial depth of cut. In contrary, the surface becomes smoother with increasing the cutting speed. From a comparison of both methods, the ANN model delivered a better accuracy than the RSM model.

Achieving more efficient operation of the nozzle vane and rotor blade rows of gas turbines through using nonaxisymmetric end wall surfaces of interblade channels

NASA Astrophysics Data System (ADS)

Inozemtsev, A. A.; Samokhvalov, N. Yu.; Tikhonov, A. S.

2012-09-01

Results from a numerical study of three versions of the end-wall generatrix of the interblade channel used in the second-stage nozzle vanes of a prospective engine's turbine are presented. Recommendations for designing nonaxisymmetric end-wall surfaces are suggested based on the obtained data.

Wall thickness measuring method and apparatus

DOEpatents

Salzer, Leander J.; Bergren, Donald A.

1989-01-01

An apparatus for measuring the wall thickness of a nonmagnetic article having a housing supporting a magnet and a contiguous supporting surface. The tubular article and the housing are releasably secured to the supporting surface and a support member of an optical comparator, respectively. To determine the wall thickness of the article at a selected point, a magnetically responsive ball is positioned within the tubular article over said point and retained therein by means of a magnetic field produced by the magnet. Thereafter, an optical comparator is employed to project a magnified image of the ball on a screen and the wall thickness at the selected point is calculated by using a ball surface measurement taken with the comparator in conjunction with a previously determined base line measurement.

Wall thickness measuring method and apparatus

DOEpatents

Salzer, L.J.; Bergren, D.A.

1987-10-06

An apparatus for measuring the wall thickness of a nonmagnetic article having a housing supporting a magnet and a contiguous supporting surface. The tubular article and the housing are releasably secured to the supporting surface and a support member of an optical comparator, respectively. To determine the wall thickness of the article at a selected point, a magnetically responsive ball is positioned within the tubular article over said point and retained therein by means of a magnetic field produced by the magnet. Thereafter, an optical comparator is employed to project a magnified image of the ball on a screen and the wall thickness at the selected point is calculated by using a ball surface measurement taken with the comparator in conjunction with a previously determined base line measurement.

Fluorescence Approaches to Growing Macromolecule Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc; Forsythe, Elizabeth; Achari, Aniruddha

2006-01-01

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

Spectroscopic investigation confirms retaining the pristine nature of single-walled carbon nanotubes on dissolution in aniline

NASA Astrophysics Data System (ADS)

Singha, Somdutta; Ghosh, Swapankumar

2017-09-01

Carbon nanotubes in all forms are very much insoluble in both organic and inorganic solvents due to its high agglomeration and entangled morphology. General methods for dissolution of single-walled carbon nanotubes (SWNTs) are mostly associated with complexation or polymerization or addition of macromolecules which change the physical or chemical properties of SWNTs and the pristine nature of SWNTs is lost. Dissolution of SWNTs in a solvent like aniline is practiced here which is a very simple reaction method. Here aniline is capable to form a SWNT-aniline charge transfer complex without attachment of macromolecules or polymer which is also soluble in other organic solvents. Solvation of SWNTs by this method is also capable of maintaining the similarity between the structure of SWNTs before and after the dissolution, which means that the pristine nature of SWNTs is preserved. Formation of charge transfer complex in this reaction has been proven by UV-Vis/NIR absorption and photoluminescence spectroscopy. Raman spectroscopy and electron microscopy (FESEM and TEM) are the evidences for protection of the pristine nature of SWNTs even after high-temperature complexation reaction with aniline and also after solubilization in organic solvents.

β-1,6-glucan synthesis-associated genes are required for proper spore wall formation in Saccharomyces cerevisiae.

PubMed

Pan, Hua-Ping; Wang, Ning; Tachikawa, Hiroyuki; Nakanishi, Hideki; Gao, Xiao-Dong

2017-11-01

The yeast spore wall is an excellent model to study the assembly of an extracellular macromolecule structure. In the present study, mutants defective in β-1,6-glucan synthesis, including kre1∆, kre6∆, kre9∆ and big1∆, were sporulated to analyse the effect of β-1,6-glucan defects on the spore wall. Except for kre6∆, these mutant spores were sensitive to treatment with ether, suggesting that the mutations perturb the integrity of the spore wall. Morphologically, the mutant spores were indistinguishable from wild-type spores. They lacked significant sporulation defects partly because the chitosan layer, which covers the glucan layer, compensated for the damage. The proof for this model was obtained from the effect of the additional deletion of CHS3 that resulted in the absence of the chitosan layer. Among the double mutants, the most severe spore wall deficiency was observed in big1∆ spores. The majority of the big1∆chs3∆ mutants failed to form visible spores at a higher temperature. Given that the big1∆ mutation caused a failure to attach a GPI-anchored reporter, Cwp2-GFP, to the spore wall, β-1,6-glucan is involved in tethering of GPI-anchored proteins in the spore wall as well as in the vegetative cell wall. Thus, β-1,6-glucan is required for proper organization of the spore wall. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Regulation of Cell Wall Biogenesis in Saccharomyces cerevisiae: The Cell Wall Integrity Signaling Pathway

PubMed Central

Levin, David E.

2011-01-01

The yeast cell wall is a strong, but elastic, structure that is essential not only for the maintenance of cell shape and integrity, but also for progression through the cell cycle. During growth and morphogenesis, and in response to environmental challenges, the cell wall is remodeled in a highly regulated and polarized manner, a process that is principally under the control of the cell wall integrity (CWI) signaling pathway. This pathway transmits wall stress signals from the cell surface to the Rho1 GTPase, which mobilizes a physiologic response through a variety of effectors. Activation of CWI signaling regulates the production of various carbohydrate polymers of the cell wall, as well as their polarized delivery to the site of cell wall remodeling. This review article centers on CWI signaling in Saccharomyces cerevisiae through the cell cycle and in response to cell wall stress. The interface of this signaling pathway with other pathways that contribute to the maintenance of cell wall integrity is also discussed. PMID:22174182

Wall teichoic acids prevent antibody binding to epitopes within the cell wall of Staphylococcus aureus.

PubMed

Gautam, Samir; Kim, Taehan; Lester, Evan; Deep, Deeksha; Spiegel, David A

2016-01-15

Staphylococcus aureus is a Gram-positive bacterial pathogen that produces a range of infections including cellulitis, pneumonia, and septicemia. The principle mechanism in antistaphylococcal host defense is opsonization with antibodies and complement proteins, followed by phagocytic clearance. Here we use a previously developed technique for installing chemical epitopes in the peptidoglycan cell wall to show that surface glycopolymers known as wall teichoic acids conceal cell wall epitopes, preventing their recognition and opsonization by antibodies. Thus, our results reveal a previously unrecognized immunoevasive role for wall teichoic acids in S. aureus: repulsion of peptidoglycan-targeted antibodies.

Interstitial distribution of charged macromolecules in the dog lung: a kinetic model.

PubMed

Parker, J C; Miniati, M; Pitt, R; Taylor, A E

1987-01-01

A mathematic model was constructed to investigate conflicting physiologic data concerning the charge effect of continuous capillaries to macromolecules in the lung. We simulated the equilibration kinetics of lactate dehydrogenase (MR 4.2 nM) isozymes LDH 1 (pI = 5.0) and LDH 5 (pI = 7.9) between plasma and lymph using previously measured permeability coefficients, lung tissue distribution volumes (VA) and plasma concentrations (CP) in lung tissue. Our hypothesis is that the fixed anionic charges in interstitium, basement membrane, and cell surfaces determine equilibration rather than charged membrane effects at the capillary barrier, so the same capillary permeability coefficients were used for both isozymes. Capillary filtration rates and protein fluxes were calculated using conventional flux equations. Initial conditions at baseline and increased left atrial pressures (PLA) were those measured in animal studies. Simulated equilibration of isozymes over 30 h in the model at baseline capillary pressures accurately predicted the observed differences in lymph/plasma concentration ratios (CL/CP) between isotopes at 4 h and equilibration of these ratios at 24 h. Quantitative prediction of isozyme CL/CP ratios was also obtained at increased PLA. However, an additional cation selective compartment representing the surface glycocalyx was required to accurately simulate the initial higher transcapillary clearances of cationic LDH 5. Thus experimental data supporting the negative barrier, positive barrier, and no charge barrier hypotheses were accurately reproduced by the model using only the observed differences in interstitial partitioning of isozymes without differences in capillary selectivity.

Food macromolecule based nanodelivery systems for enhancing the bioavailability of polyphenols.

PubMed

Hu, Bing; Liu, Xixia; Zhang, Chunlan; Zeng, Xiaoxiong

2017-01-01

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. Copyright © 2016. Published by Elsevier B.V.

Interspecies scaling and prediction of human clearance: comparison of small- and macro-molecule drugs

PubMed Central

Huh, Yeamin; Smith, David E.; Feng, Meihau Rose

2014-01-01

Human clearance prediction for small- and macro-molecule drugs was evaluated and compared using various scaling methods and statistical analysis.Human clearance is generally well predicted using single or multiple species simple allometry for macro- and small-molecule drugs excreted renally.The prediction error is higher for hepatically eliminated small-molecules using single or multiple species simple allometry scaling, and it appears that the prediction error is mainly associated with drugs with low hepatic extraction ratio (Eh). The error in human clearance prediction for hepatically eliminated small-molecules was reduced using scaling methods with a correction of maximum life span (MLP) or brain weight (BRW).Human clearance of both small- and macro-molecule drugs is well predicted using the monkey liver blood flow method. Predictions using liver blood flow from other species did not work as well, especially for the small-molecule drugs. PMID:21892879

Study of Unsteady Flows with Concave Wall Effect

NASA Technical Reports Server (NTRS)

Wang, Chi R.

2003-01-01

This paper presents computational fluid dynamic studies of the inlet turbulence and wall curvature effects on the flow steadiness at near wall surface locations in boundary layer flows. The time-stepping RANS numerical solver of the NASA Glenn-HT RANS code and a one-equation turbulence model, with a uniform inlet turbulence modeling level of the order of 10 percent of molecular viscosity, were used to perform the numerical computations. The approach was first calibrated for its predictabilities of friction factor, velocity, and temperature at near surface locations within a transitional boundary layer over concave wall. The approach was then used to predict the velocity and friction factor variations in a boundary layer recovering from concave curvature. As time iteration proceeded in the computations, the computed friction factors converged to their values from existing experiments. The computed friction factors, velocity, and static temperatures at near wall surface locations oscillated periodically in terms of time iteration steps and physical locations along the span-wise direction. At the upstream stations, the relationship among the normal and tangential velocities showed vortices effects on the velocity variations. Coherent vortices effect on the velocity components broke down at downstream stations. The computations also predicted the vortices effects on the velocity variations within a boundary layer flow developed along a concave wall surface with a downstream recovery flat wall surface. It was concluded that the computational approach might have the potential to analyze the flow steadiness in a turbine blade flow.

Rigidity of Glasses and Macromolecules

NASA Astrophysics Data System (ADS)

Thorpe, M. F.

1998-03-01

The simple yet powerful ideas of percolation theory have found their way into many different areas of research. In this talk we show how RIGIDITY PERCOLATION can be studied at a similar level of sophistication, using a powerful new program THE PEBBLE GAME (D. J. Jacobs and M. F. Thorpe, Phys. Rev. E) 53, 3682 (1996). that uses an integer algorithm. This program can analyse the rigidity of two and three dimensional networks containing more than one million bars and joints. We find the total number of floppy modes, and find the critical behavior as the network goes from floppy to rigid as more bars are added. We discuss the relevance of this work to network glasses, and how it relates to experiments that involve the mechanical properties like hardness and elasticity of covalent glassy networks like Ge_xAs_ySe_1-x-y and dicuss recent experiments that suggest that the rigidity transition may be first order (Xingwei Feng, W. J.Bresser and P. Boolchand, Phys. Rev. Lett 78), 4422 (1997).. This approach is also useful in macromolecules and proteins, where detailed information about the rigid domain structure can be obtained.

Investigation into the influence of laser energy input on selective laser melted thin-walled parts by response surface method

NASA Astrophysics Data System (ADS)

Liu, Yang; Zhang, Jian; Pang, Zhicong; Wu, Weihui

2018-04-01

Selective laser melting (SLM) provides a feasible way for manufacturing of complex thin-walled parts directly, however, the energy input during SLM process, namely derived from the laser power, scanning speed, layer thickness and scanning space, etc. has great influence on the thin wall's qualities. The aim of this work is to relate the thin wall's parameters (responses), namely track width, surface roughness and hardness to the process parameters considered in this research (laser power, scanning speed and layer thickness) and to find out the optimal manufacturing conditions. Design of experiment (DoE) was used by implementing composite central design to achieve better manufacturing qualities. Mathematical models derived from the statistical analysis were used to establish the relationships between the process parameters and the responses. Also, the effects of process parameters on each response were determined. Then, a numerical optimization was performed to find out the optimal process set at which the quality features are at their desired values. Based on this study, the relationship between process parameters and SLMed thin-walled structure was revealed and thus, the corresponding optimal process parameters can be used to manufactured thin-walled parts with high quality.

Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses

DOE PAGES

Nafisi, Majse; Stranne, Maria; Fimognari, Lorenzo; ...

2015-07-22

Here we report that the epidermis on leaves protects plants from pathogen invasion and provides a waterproof barrier. It consists of a layer of cells that is surrounded by thick cell walls, which are partially impregnated by highly hydrophobic cuticular components. We show that the Arabidopsis T-DNA insertion mutants of REDUCED WALL ACETYLATION 2 (rwa2), previously identified as having reduced O-acetylation of both pectins and hemicelluloses, exhibit pleiotrophic phenotype on the leaf surface. The cuticle layer appeared diffused and was significantly thicker and underneath cell wall layer was interspersed with electron-dense deposits. A large number of trichomes were collapsed andmore » surface permeability of the leaves was enhanced in rwa2 as compared to the wild type. A massive reprogramming of the transcriptome was observed in rwa2 as compared to the wild type, including a coordinated up-regulation of genes involved in responses to abiotic stress, particularly detoxification of reactive oxygen species and defense against microbial pathogens (e.g., lipid transfer proteins, peroxidases). In accordance, peroxidase activities were found to be elevated in rwa2 as compared to the wild type. These results indicate that cell wall acetylation is essential for maintaining the structural integrity of leaf epidermis, and that reduction of cell wall acetylation leads to global stress responses in Arabidopsis.« less

Comparative inhalation toxicity of multi-wall carbon nanotubes, graphene, graphite nanoplatelets and low surface carbon black

PubMed Central

2013-01-01

Background Carbon nanotubes, graphene, graphite nanoplatelets and carbon black are seemingly chemically identical carbon-based nano-materials with broad technological applications. Carbon nanotubes and carbon black possess different inhalation toxicities, whereas little is known about graphene and graphite nanoplatelets. Methods In order to compare the inhalation toxicity of the mentioned carbon-based nanomaterials, male Wistar rats were exposed head-nose to atmospheres of the respective materials for 6 hours per day on 5 consecutive days. Target concentrations were 0.1, 0.5, or 2.5 mg/m3 for multi-wall carbon nanotubes and 0.5, 2.5, or 10 mg/m3 for graphene, graphite nanoplatelets and low-surface carbon black. Toxicity was determined after end of exposure and after three-week recovery using broncho-alveolar lavage fluid and microscopic examinations of the entire respiratory tract. Results No adverse effects were observed after inhalation exposure to 10 mg/m3 graphite nanoplatelets or relatively low specific surface area carbon black. Increases of lavage markers indicative for inflammatory processes started at exposure concentration of 0.5 mg/m3 for multi-wall carbon nanotubes and 10 mg/m3 for graphene. Consistent with the changes in lavage fluid, microgranulomas were observed at 2.5 mg/m3 multi-wall carbon nanotubes and 10 mg/m3 graphene. In order to evaluate volumetric loading of the lung as the key parameter driving the toxicity, deposited particle volume was calculated, taking into account different methods to determine the agglomerate density. However, the calculated volumetric load did not correlate to the toxicity, nor did the particle surface burden of the lung. Conclusions The inhalation toxicity of the investigated carbon-based materials is likely to be a complex interaction of several parameters. Until the properties which govern the toxicity are identified, testing by short-term inhalation is the best option to identify hazardous properties in

Comparative inhalation toxicity of multi-wall carbon nanotubes, graphene, graphite nanoplatelets and low surface carbon black.

PubMed

Ma-Hock, Lan; Strauss, Volker; Treumann, Silke; Küttler, Karin; Wohlleben, Wendel; Hofmann, Thomas; Gröters, Sibylle; Wiench, Karin; van Ravenzwaay, Bennard; Landsiedel, Robert

2013-06-17

Carbon nanotubes, graphene, graphite nanoplatelets and carbon black are seemingly chemically identical carbon-based nano-materials with broad technological applications. Carbon nanotubes and carbon black possess different inhalation toxicities, whereas little is known about graphene and graphite nanoplatelets. In order to compare the inhalation toxicity of the mentioned carbon-based nanomaterials, male Wistar rats were exposed head-nose to atmospheres of the respective materials for 6 hours per day on 5 consecutive days. Target concentrations were 0.1, 0.5, or 2.5 mg/m3 for multi-wall carbon nanotubes and 0.5, 2.5, or 10 mg/m3 for graphene, graphite nanoplatelets and low-surface carbon black. Toxicity was determined after end of exposure and after three-week recovery using broncho-alveolar lavage fluid and microscopic examinations of the entire respiratory tract. No adverse effects were observed after inhalation exposure to 10 mg/m3 graphite nanoplatelets or relatively low specific surface area carbon black. Increases of lavage markers indicative for inflammatory processes started at exposure concentration of 0.5 mg/m3 for multi-wall carbon nanotubes and 10 mg/m3 for graphene. Consistent with the changes in lavage fluid, microgranulomas were observed at 2.5 mg/m3 multi-wall carbon nanotubes and 10 mg/m3 graphene. In order to evaluate volumetric loading of the lung as the key parameter driving the toxicity, deposited particle volume was calculated, taking into account different methods to determine the agglomerate density. However, the calculated volumetric load did not correlate to the toxicity, nor did the particle surface burden of the lung. The inhalation toxicity of the investigated carbon-based materials is likely to be a complex interaction of several parameters. Until the properties which govern the toxicity are identified, testing by short-term inhalation is the best option to identify hazardous properties in order to avoid unsafe applications or select

The surface chemical properties of multi-walled carbon nanotubes modified by thermal fluorination for electric double-layer capacitor

NASA Astrophysics Data System (ADS)

Jung, Min-Jung; Jeong, Euigyung; Lee, Young-Seak

2015-08-01

The surfaces of multi-walled carbon nanotubes (MWCNTs) were thermally fluorinated at various temperatures to enhance the electrochemical properties of the MWCNTs for use as electric double-layer capacitor (EDLC) electrodes. The fluorine functional groups were added to the surfaces of the MWCNTs via thermal fluorination. The thermal fluorination exposed the Fe catalyst on MWCNTs, and the specific surface area increased due to etching during the fluorination. The specific capacitances of the thermally fluorinated at 100 °C, MWCNT based electrode increased from 57 to 94 F/g at current densities of 0.2 A/g, respectively. This enhancement in capacitance can be attributed to increased polarization of the thermally fluorinated MWCNT surface, which increased the affinity between the electrode surface and the electrolyte ions.

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

PubMed

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. Copyright © 2015 Elsevier B.V. All rights reserved.

Capturing strain localization behind a geosynthetic-reinforced soil wall

NASA Astrophysics Data System (ADS)

Lai, Timothy Y.; Borja, Ronaldo I.; Duvernay, Blaise G.; Meehan, Richard L.

2003-04-01

This paper presents the results of finite element (FE) analyses of shear strain localization that occurred in cohesionless soils supported by a geosynthetic-reinforced retaining wall. The innovative aspects of the analyses include capturing of the localized deformation and the accompanying collapse mechanism using a recently developed embedded strong discontinuity model. The case study analysed, reported in previous publications, consists of a 3.5-m tall, full-scale reinforced wall model deforming in plane strain and loaded by surcharge at the surface to failure. Results of the analysis suggest strain localization developing from the toe of the wall and propagating upward to the ground surface, forming a curved failure surface. This is in agreement with a well-documented failure mechanism experienced by the physical wall model showing internal failure surfaces developing behind the wall as a result of the surface loading. Important features of the analyses include mesh sensitivity studies and a comparison of the localization properties predicted by different pre-localization constitutive models, including a family of three-invariant elastoplastic constitutive models appropriate for frictional/dilatant materials. Results of the analysis demonstrate the potential of the enhanced FE method for capturing a collapse mechanism characterized by the presence of a failure, or slip, surface through earthen materials.

Modeling shape and topology of low-resolution density maps of biological macromolecules.

PubMed Central

De-Alarcón, Pedro A; Pascual-Montano, Alberto; Gupta, Amarnath; Carazo, Jose M

2002-01-01

In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory. PMID:12124252

Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Pusheng; Asher, Sanford A.

1999-01-01

The separation of macromolecules such as polymers and DNA by means of electrophoresis, gel permeation chromatography or filtration exploits size-dependent differences in the time it takes for the molecules to migrate through a random porous network. Transport through the gel matrices, which usually consist of full swollen crosslinked polymers, depends on the relative size of the macromolecule compared with the pore radius. Sufficiently small molecules are thought to adopt an approximately spherical conformation when diffusing through the gel matrix, whereas larger ones are forced to migrate in a snake-like fashion. Molecules of intermediate size, however, can get temporarily trapped in the largest pores of the matrix, where the molecule can extend and thus maximize its conformational entropy. This `entropic trapping' is thought to increase the dependence of diffusion rate on molecular size. Here we report the direct experimental verification of this phenomenon. Bragg diffraction from a hydrogel containing a periodic array of monodisperse water voids confirms that polymers of different weights partition between the hydrogel matrix and the water voids according to the predictions of the entropic trapping theory. Our approach might also lead to the design of improved separation media based on entropic trapping.

Diffusion profile of macromolecules within and between human skin layers for (trans)dermal drug delivery.

PubMed

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.

The role of Listeria monocytogenes cell wall surface anchor protein LapB in virulence, adherence, and intracellular replication

USDA-ARS?s Scientific Manuscript database

Lmof2365_2117 is a Listeria monocytogenes putative cell wall surface anchor protein with a conserved domain found in collagen binding proteins. We constructed a deletion mutation in lmof2365_2117 in serotype 4b strain F2365, evaluated its virulence, and determined its ability to adhere and invade co...

Post-cast EDM method for reducing the thickness of a turbine nozzle wall

DOEpatents

Jones, Raymond Joseph; Bojappa, Parvangada Ganapathy; Kirkpatrick, Francis Lawrence; Schotsch, Margaret Jones; Rajan, Rajiv; Wei, Bin

2002-01-01

A post-cast EDM process is used to remove material from the interior surface of a nozzle vane cavity of a turbine. A thin electrode is passed through the cavity between opposite ends of the nozzle vane and displaced along the interior nozzle wall to remove the material along a predetermined path, thus reducing the thickness of the wall between the cavity and the external surface of the nozzle. In another form, an EDM process employing a profile as an electrode is disposed in the cavity and advanced against the wall to remove material from the wall until the final wall thickness is achieved, with the interior wall surface being complementary to the profile surface.

Fucosylated chondroitin sulfate is covalently associated with collagen fibrils in sea cucumber Apostichopus japonicus body wall.

PubMed

Wang, Jun; Chang, Yaoguang; Wu, Fanxiu; Xu, Xiaoqi; Xue, Changhu

2018-04-15

Fucosylated chondroitin sulfate (fCS) is the major carbohydrate constituent of sea cucumber. However, the distribution of fCS in the sea cucumber body wall has not been fully described. We addressed this in the present study employing Apostichopus japonicus as the material, a sea cucumber species with significant commercial importance. It was found that fCS was covalently attached to collagen fibrils via O-glycosidic linkages. Transmission electron microscopy analysis revealed that fCS precipitate was present in gap regions of collagen fibrils as roughly globular or ellipsoidal dots. The fCS dots arranged circumferentially around the fibrils with an axial repeat period that matched the periodicity of the fibrils. Physicochemical analysis indicated that the presence of fCS significantly increased the negative charge of the fibrils. These findings provide novel insight into fCS distribution in the sea cucumber body wall and its supramolecular organization with other macromolecules. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Versatile Technique for the In Vivo Imaging of Human Tumor Xenografts Using Near-Infrared Fluorochrome-Conjugated Macromolecule Probes

PubMed Central

Suemizu, Hiroshi; Kawai, Kenji; Higuchi, Yuichiro; Hashimoto, Haruo; Ogura, Tomoyuki; Itoh, Toshio; Sasaki, Erika; Nakamura, Masato

2013-01-01

Here, we present a versatile method for detecting human tumor xenografts in vivo, based on the enhanced permeability and retention (EPR) effect, using near-infrared (NIR) fluorochrome-conjugated macromolecule probes. Bovine serum albumin (BSA) and two immunoglobulins—an anti-human leukocyte antigen (HLA) monoclonal antibody and isotype control IgG2a—were labeled with XenoLight CF770 fluorochrome and used as NIR-conjugated macromolecule probes to study whole-body imaging in a variety of xenotransplantation mouse models. NIR fluorescent signals were observed in subcutaneously transplanted BxPC-3 (human pancreatic cancer) cells and HCT 116 (colorectal cancer) cells within 24 h of NIR-macromolecule probe injection, but the signal from the fluorochrome itself or from the NIR-conjugated small molecule (glycine) injection was not observed. The accuracy of tumor targeting was confirmed by the localization of the NIR-conjugated immunoglobulin within the T-HCT 116 xenograft (in which the orange-red fluorescent protein tdTomato was stably expressed by HCT 116 cells) in the subcutaneous transplantation model. However, there was no significant difference in the NIR signal intensity of the region of interest between the anti-HLA antibody group and the isotype control group in the subcutaneous transplantation model. Therefore, the antibody accumulation within the tumor in vivo is based on the EPR effect. The liver metastasis generated by an intrasplenic injection of T-HCT 116 cells was clearly visualized by the NIR-conjugated anti-HLA probe but not by the orange-red fluorescent signal derived from the tdTomato reporter. This result demonstrated the superiority of the NIR probes over the tdTomato reporter protein at enhancing tissue penetration. In another xenograft model, patient-derived xenografts (PDX) of LC11-JCK (human non-small cell lung cancer) were successfully visualized using the NIR-conjugated macromolecule probe without any genetic modification. These results

Nano-Welding of Multi-Walled Carbon Nanotubes on Silicon and Silica Surface by Laser Irradiation.

PubMed

Yuan, Yanping; Chen, Jimin

2016-02-24

In this study, a continuous fiber laser (1064 nm wavelength, 30 W/cm²) is used to irradiate multi-walled carbon nanotubes (MWCNTs) on different substrate surfaces. Effects of substrates on nano-welding of MWCNTs are investigated by scanning electron microscope (SEM). For MWCNTs on silica, after 3 s irradiation, nanoscale welding with good quality can be achieved due to breaking C-C bonds and formation of new graphene layers. While welding junctions can be formed until 10 s for the MWCNTs on silicon, the difference of irradiation time to achieve welding is attributed to the difference of thermal conductivity for silica and silicon. As the irradiation time is prolonged up to 12.5 s, most of the MWCNTs are welded to a silicon substrate, which leads to their frameworks of tube walls on the silicon surface. This is because the accumulation of absorbed energy makes the temperature rise. Then chemical reactions among silicon, carbon and nitrogen occur. New chemical bonds of Si-N and Si-C achieve the welding between the MWCNTs and silicon. Vibration modes of Si₃N₄ appear at peaks of 363 cm -1 and 663 cm -1 . There are vibration modes of SiC at peaks of 618 cm -1 , 779 cm -1 and 973 cm -1 . The experimental observation proves chemical reactions and the formation of Si₃N₄ and SiC by laser irradiation.

The Draft Genome of the Invasive Walking Stick, Medauroidea extradendata, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea

PubMed Central

Brand, Philipp; Lin, Wei; Johnson, Brian R.

2018-01-01

Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components. PMID:29588379

Wall conditioning in ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Rohde, V.; Dux, R.; Kallenbach, A.; Krieger, K.; Neu, R.; ASDEX Upgrade Team

2007-06-01

An overview on wall conditioning in ASDEX Upgrade is presented. Helium glow discharges (HeGD) are needed mostly for plasma start up after high density discharges, disruptions and disruption mitigation gas puffs. Boronisation is routinely applied. The reduction of the oxygen content is a minor effect. Strong variation of the wall pumping is observed for tungsten first wall materials. The uncoated tungsten surface stores and releases large amounts of He, which can disturb the plasma. The released He causes the modification in the wall pumping. By reducing HeGD this effect could be minimized. Advanced and natural density scenarios are sensitive to the status of the wall coating. Accumulation of impurities at the pedestal influences the ELM frequency and finally causes radiation unstable discharges.

Surface-enhanced Raman scattering on single-wall carbon nanotubes.

PubMed

Kneipp, Katrin; Kneipp, Harald; Dresselhaus, Mildred S; Lefrant, Serge

2004-11-15

Exploiting the effect of surface-enhanced Raman scattering (SERS), the Raman signal of single-wall carbon nanotubes (SWNTs) can be enhanced by up to 14 orders of magnitude when the tubes are in contact with silver or gold nanostructures and Raman scattering takes place predominantly in the enhanced local optical fields of the nanostructures. Such a level of enhancement offers exciting opportunities for ultrasensitive Raman studies on SWNTs and allows resonant and non-resonant Raman experiments to be done on single SWNTs at relatively high signal levels. Since the optical fields are highly localized within so-called "hot spots" on fractal silver colloidal clusters, lateral confinement of the Raman scattering can be as small as 5 nm, allowing spectroscopic selection of a single nanotube from a larger population. Moreover, since SWNTs are very stable "artificial molecules" with a high aspect ratio and a strong electron-phonon coupling, they are unique "test molecules" for investigating the SERS effect itself and for probing the "electromagnetic field contribution" and "charge transfer contribution" to the effect. SERS is also a powerful tool for monitoring the "chemical" interaction between the nanotube and the metal nanostructure.

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

ERIC Educational Resources Information Center

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…

Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution.

PubMed

Jelsch, C

2001-09-01

The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 A resolution, the elements are reduced by two orders of magnitude for distances above 1.5 A. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.

Analysis of a dusty wall jet

NASA Technical Reports Server (NTRS)

Lim, Hock-Bin; Roberts, Leonard

1991-01-01

An analysis is given for the entrainment of dust into a turbulent radial wall jet. Equations are solved based on incompressible flow of a radial wall jet into which dust is entrained from the wall and transported by turbulent diffusion and convection throughout the flow. It is shown that the resulting concentration of dust particles in the flow depends on the difference between the applied shear stress at the surface and the maximum level of shear stress that the surface can withstand (varies as rho(sub d)a(sub g)D) i.e., the pressure due to the weight of a single layer of dust. The analysis is expected to have application to the downflow that results from helicopter and VTOL aircraft.

Plasma Surface Interactions Common to Advanced Fusion Wall Materials and EUV Lithography - Lithium and Tin

NASA Astrophysics Data System (ADS)

Ruzic, D. N.; Alman, D. A.; Jurczyk, B. E.; Stubbers, R.; Coventry, M. D.; Neumann, M. J.; Olczak, W.; Qiu, H.

2004-09-01

Advanced plasma facing components (PFCs) are needed to protect walls in future high power fusion devices. In the semiconductor industry, extreme ultraviolet (EUV) sources are needed for next generation lithography. Lithium and tin are candidate materials in both areas, with liquid Li and Sn plasma material interactions being critical. The Plasma Material Interaction Group at the University of Illinois is leveraging liquid metal experimental and computational facilities to benefit both fields. The Ion surface InterAction eXperiment (IIAX) has measured liquid Li and Sn sputtering, showing an enhancement in erosion with temperature for light ion bombardment. Surface Cleaning of Optics by Plasma Exposure (SCOPE) measures erosion and damage of EUV mirror samples, and tests cleaning recipes with a helicon plasma. The Flowing LIquid surface Retention Experiment (FLIRE) measures the He and H retention in flowing liquid metals, with retention coefficients varying between 0.001 at 500 eV to 0.01 at 4000 eV.

Mass Transport of Macromolecules within an In Vitro Model of Supragingival Plaque

PubMed Central

Thurnheer, Thomas; Gmür, Rudolf; Shapiro, Stuart; Guggenheim, Bernhard

2003-01-01

The aim of this study was to examine the diffusion of macromolecules through an in vitro biofilm model of supragingival plaque. Polyspecies biofilms containing Actinomyces naeslundii, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus sobrinus, Veillonella dispar, and Candida albicans were formed on sintered hydroxyapatite disks and then incubated at room temperature for defined periods with fluorescent markers with molecular weights ranging from 3,000 to 900,000. Subsequent examination by confocal laser scanning microscopy revealed that the mean square penetration depths for all tested macromolecules except immunoglobulin M increased linearly with time, diffusion coefficients being linearly proportional to the cube roots of the molecular weights of the probes (range, 10,000 to 240,000). Compared to diffusion in bulk water, diffusion in the biofilms was markedly slower. The rate of diffusion for each probe appeared to be constant and not a function of biofilm depth. Analysis of diffusion phenomena through the biofilms suggested tortuosity as the most probable explanation for retarded diffusion. Selective binding of probes to receptors present in the biofilms could not explain the observed extent of retardation of diffusion. These results are relevant to oral health, as selective attenuated diffusion of fermentable carbohydrates and acids produced within dental plaque is thought to be essential for the development of carious lesions. PMID:12620862

A dural lymphatic vascular system that drains brain interstitial fluid and macromolecules

PubMed Central

Aspelund, Aleksanteri; Antila, Salli; Proulx, Steven T.; Karlsen, Tine Veronica; Karaman, Sinem; Detmar, Michael; Wiig, Helge

2015-01-01

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. PMID:26077718

A dural lymphatic vascular system that drains brain interstitial fluid and macromolecules.

PubMed

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. © 2015 Aspelund et al.

Ultrasensitive Detection of Single-Walled Carbon Nanotubes Using Surface Plasmon Resonance.

PubMed

Jang, Daeho; Na, Wonhwi; Kang, Minwook; Kim, Namjoon; Shin, Sehyun

2016-01-05

Because single-walled carbon nanotubes (SWNTs) are known to be a potentially dangerous material, inducing cancers and other diseases, any possible leakage of SWNTs through an aquatic medium such as drinking water will result in a major public threat. To solve this problem, for the present study, a highly sensitive, quantitative detection method of SWNTs in an aqueous solution was developed using surface plasmon resonance (SPR) spectroscopy. For a highly sensitive and specific detection, a strong affinity conjugation with biotin-streptavidin was adopted on an SPR sensing mechanism. During the pretreatment process, the SWNT surface was functionalized and hydrophilized using a thymine-chain based biotinylated single-strand DNA linker (B-ssDNA) and bovine serum albumin (BSA). The pretreated SWNTs were captured on a sensing film, the surface of which was immobilized with streptavidin on biotinylated gold film. The captured SWNTs were measured in real-time using SPR spectroscopy. Specific binding with SWNTs was verified through several validation experiments. The present method using an SPR sensor is capable of detecting SWNTs of as low as 100 fg/mL, which is the lowest level reported thus far for carbon-nanotube detection. In addition, the SPR sensor showed a linear characteristic within the range of 100 pg/mL to 200 ng/mL. These findings imply that the present SPR sensing method can detect an extremely low level of SWNTs in an aquatic environment with high sensitivity and high specificity, and thus any potential leakage of SWNTs into an aquatic environment can be precisely monitored within a couple of hours.

Poiseuille, thermal transpiration and Couette flows of a rarefied gas between plane parallel walls with nonuniform surface properties in the transverse direction and their reciprocity relations

NASA Astrophysics Data System (ADS)

Doi, Toshiyuki

2018-04-01

Slow flows of a rarefied gas between two plane parallel walls with nonuniform surface properties are studied based on kinetic theory. It is assumed that one wall is a diffuse reflection boundary and the other wall is a Maxwell-type boundary whose accommodation coefficient varies periodically in the direction perpendicular to the flow. The time-independent Poiseuille, thermal transpiration and Couette flows are considered. The flow behavior is numerically studied based on the linearized Bhatnagar-Gross-Krook-Welander model of the Boltzmann equation. The flow field, the mass and heat flow rates in the gas, and the tangential force acting on the wall surface are studied over a wide range of the gas rarefaction degree and the parameters characterizing the distribution of the accommodation coefficient. The locally convex velocity distribution is observed in Couette flow of a highly rarefied gas, similarly to Poiseuille flow and thermal transpiration. The reciprocity relations are numerically confirmed over a wide range of the flow parameters.

Organization of pectic arabinan and galactan side chains in association with cellulose microfibrils in primary cell walls and related models envisaged.

PubMed

Zykwinska, Agata; Thibault, Jean-François; Ralet, Marie-Christine

2007-01-01

The structure of arabinan and galactan domains in association with cellulose microfibrils was investigated using enzymatic and alkali degradation procedures. Sugar beet and potato cell wall residues (called 'natural' composites), rich in pectic neutral sugar side chains and cellulose, as well as 'artificial' composites, created by in vitro adsorption of arabinan and galactan side chains onto primary cell wall cellulose, were studied. These composites were sequentially treated with enzymes specific for pectic side chains and hot alkali. The degradation approach used showed that most of the arabinan and galactan side chains are in strong interaction with cellulose and are not hydrolysed by pectic side chain-degrading enzymes. It seems unlikely that isolated arabinan and galactan chains are able to tether adjacent microfibrils. However, cellulose microfibrils may be tethered by different pectic side chains belonging to the same pectic macromolecule.

Progress Towards an LES Wall Model Including Unresolved Roughness

NASA Astrophysics Data System (ADS)

Craft, Kyle; Redman, Andrew; Aikens, Kurt

2015-11-01

Wall models used in large eddy simulations (LES) are often based on theories for hydraulically smooth walls. While this is reasonable for many applications, there are also many where the impact of surface roughness is important. A previously developed wall model has been used primarily for jet engine aeroacoustics. However, jet simulations have not accurately captured thick initial shear layers found in some experimental data. This may partly be due to nozzle wall roughness used in the experiments to promote turbulent boundary layers. As a result, the wall model is extended to include the effects of unresolved wall roughness through appropriate alterations to the log-law. The methodology is tested for incompressible flat plate boundary layers with different surface roughness. Correct trends are noted for the impact of surface roughness on the velocity profile. However, velocity deficit profiles and the Reynolds stresses do not collapse as well as expected. Possible reasons for the discrepancies as well as future work will be presented. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575. Computational resources on TACC Stampede were provided under XSEDE allocation ENG150001.

Nano-Welding of Multi-Walled Carbon Nanotubes on Silicon and Silica Surface by Laser Irradiation

PubMed Central

Yuan, Yanping; Chen, Jimin

2016-01-01

In this study, a continuous fiber laser (1064 nm wavelength, 30 W/cm2) is used to irradiate multi-walled carbon nanotubes (MWCNTs) on different substrate surfaces. Effects of substrates on nano-welding of MWCNTs are investigated by scanning electron microscope (SEM). For MWCNTs on silica, after 3 s irradiation, nanoscale welding with good quality can be achieved due to breaking C–C bonds and formation of new graphene layers. While welding junctions can be formed until 10 s for the MWCNTs on silicon, the difference of irradiation time to achieve welding is attributed to the difference of thermal conductivity for silica and silicon. As the irradiation time is prolonged up to 12.5 s, most of the MWCNTs are welded to a silicon substrate, which leads to their frameworks of tube walls on the silicon surface. This is because the accumulation of absorbed energy makes the temperature rise. Then chemical reactions among silicon, carbon and nitrogen occur. New chemical bonds of Si–N and Si–C achieve the welding between the MWCNTs and silicon. Vibration modes of Si3N4 appear at peaks of 363 cm−1 and 663 cm−1. There are vibration modes of SiC at peaks of 618 cm−1, 779 cm−1 and 973 cm−1. The experimental observation proves chemical reactions and the formation of Si3N4 and SiC by laser irradiation. PMID:28344293

Thermal treatment wall

DOEpatents

Aines, Roger D.; Newmark, Robin L.; Knauss, Kevin G.

2000-01-01

A thermal treatment wall emplaced to perform in-situ destruction of contaminants in groundwater. Thermal destruction of specific contaminants occurs by hydrous pyrolysis/oxidation at temperatures achievable by existing thermal remediation techniques (electrical heating or steam injection) in the presence of oxygen or soil mineral oxidants, such as MnO.sub.2. The thermal treatment wall can be installed in a variety of configurations depending on the specific objectives, and can be used for groundwater cleanup, wherein in-situ destruction of contaminants is carried out rather than extracting contaminated fluids to the surface, where they are to be cleaned. In addition, the thermal treatment wall can be used for both plume interdiction and near-wellhead in-situ groundwater treatment. Thus, this technique can be utilized for a variety of groundwater contamination problems.

Entomological efficacy of durable wall lining with reduced wall surface coverage for strengthening visceral leishmaniasis vector control in Bangladesh, India and Nepal.

PubMed

Huda, M Mamun; Kumar, Vijay; Das, Murari Lal; Ghosh, Debashis; Priyanka, Jyoti; Das, Pradeep; Alim, Abdul; Matlashewski, Greg; Kroeger, Axel; Alfonso-Sierra, Eduardo; Mondal, Dinesh

2016-10-06

New methods for controlling sand fly are highly desired by the Visceral Leishmaniasis (VL) elimination program of Bangladesh, India and Nepal for its consolidation and maintenance phases. To support the program we investigated safety, efficacy and cost of Durable Wall Lining to control sand fly. This multicentre randomized controlled study in Bangladesh, India and Nepal included randomized two intervention clusters and one control cluster. Each cluster had 50 households except full wall surface coverage (DWL-FWSC) cluster in Nepal which had 46 households. Ten of 50 households were randomly selected for entomological activities except India where it was 6 households. Interventions were DWL-FWSC and reduced wall surface coverage (DWL-RWSC) with DWL which covers 1.8 m and 1.5 m height from floor respectively. Efficacy was measured by reduction in sand fly density by intervention and sand fly mortality assessment by the WHO cone bioassay test at 1 month after intervention. Trained field research assistants interviewed household heads for socio-demographic information, knowledge and practice about VL, vector control, and for their experience following the intervention. Cost data was collected using cost data collection tool which was designed for this study. Statistical analysis included difference-in-differences estimate, bivariate analysis, Poisson regression model and incremental cost-efficacy ratio calculation. Mean sand fly density reduction by DWL-FWSC and DWL-RWSC was respectively -4.96 (95 % CI, -4.54, -5.38) and -5.38 (95 % CI, -4.89, -5.88). The sand fly density reduction attributed by both the interventions were statistically significant after adjusting for covariates (IRR = 0.277, p < 0.001 for DWL-RWSC and IRR = 0.371, p < 0.001 for DWL-FWSC). The efficacy of DWL-RWSC and DWL-FWSC on sand fly density reduction was statistically comparable (p = 0.214). The acceptability of both interventions was high. Transient burning sensations

Cell wall formation in zoospores of Allomyces arbuscula. II. Development of surface structure of encysted haploid zoospores, rhizoids, and hyphae.

PubMed

Kroh, M; Hendriks, H; Kirby, E G; Sassen, M M

1976-08-01

Development of haploid meiospores of Allomyces arbuscula into germling cells with rhizoids and hyphae was followed during incubation in complete growth medium. The surface structure of encysted meiospores, rhizoids and hyphae before and after extraction of amorphous materials with ethanolic KOH was studied by means of carbon-platinum replicas. After 2--3 min incubation in complete medium 10% of the meiospores were surrounded by a cell wall containing microfibrils embedded in a matrix. Structure of cell walls of encysted meiospores, rhizoids, and hyphae differ from one another by the location of amorphous materials and by the arrangement of chitin microfibrils.

[Hydroxyproline: Rich glycoproteins of the plant and cell wall

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

Varner, J.E.

1993-01-01

Since xylem tissue includes the main cell types which are lignified, we are interested in gene expression of glycine-rich proteins and proline-rich proteins, and other proteins which are involved in secondary cell wall thickening during xylogenesis. Since the main feature of xylogenesis is the deposition of additional wall components, study of the mechanism of xylogenesis will greatly advance our knowledge of the synthesis and assembly of wall macromolecules. We are using the in vitro xylogenesis system from isolated Zinnia mesophyll cells to isolate genes which are specifically expressed during xylogenesis. We have used subtractive hybridization methods to isolate a numbermore » of cDNA clones for differentially regulated genes from the cells after hormonal induction. So far, we have partially characterized 18 different cDNA clones from 239 positive clones. These differentially regulated genes can be divided into three sets according to the characteristics of gene expression in the induction medium and the control medium. The first set is induced in both the induction medium and the control medium without hormones. The second set is induced mainly in the induction medium and in the control medium with the addition of NAA alone. Two of thesegenes are exclusively induced by auxin. The third set of genes is induced mainly in the induction medium. Since these genes are not induced by either auxin or cytokinin alone, they may be directly involved in the process of xylogenesis. Our experiments on the localization of H[sub 2]O[sub 2] production reinforce the earlier ideas of others that H[sub 2]O[sub 2] is involved in normal lignification.« less

15. MASONRY DETAIL NO. 1, NORTH TRAINING WALL, LOOKING DOWN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. MASONRY DETAIL NO. 1, NORTH TRAINING WALL, LOOKING DOWN UPON THE WALL SURFACE FROM THE ADJACENT RIPRAP. - Oakland Harbor Training Walls, Mouth of Federal Channel to Inner Harbor, Oakland, Alameda County, CA

Technical note: Influence of surface roughness and local turbulence on coated-wall flow tube experiments for gas uptake and kinetic studies

NASA Astrophysics Data System (ADS)

Li, Guo; Su, Hang; Kuhn, Uwe; Meusel, Hannah; Ammann, Markus; Shao, Min; Pöschl, Ulrich; Cheng, Yafang

2018-02-01

Coated-wall flow tube reactors are frequently used to investigate gas uptake and heterogeneous or multiphase reaction kinetics under laminar flow conditions. Coating surface roughness may potentially distort the laminar flow pattern, induce turbulence and introduce uncertainties in the calculated uptake coefficient based on molecular diffusion assumptions (e.g., Brown/Cooney-Kim-Davis (CKD)/Knopf-Pöschl-Shiraiwa (KPS) methods), which has not been fully resolved in earlier studies. Here, we investigate the influence of surface roughness and local turbulence on coated-wall flow tube experiments for gas uptake and kinetic studies. According to laminar boundary theory and considering the specific flow conditions in a coated-wall flow tube, we derive and propose a critical height δc to evaluate turbulence effects in the design and analysis of coated-wall flow tube experiments. If a geometric coating thickness δg is larger than δc, the roughness elements of the coating may cause local turbulence and result in overestimation of the real uptake coefficient (γ). We further develop modified CKD/KPS methods (i.e., CKD-LT/KPS-LT) to account for roughness-induced local turbulence effects. By combination of the original methods and their modified versions, the maximum error range of γCKD (derived with the CKD method) or γKPS (derived with the KPS method) can be quantified and finally γ can be constrained. When turbulence is generated, γCKD or γKPS can bear large difference compared to γ. Their difference becomes smaller for gas reactants with lower uptake (i.e., smaller γ) and/or for a smaller ratio of the geometric coating thickness to the flow tube radius (δg / R0). On the other hand, the critical height δc can also be adjusted by optimizing flow tube configurations and operating conditions (i.e., tube diameter, length, and flow velocity), to ensure not only unaffected laminar flow patterns but also other specific requirements for an individual flow tube

Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules.

PubMed

Trovato, Fabio; Tozzini, Valentina

2014-12-02

Recent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic molecular-dynamics simulations of a virtual cytoplasm we are able to track the single biomolecule motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coefficients, anomalous exponents, and the effective viscosity experienced by biomolecules in the cytoplasm is fine-tuned by the intermolecular interactions. Accounting only for excluded volume in these potentials gives a weaker size-dependence than that expected from experimental data. On the contrary, adding nonspecific attraction in the range of 1-10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromolecular concentration, poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Enhanced dielectric-wall linear accelerator

DOEpatents

Sampayan, Stephen E.; Caporaso, George J.; Kirbie, Hugh C.

1998-01-01

A dielectric-wall linear accelerator is enhanced by a high-voltage, fast e-time switch that includes a pair of electrodes between which are laminated alternating layers of isolated conductors and insulators. A high voltage is placed between the electrodes sufficient to stress the voltage breakdown of the insulator on command. A light trigger, such as a laser, is focused along at least one line along the edge surface of the laminated alternating layers of isolated conductors and insulators extending between the electrodes. The laser is energized to initiate a surface breakdown by a fluence of photons, thus causing the electrical switch to close very promptly. Such insulators and lasers are incorporated in a dielectric wall linear accelerator with Blumlein modules, and phasing is controlled by adjusting the length of fiber optic cables that carry the laser light to the insulator surface.

Reaction-Mediated Desorption of Macromolecules: Novel Phenomenon Enabling Simultaneous Reaction and Separation.

PubMed

Isakari, Yu; Kishi, Yuhi; Yoshimoto, Noriko; Yamamoto, Shuichi; Podgornik, Aleš

2018-02-02

Combining chemical reaction with separation offers several advantages. In this work possibility to induce spontaneous desorption of adsorbed macromolecules, once being PEGylated, through adjustment of the reagent composition is investigated. Bovine serum albumin (BSA) and activated oligonucleotide, 9T, are used as the test molecules and 20 kDa linear activated PEG is used for their PEGylation. BSA solid-phase PEGylation is performed on Q Sepharose HP. Distribution coefficient of BSA and PEG-BSA as a function of NaCl is determined using linear gradient elution (LGE) experiments and Yamamoto model. According to the distribution coefficient the selectivity between BSA and PEG - BSA of around 15 is adjusted by using NaCl. Spontaneous desorption of PEG - BSA is detected with no presence of BSA. However, due to a rather low selectivity, also desorption of BSA occurred at high elution volume. A similar procedure is applied for activated 9T oligonucleotide, this time using monolithic CIM QA disk monolithic column for adsorption. Selectivity of over 2000 is obtained by proper adjustment of PEG reagent composition. High selectivity enables spontaneous desorption of PEG-9T without any desorption of activated 9T. Both experiments demonstrates that reaction-mediated desorption of macromolecules is possible when the reaction conditions are properly tuned. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Technical Reports Server (NTRS)

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.

Nonlinear fracture mechanics-based analysis of thin wall cylinders

NASA Technical Reports Server (NTRS)

Brust, Frederick W.; Leis, Brian N.; Forte, Thomas P.

1994-01-01

This paper presents a simple analysis technique to predict the crack initiation, growth, and rupture of large-radius, R, to thickness, t, ratio (thin wall) cylinders. The method is formulated to deal both with stable tearing as well as fatigue mechanisms in applications to both surface and through-wall axial cracks, including interacting surface cracks. The method can also account for time-dependent effects. Validation of the model is provided by comparisons of predictions to more than forty full scale experiments of thin wall cylinders pressurized to failure.

Some Fundamental Molecular Mechanisms of Contractility in Fibrous Macromolecules

PubMed Central

Mandelkern, L.

1967-01-01

The fundamental molecular mechanisms of contractility and tension development in fibrous macromolecules are developed from the point of view of the principles of polymer physical chemistry. The problem is treated in a general manner to encompass the behavior of all macromolecular systems irrespective of their detailed chemical structure and particular function, if any. Primary attention is given to the contractile process which accompanies the crystal-liquid transition in axially oriented macromolecular systems. The theoretical nature of the process is discussed, and many experimental examples are given from the literature which demonstrate the expected behavior. Experimental attention is focused on the contraction of fibrous proteins, and the same underlying molecular mechanism is shown to be operative for a variety of different systems. PMID:6050598

Electromagnetic approaches to wall characterization, wall mitigation, and antenna design for through-the-wall radar systems

NASA Astrophysics Data System (ADS)

Thajudeen, Christopher

of ground reflections, and situations where they may be applied to the estimation of the parameters associated with an interior wall. It is demonstrated through extensive computer simulations and laboratory experiments that, by proper exploitation of the electromagnetic characteristics of walls, one can efficiently extract the constitutive parameters associated with unknown wall(s) as well as to characterize and image the intra-wall region. Additionally, it is possible, to a large extent, to remove the negative wall effects, such as shadowing and incorrect target localization, as well as to enhance the imaging and classification of targets behind walls. In addition to the discussion of post processing the radar data to account for wall effects, the design of antenna elements used for transmit (Tx) and receive (Rx) operations in TWR radars is also discussed but limited to antennas for mobile, handheld, or UAV TWR systems which impose design requirements such as low profiles, wide operational bands, and in most cases lend themselves to fabrication using surface printing techniques. A new class of wideband antennas, formed though the use of printed metallic paths in the form of Peano and Hilbert space-filling curves (SFC) to provide top-loading properties that miniaturize monopole antenna elements, has been developed for applications in conformal and/or low profile antennas systems, such as mobile platforms for TWRI and communication systems. Additionally, boresight gain enhancements of a stair-like antenna geometry, through the addition of parasitic self-similar patches and gate like ground plane structures, are presented.

Near-wall serpentine cooled turbine airfoil

DOEpatents

Lee, Ching-Pang

2013-09-17

A serpentine coolant flow path (54A-54G) formed by inner walls (50, 52) in a cavity (49) between pressure and suction side walls (22, 24) of a turbine airfoil (20A). A coolant flow (58) enters (56) an end of the airfoil, flows into a span-wise channel (54A), then flows forward (54B) over the inner surface of the pressure side wall, then turns behind the leading edge (26), and flows back along a forward part of the suction side wall, then follows a loop (54E) forward and back around an inner wall (52), then flows along an intermediate part of the suction side wall, then flows into an aft channel (54G) between the pressure and suction side walls, then exits the trailing edge (28). This provides cooling matched to the heating topography of the airfoil, minimizes differential thermal expansion, revives the coolant, and minimizes the flow volume needed.

Wall roughness induces asymptotic ultimate turbulence

NASA Astrophysics Data System (ADS)

Zhu, Xiaojue; Verschoof, Ruben A.; Bakhuis, Dennis; Huisman, Sander G.; Verzicco, Roberto; Sun, Chao; Lohse, Detlef

2018-04-01

Turbulence governs the transport of heat, mass and momentum on multiple scales. In real-world applications, wall-bounded turbulence typically involves surfaces that are rough; however, characterizing and understanding the effects of wall roughness on turbulence remains a challenge. Here, by combining extensive experiments and numerical simulations, we examine the paradigmatic Taylor-Couette system, which describes the closed flow between two independently rotating coaxial cylinders. We show how wall roughness greatly enhances the overall transport properties and the corresponding scaling exponents associated with wall-bounded turbulence. We reveal that if only one of the walls is rough, the bulk velocity is slaved to the rough side, due to the much stronger coupling to that wall by the detaching flow structures. If both walls are rough, the viscosity dependence is eliminated, giving rise to asymptotic ultimate turbulence—the upper limit of transport—the existence of which was predicted more than 50 years ago. In this limit, the scaling laws can be extrapolated to arbitrarily large Reynolds numbers.

Chest wall segmentation in automated 3D breast ultrasound scans.

PubMed

Tan, Tao; Platel, Bram; Mann, Ritse M; Huisman, Henkjan; Karssemeijer, Nico

2013-12-01

In this paper, we present an automatic method to segment the chest wall in automated 3D breast ultrasound images. Determining the location of the chest wall in automated 3D breast ultrasound images is necessary in computer-aided detection systems to remove automatically detected cancer candidates beyond the chest wall and it can be of great help for inter- and intra-modal image registration. We show that the visible part of the chest wall in an automated 3D breast ultrasound image can be accurately modeled by a cylinder. We fit the surface of our cylinder model to a set of automatically detected rib-surface points. The detection of the rib-surface points is done by a classifier using features representing local image intensity patterns and presence of rib shadows. Due to attenuation of the ultrasound signal, a clear shadow is visible behind the ribs. Evaluation of our segmentation method is done by computing the distance of manually annotated rib points to the surface of the automatically detected chest wall. We examined the performance on images obtained with the two most common 3D breast ultrasound devices in the market. In a dataset of 142 images, the average mean distance of the annotated points to the segmented chest wall was 5.59 ± 3.08 mm. Copyright © 2012 Elsevier B.V. All rights reserved.

A Structurally Specialized Uniform Wall Layer is Essential for Constructing Wall Ingrowth Papillae in Transfer Cells

PubMed Central

Xia, Xue; Zhang, Hui-Ming; Offler, Christina E.; Patrick, John W.

2017-01-01

Transfer cells are characterized by wall labyrinths with either a flange or reticulate architecture. A literature survey established that reticulate wall ingrowth papillae ubiquitously arise from a modified component of their wall labyrinth, termed the uniform wall layer; a structure absent from flange transfer cells. This finding sparked an investigation of the deposition characteristics and role of the uniform wall layer using a Vicia faba cotyledon culture system. On transfer of cotyledons to culture, their adaxial epidermal cells spontaneously trans-differentiate to a reticulate architecture comparable to their abaxial epidermal transfer cell counterparts formed in planta. Uniform wall layer construction commenced once adaxial epidermal cell expansion had ceased to overlay the original outer periclinal wall on its inner surface. In contrast to the dense ring-like lattice of cellulose microfibrils in the original primary wall, the uniform wall layer was characterized by a sparsely dispersed array of linear cellulose microfibrils. A re-modeled cortical microtubule array exerted no influence on uniform wall layer formation or on its cellulose microfibril organization. Surprisingly, formation of the uniform wall layer was not dependent upon depositing a cellulose scaffold. In contrast, uniform wall cellulose microfibrils were essential precursors for constructing wall ingrowth papillae. On converging to form wall ingrowth papillae, the cellulose microfibril diameters increased 3-fold. This event correlated with up-regulated differential, and transfer-cell specific, expression of VfCesA3B while transcript levels of other cellulose biosynthetic-related genes linked with primary wall construction were substantially down-regulated. PMID:29259611

A Structurally Specialized Uniform Wall Layer is Essential for Constructing Wall Ingrowth Papillae in Transfer Cells.

PubMed

Xia, Xue; Zhang, Hui-Ming; Offler, Christina E; Patrick, John W

2017-01-01

Transfer cells are characterized by wall labyrinths with either a flange or reticulate architecture. A literature survey established that reticulate wall ingrowth papillae ubiquitously arise from a modified component of their wall labyrinth, termed the uniform wall layer; a structure absent from flange transfer cells. This finding sparked an investigation of the deposition characteristics and role of the uniform wall layer using a Vicia faba cotyledon culture system. On transfer of cotyledons to culture, their adaxial epidermal cells spontaneously trans -differentiate to a reticulate architecture comparable to their abaxial epidermal transfer cell counterparts formed in planta . Uniform wall layer construction commenced once adaxial epidermal cell expansion had ceased to overlay the original outer periclinal wall on its inner surface. In contrast to the dense ring-like lattice of cellulose microfibrils in the original primary wall, the uniform wall layer was characterized by a sparsely dispersed array of linear cellulose microfibrils. A re-modeled cortical microtubule array exerted no influence on uniform wall layer formation or on its cellulose microfibril organization. Surprisingly, formation of the uniform wall layer was not dependent upon depositing a cellulose scaffold. In contrast, uniform wall cellulose microfibrils were essential precursors for constructing wall ingrowth papillae. On converging to form wall ingrowth papillae, the cellulose microfibril diameters increased 3-fold. This event correlated with up-regulated differential, and transfer-cell specific, expression of VfCesA3B while transcript levels of other cellulose biosynthetic-related genes linked with primary wall construction were substantially down-regulated.

The laboratory investigation of surface envelope solitons: reflection from a vertical wall and collisions of solitons

NASA Astrophysics Data System (ADS)

Slunyaev, Alexey; Klein, Marco; Clauss, Günther F.

2016-04-01

Envelope soliton solutions are key elements governing the nonlinear wave dynamics within a simplified theory for unidirectional weakly modulated weakly nonlinear wave groups on the water surface. Within integrable models the solitons preserve their structure in collisions with other waves; they do not disperse and can carry energy infinitively long. Steep and short soliton-like wave groups have been shown to exist in laboratory tests [1] and, even earlier, in numerical simulations [2, 3]. Thus, long-living wave groups may play important role in the dynamics of intense sea waves and wave-structure interactions. The solitary wave groups may change the wave statistics and can be taken into account when developing approaches for the deterministic forecasting of dangerous waves, including so-called rogue waves. An experimental campaign has been conducted in the wave basin of the Technical University of Berlin on simulations of intense solitary wave groups. The first successful experimental observation of intense envelope solitons took place in this facility [1]. The new experiments aimed at following main goals: 1) to reproduce intense envelope solitons with different carrier wave lengths; 2) to estimate the rate of envelope soliton dissipation; 3) to consider the reflection of envelope solitons on a vertical wall; 4) to consider head-on collisions of envelope solitons, and 5) to consider overtaking interactions of envelope solitons. Up to 9 wave gauges were used in each experimental run, which enabled registration of the surface movement at different distances from the wavemaker, at different locations across the wave flume and near the wall. Besides surface displacements, the group envelope shapes were directly recorded, with use of phase shifts applied to the modulated waves generated by the wavemaker. [1] A. Slunyaev, G.F. Clauss, M. Klein, M. Onorato, Simulations and experiments of short intense envelope solitons of surface water waves. Phys. Fluids 25, 067105

Enhanced dielectric-wall linear accelerator

DOEpatents

Sampayan, S.E.; Caporaso, G.J.; Kirbie, H.C.

1998-09-22

A dielectric-wall linear accelerator is enhanced by a high-voltage, fast e-time switch that includes a pair of electrodes between which are laminated alternating layers of isolated conductors and insulators. A high voltage is placed between the electrodes sufficient to stress the voltage breakdown of the insulator on command. A light trigger, such as a laser, is focused along at least one line along the edge surface of the laminated alternating layers of isolated conductors and insulators extending between the electrodes. The laser is energized to initiate a surface breakdown by a fluence of photons, thus causing the electrical switch to close very promptly. Such insulators and lasers are incorporated in a dielectric wall linear accelerator with Blumlein modules, and phasing is controlled by adjusting the length of fiber optic cables that carry the laser light to the insulator surface. 6 figs.

Wall conditioning and particle control in Extrap T2

NASA Astrophysics Data System (ADS)

Bergsåker, H.; Larsson, D.; Brunsell, P.; Möller, A.; Tramontin, L.

1997-02-01

The Extrap T2 reversed field pinch experiment is operated with the former OHTE vacuum vessel, of dimensions R = 1.24 m and a = 0.18 m and with a complete graphite liner. It is shown that a rudimentary density control can be achieved by means of frequent helium glow discharge conditioning of the wall. The standard He-GDC is well characterized and reproducible. The trapping and release of hydrogen and impurities at the wall surfaces have been studied by mass spectrometry and surface analysis. The shot to shot particle exchange between wall and plasma can be approximately accounted for.

Translational Diffusion of Macromolecule-sized Solutes in Cytoplasm and Nucleus

PubMed Central

Seksek, Olivier; Biwersi, Joachim; Verkman, A.S.

1997-01-01

Fluorescence recovery after photobleaching (FRAP) was used to quantify the translational diffusion of microinjected FITC-dextrans and Ficolls in the cytoplasm and nucleus of MDCK epithelial cells and Swiss 3T3 fibroblasts. Absolute diffusion coefficients (D) were measured using a microsecond-resolution FRAP apparatus and solution standards. In aqueous media (viscosity 1 cP), D for the FITC-dextrans decreased from 75 to 8.4 × 10−7 cm2/s with increasing dextran size (4–2,000 kD). D in cytoplasm relative to that in water (D/Do) was 0.26 ± 0.01 (MDCK) and 0.27 ± 0.01 (fibroblasts), and independent of FITC-dextran and Ficoll size (gyration radii [RG] 40–300 Å). The fraction of mobile FITC-dextran molecules (fmob), determined by the extent of fluorescence recovery after spot photobleaching, was >0.75 for RG < 200 Å, but decreased to <0.5 for RG > 300 Å. The independence of D/Do on FITC-dextran and Ficoll size does not support the concept of solute “sieving” (size-dependent diffusion) in cytoplasm. Photobleaching measurements using different spot diameters (1.5–4 μm) gave similar D/Do, indicating that microcompartments, if present, are of submicron size. Measurements of D/Do and fmob in concentrated dextran solutions, as well as in swollen and shrunken cells, suggested that the low fmob for very large macromolecules might be related to restrictions imposed by immobile obstacles (such as microcompartments) or to anomalous diffusion (such as percolation). In nucleus, D/Do was 0.25 ± 0.02 (MDCK) and 0.27 ± 0.03 (fibroblasts), and independent of solute size (RG 40–300 Å). Our results indicate relatively free and rapid diffusion of macromolecule-sized solutes up to approximately 500 kD in cytoplasm and nucleus. PMID:9214387

Wall turbulence control

NASA Technical Reports Server (NTRS)

Wilkinson, Stephen P.; Lindemann, A. Margrethe; Beeler, George B.; Mcginley, Catherine B.; Goodman, Wesley L.; Balasubramanian, R.

1986-01-01

A variety of wall turbulence control devices which were experimentally investigated are discussed; these include devices for burst control, alteration of outer flow structures, large eddy substitution, increased heat transfer efficiency, and reduction of wall pressure fluctuations. Control of pre-burst flow was demonstrated with a single, traveling surface depression which is phase-locked to elements of the burst production process. Another approach to wall turbulence control is to interfere with the outer layer coherent structures. A device in the outer part of a boundary layer was shown to suppress turbulence and reduce drag by opposing both the mean and unsteady vorticity in the boundary layer. Large eddy substitution is a method in which streamline curvature is introduced into the boundary layer in the form of streamwise vortices. Riblets, which were already shown to reduce turbulent drag, were also shown to exhibit superior heat transfer characteristics. Heat transfer efficiency as measured by the Reynolds Analogy Factor was shown to be as much as 36 percent greater than a smooth flat plate in a turbulent boundary layer. Large Eddy Break-Up (LEBU) which are also known to reduce turbulent drag were shown to reduce turbulent wall pressure fluctuation.

Is the great attractor really a great wall

NASA Technical Reports Server (NTRS)

Stebbins, Albert; Turner, Michael S.

1988-01-01

Some of the cosmological consequences are discussed of a late time phase transition which produces light domain walls. The observed peculiar velocity field of the Universe and the observed isotropy of the microwave background radiation severely constrain the wall surface density in such a scenario. The most interesting consequence of such a phase transition is the possibility that the local, coherent streaming motion reported by the Seven Samurai could be explained by the repulsive effect of a relic domain wall with the Hubble volume (the Great Wall).

Problems And Their Solutions When Thin-Walled Turned Parts Of High Precision With Quasi-Optical Surfaces Are Manufactured On A CNC Automatic Lathe Under Workshop Conditions

NASA Astrophysics Data System (ADS)

Jaeger, Valentin E.

1989-04-01

The geometrical accuracy and surface roughness of diamond-turned workpieces is influenced by several parameters: the properties of the machine tool, the cutting process and the environmental conditions. A thin-walled electrode made from an aluminium alloy (wall thickness: 1 mm, length: 169 mm, outer diameter: 126 mm) and intended for an electrostatic measuring instrument, serves as an example to show how quasi-optical surfaces with a surface roughness Rα < 10 nm and deviations from roundness of <= 5 μm can be achieved when some of these influence quantities are optimized. The cylindrical part of the electrode was turned by means of a rounded mirror-finish diamond tool, the width of the cutting edge being 2 mm, the rake angle -6° and the clearance angle 2°. Compliance with the tolerances of geometrical accuracy was particularly difficult. As age-hardened wrought aluminium alloys cannot be stress-relieved by annealing, or only insufficiently, the geometrical accuracy - in particular the roundness - of thin-walled, rotationally symmetric bodies decisively depends on the state of stress of the workpiece material, on the clamping fixture and on the balanced condition of this clamping fixture.

Research status and future trends on surface pre-grouting technology in reforming wall rock of vertical shafts in coal mines in China

NASA Astrophysics Data System (ADS)

Wang, Hua

2018-02-01

In the mine construction, the surface pre-grouting technology is an important method to prevent water blast in excavation process of vertical shaft when the shaft must pass through the thick, water-rich and high water-pressure bedrock aquifer. It has been nearly 60 years since the technology was used to reform wall rock of vertical shaft in coal mine in China for the first time, and the existing technology can basically meet the needs of constructing 1000m deep vertical shaft. Firstly, the article introduces that in view of Magg’s spherical seepage theory and Karol’s spherical seepage theory, Chinese scholars found that the diffusion of grout from borehole into the surrounding strata in horizontal direction is irregular through a lot of research and engineering practice of using the surface pre-grouting technology to reform wall rock of vertical shafts, and put forward the selecting principles of grout’s effective diffusion radius in one grouting engineering; Secondly, according to the shape of the grouting boreholes, surface pre-grouting technology of vertical shaft is divided into two stages: vertical borehole stage and S-type borehole stage. Thirdly, the development status of grouting materials and grouting equipment for the technology is introduced. Fourthly, grouting mode, stage height and pressure of the technology are introduced. Finally, it points out that with the increasing depth of coal mining in China, the technology of reforming wall rock of 1000~2000m deep vertical shafts will face many problems, such as grouting theory, grouting equipment, grouting finishing standard, testing and evaluation of grouting effect, and so on. And it put forward a preliminary approach to solving these problems. This paper points out future research directions of the surface pre-grouting technology in China.

Is it Possible to have the Similar Unit Cell in Crystals of Different form from the same Macromolecule? (A Case Study of Ribosome Crystals)

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Three different types of ribosome crystals were grown by the vapor diffusion technique in hanging drops as described in (1,2). The ribosome is a large asymmetric RNA-protein complex (2.3 million Da), which is protein syntheses machinery of the cell. In this poster we would like to discuss the features of ribosome crystallization. Ribosomes were purified from the thermophilic bacteria Thermus thermophilus by centrifugation (3). Three types of crystals (needle, flat tetragonal and tetragonal-like pyramid) can be grown from the same solution; furthermore, in the same drop using 10-15% 2-methyl-2,4- pentanediol as a precipitant. The crystals appeared in 5-48 hours. The crystals were stable and can co-exist in solution over long period of time. The kinetics of appearance of different crystal forms was different: first the needle crystals were grown, then the tetragonal, and finally the tetragonal pyramids. Later studies of the process of ribosome crystal growth depending on supersaturation showed that low supersaturation results in the appearance of tetragonal plates or tetragonal-like pyramids. An electron microscopy study, together with computer modeling, has shown that crystals of different forms have a high probability of having the same unit cell parameters. According to these experiments the following conclusion can be dranvn: the level of supersaturation of the macromolecule in a crystallizing solution is one of the major factors for forming three-dimensional crystals convenient for X-rays diffraction analysis. From the same macromolecule solution, crystals of different forms can be grown at approximately the same conditions by varying the concentration of macromolecule in the solution. Ion-macromolecule and water-macromolecule interactions, apparently, play the main role in the formation of the unit cell of the crystals.

Experimental investigation of turbulent wall jet

NASA Astrophysics Data System (ADS)

Andre, Matthieu A.; Bardet, Philippe M.

2011-11-01

Water jet flowing on a flat plate surrounded by quiescent air constitutes a standard case for the study of the interaction between turbulence and the liquid-air interface. This is of particular interest in the understanding of heat and mass transfers across interfaces. The structure of the surface has a great influence on the rate of the transfers which is critical for chemical processes like separation or absorption; pool-type nuclear reactor; climate modeling etc. This study focuses on high Froude (8 to 12) and Weber (3300 to 7400) numbers at which the surface exhibits small wavelength and large amplitude deformations, such as ligaments, surface break up with air entrainment and droplets projection. The experiment features a high velocity (up to 7.5 m/s) water wall jet (19.05mm thick at the nozzle exit) flowing on a flat plate (Re =105 to 1 . 5 .105). High speed movies and PLIF visualization show the evolution of the surface from smooth to 2D structures, then 3D disturbances as the turbulence arising from the wall interacts with the surface.

Comparative analysis of cell wall surface glycan expression in Candida albicans and Saccharomyces cerevisiae yeasts by flow cytometry.

PubMed

Martínez-Esparza, M; Sarazin, A; Jouy, N; Poulain, D; Jouault, T

2006-07-31

The yeast Candida albicans is an opportunistic pathogen, part of the normal human microbial flora that causes infections in immunocompromised individuals with a high morbidity and mortality levels. Recognition of yeasts by host cells is based on components of the yeast cell wall, which are considered part of its virulence attributes. Cell wall glycans play an important role in the continuous interchange that regulates the balance between saprophytism and parasitism, and also between resistance and infection. Some of these molecular entities are expressed both by the pathogenic yeast C. albicans and by Saccharomyces cerevisiae, a related non-pathogenic yeast, involving similar molecular mechanisms and receptors for recognition. In this work we have exploited flow cytometry methods for probing surface glycans of the yeasts. We compared glycan expression by C. albicans and by S. cerevisiae, and studied the effect of culture conditions. Our results show that the expression levels of alpha- and beta-linked mannosides as well as beta-glucans can be successfully evaluated by flow cytometry methods using different antibodies independent of agglutination reactions. We also found that the surface expression pattern of beta-mannosides detected by monoclonal or polyclonal antibodies are differently modulated during the growth course. These data indicate that the yeast beta-mannosides exposed on mannoproteins and/or phospholipomannan are increased in stationary phase, whereas those linked to mannan are not affected by the yeast growth phase. The cytometric method described here represents a useful tool to investigate to what extent C. albicans is able to regulate its glycan surface expression and therefore modify its virulence properties.

Construction of Extended 3D Field of Views of the Internal Bladder Wall Surface: A Proof of Concept

NASA Astrophysics Data System (ADS)

Ben-Hamadou, Achraf; Daul, Christian; Soussen, Charles

2016-09-01

3D extended field of views (FOVs) of the internal bladder wall facilitate lesion diagnosis, patient follow-up and treatment traceability. In this paper, we propose a 3D image mosaicing algorithm guided by 2D cystoscopic video-image registration for obtaining textured FOV mosaics. In this feasibility study, the registration makes use of data from a 3D cystoscope prototype providing, in addition to each small FOV image, some 3D points located on the surface. This proof of concept shows that textured surfaces can be constructed with minimally modified cystoscopes. The potential of the method is demonstrated on numerical and real phantoms reproducing various surface shapes. Pig and human bladder textures are superimposed on phantoms with known shape and dimensions. These data allow for quantitative assessment of the 3D mosaicing algorithm based on the registration of images simulating bladder textures.

Focal macromolecule delivery in neuronal tissue using simultaneous pressure ejection and local electroporation

PubMed Central

Barker, Matthew; Billups, Brian; Hamann, Martine

2009-01-01

Electroporation creates transient pores in the plasma membrane to introduce macromolecules within a cell or cell population. Generally, electrical pulses are delivered between two electrodes separated from each other, making electroporation less likely to be localised. We have developed a new device combining local pressure ejection with local electroporation through a double-barrelled glass micropipette to transfer impermeable macromolecules in brain slices or in cultured HEK293 cells. The design achieves better targeting of the site of pressure ejection with that of electroporation. With this technique, we have been able to limit the delivery of propidium iodide or dextran amine within areas of 100–200 μm diameter. We confirm that local electroporation is transient and show that when combined with pressure ejection, it allows local transfection of EGFP plasmids within HEK293 cells or within cerebellar and hippocampal slice cultures. We further show that local electroporation is less damaging when compared to global electroporation using two separate electrodes. Focal delivery of dextran amine dyes within trapezoid body fibres allowed tracing axonal tracts within brainstem slices, enabling the study of identified calyx of Held presynaptic terminals in living brain tissue. This labelling method can be used to target small nuclei in neuronal tissue and is generally applicable to the study of functional synaptic connectivity, or live axonal tracing in a variety of brain areas. PMID:19014970

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

NASA Astrophysics Data System (ADS)

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.

Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

NASA Astrophysics Data System (ADS)

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.

The Question of Impurities in Macromolecule Crystal Quality Improvement in Microgravity

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, Edward H.; Pusey, Marc L.; Sportiello, Michael G.; Todd, Paul; Bellamy, Henry; Borgstahl, Gloria E.; Pokros, Matthew; Cassanto, John M.

2000-01-01

While macromolecule impurities may affect crystal size and morphology the over-riding question is how do macromolecule impurities effect crystal X-ray quality and diffraction resolution. In the case of chicken egg white lysozyme previous researchers have reported that crystals grown in the presence of ovalbumin, ovotransferrin, and turkey egg white lysozyme show no difference in diffraction resolution compared to those grown in pure solutions. One impurity however, a naturally occurring lysozyme dimer, does negatively impact the X-ray crystal properties. For this impurity it has been reported that crystal quality improvement in microgravity may be due to improved impurity partitioning during crystallization. In this study we have examined the incorporation of the dimer into lysozyme crystals, both on the ground and in microgravity experiments, and have performed detailed X-ray analysis of the crystals using a new technique for finely probing the mosaicity of the crystal at the Stanford Synchrotron Radiation Laboratory. Dimer partitioning was not significantly different in microgravity compared to the ground based experiments, although it is significantly better than that previously reported in microgravity. Mosaicity analysis of pure crystals, 1422 indexed reflections (microgravity) and 752 indexed reflections (ground), gave average results of 0.0066 and 0.0092 degrees (FWHM) respectively. The microgravity crystals also provided an increased signal to noise. Dimer incorporation increased the average mosaicity in microgravity but not on the ground. However, dimer incorporation did greatly reduce the resolution limit in both ground and microgravity grown crystals. The data is being treated anisotropically to explore these effects. These results indicate that impurity effects in microgravity are complex and that the conditions or techniques employed may greatly affect the role of impurities.

Reynolds number invariance of the structure inclination angle in wall turbulence.

PubMed

Marusic, Ivan; Heuer, Weston D C

2007-09-14

Cross correlations of the fluctuating wall-shear stress and the streamwise velocity in the logarithmic region of turbulent boundary layers are reported over 3 orders of magnitude change in Reynolds number. These results are obtained using hot-film and hot-wire anemometry in a wind tunnel facility, and sonic anemometers and a purpose-built wall-shear stress sensor in the near-neutral atmospheric surface layer on the salt flats of Utah's western desert. The direct measurement of fluctuating wall-shear stress in the atmospheric surface layer has not been available before. Structure inclination angles are inferred from the cross correlation results and are found to be invariant over the large range of Reynolds number. The findings justify the prior use of low Reynolds number experiments for obtaining structure angles for near-wall models in the large-eddy simulation of atmospheric surface layer flows.

A model for cell wall dissolution in mating yeast cells: polarized secretion and restricted diffusion of cell wall remodeling enzymes induces local dissolution.

PubMed

Huberman, Lori B; Murray, Andrew W

2014-01-01

Mating of the budding yeast, Saccharomyces cerevisiae, occurs when two haploid cells of opposite mating types signal using reciprocal pheromones and receptors, grow towards each other, and fuse to form a single diploid cell. To fuse, both cells dissolve their cell walls at the point of contact. This event must be carefully controlled because the osmotic pressure differential between the cytoplasm and extracellular environment causes cells with unprotected plasma membranes to lyse. If the cell wall-degrading enzymes diffuse through the cell wall, their concentration would rise when two cells touched each other, such as when two pheromone-stimulated cells adhere to each other via mating agglutinins. At the surfaces that touch, the enzymes must diffuse laterally through the wall before they can escape into the medium, increasing the time the enzymes spend in the cell wall, and thus raising their concentration at the point of attachment and restricting cell wall dissolution to points where cells touch each other. We tested this hypothesis by studying pheromone treated cells confined between two solid, impermeable surfaces. This confinement increases the frequency of pheromone-induced cell death, and this effect is diminished by reducing the osmotic pressure difference across the cell wall or by deleting putative cell wall glucanases and other genes necessary for efficient cell wall fusion. Our results support the model that pheromone-induced cell death is the result of a contact-driven increase in the local concentration of cell wall remodeling enzymes and suggest that this process plays an important role in regulating cell wall dissolution and fusion in mating cells.

A Model for Cell Wall Dissolution in Mating Yeast Cells: Polarized Secretion and Restricted Diffusion of Cell Wall Remodeling Enzymes Induces Local Dissolution

PubMed Central

Huberman, Lori B.; Murray, Andrew W.

2014-01-01

Mating of the budding yeast, Saccharomyces cerevisiae, occurs when two haploid cells of opposite mating types signal using reciprocal pheromones and receptors, grow towards each other, and fuse to form a single diploid cell. To fuse, both cells dissolve their cell walls at the point of contact. This event must be carefully controlled because the osmotic pressure differential between the cytoplasm and extracellular environment causes cells with unprotected plasma membranes to lyse. If the cell wall-degrading enzymes diffuse through the cell wall, their concentration would rise when two cells touched each other, such as when two pheromone-stimulated cells adhere to each other via mating agglutinins. At the surfaces that touch, the enzymes must diffuse laterally through the wall before they can escape into the medium, increasing the time the enzymes spend in the cell wall, and thus raising their concentration at the point of attachment and restricting cell wall dissolution to points where cells touch each other. We tested this hypothesis by studying pheromone treated cells confined between two solid, impermeable surfaces. This confinement increases the frequency of pheromone-induced cell death, and this effect is diminished by reducing the osmotic pressure difference across the cell wall or by deleting putative cell wall glucanases and other genes necessary for efficient cell wall fusion. Our results support the model that pheromone-induced cell death is the result of a contact-driven increase in the local concentration of cell wall remodeling enzymes and suggest that this process plays an important role in regulating cell wall dissolution and fusion in mating cells. PMID:25329559

Wall-crossing in coupled 2d-4d systems

NASA Astrophysics Data System (ADS)

Gaiotto, Davide; Moore, Gregory W.; Neitzke, Andrew

2012-12-01

We introduce a new wall-crossing formula which combines and generalizes the Cecotti-Vafa and Kontsevich-Soibelman formulas for supersymmetric 2d and 4d systems respectively. This 2d-4d wall-crossing formula governs the wall-crossing of BPS states in an {N}=2 supersymmetric 4d gauge theory coupled to a supersymmetric surface defect. When the theory and defect are compactified on a circle, we get a 3d theory with a supersymmetric line operator, corresponding to a hyperholomorphic connection on a vector bundle over a hyperkähler space. The 2d-4d wall-crossing formula can be interpreted as a smoothness condition for this hyperholomorphic connection. We explain how the 2d-4d BPS spectrum can be determined for 4d theories of class {S} , that is, for those theories obtained by compactifying the six-dimensional (0, 2) theory with a partial topological twist on a punctured Riemann surface C. For such theories there are canonical surface defects. We illustrate with several examples in the case of A 1 theories of class {S} . Finally, we indicate how our results can be used to produce solutions to the A 1 Hitchin equations on the Riemann surface C.

Exploratory visualization of astronomical data on ultra-high-resolution wall displays

NASA Astrophysics Data System (ADS)

Pietriga, Emmanuel; del Campo, Fernando; Ibsen, Amanda; Primet, Romain; Appert, Caroline; Chapuis, Olivier; Hempel, Maren; Muñoz, Roberto; Eyheramendy, Susana; Jordan, Andres; Dole, Hervé

2016-07-01

Ultra-high-resolution wall displays feature a very high pixel density over a large physical surface, which makes them well-suited to the collaborative, exploratory visualization of large datasets. We introduce FITS-OW, an application designed for such wall displays, that enables astronomers to navigate in large collections of FITS images, query astronomical databases, and display detailed, complementary data and documents about multiple sources simultaneously. We describe how astronomers interact with their data using both the wall's touchsensitive surface and handheld devices. We also report on the technical challenges we addressed in terms of distributed graphics rendering and data sharing over the computer clusters that drive wall displays.

Esophageal wall dose-surface maps do not improve the predictive performance of a multivariable NTCP model for acute esophageal toxicity in advanced stage NSCLC patients treated with intensity-modulated (chemo-)radiotherapy.

PubMed

Dankers, Frank; Wijsman, Robin; Troost, Esther G C; Monshouwer, René; Bussink, Johan; Hoffmann, Aswin L

2017-05-07

In our previous work, a multivariable normal-tissue complication probability (NTCP) model for acute esophageal toxicity (AET) Grade  ⩾2 after highly conformal (chemo-)radiotherapy for non-small cell lung cancer (NSCLC) was developed using multivariable logistic regression analysis incorporating clinical parameters and mean esophageal dose (MED). Since the esophagus is a tubular organ, spatial information of the esophageal wall dose distribution may be important in predicting AET. We investigated whether the incorporation of esophageal wall dose-surface data with spatial information improves the predictive power of our established NTCP model. For 149 NSCLC patients treated with highly conformal radiation therapy esophageal wall dose-surface histograms (DSHs) and polar dose-surface maps (DSMs) were generated. DSMs were used to generate new DSHs and dose-length-histograms that incorporate spatial information of the dose-surface distribution. From these histograms dose parameters were derived and univariate logistic regression analysis showed that they correlated significantly with AET. Following our previous work, new multivariable NTCP models were developed using the most significant dose histogram parameters based on univariate analysis (19 in total). However, the 19 new models incorporating esophageal wall dose-surface data with spatial information did not show improved predictive performance (area under the curve, AUC range 0.79-0.84) over the established multivariable NTCP model based on conventional dose-volume data (AUC  =  0.84). For prediction of AET, based on the proposed multivariable statistical approach, spatial information of the esophageal wall dose distribution is of no added value and it is sufficient to only consider MED as a predictive dosimetric parameter.

Esophageal wall dose-surface maps do not improve the predictive performance of a multivariable NTCP model for acute esophageal toxicity in advanced stage NSCLC patients treated with intensity-modulated (chemo-)radiotherapy

NASA Astrophysics Data System (ADS)

Dankers, Frank; Wijsman, Robin; Troost, Esther G. C.; Monshouwer, René; Bussink, Johan; Hoffmann, Aswin L.

2017-05-01

In our previous work, a multivariable normal-tissue complication probability (NTCP) model for acute esophageal toxicity (AET) Grade  ⩾2 after highly conformal (chemo-)radiotherapy for non-small cell lung cancer (NSCLC) was developed using multivariable logistic regression analysis incorporating clinical parameters and mean esophageal dose (MED). Since the esophagus is a tubular organ, spatial information of the esophageal wall dose distribution may be important in predicting AET. We investigated whether the incorporation of esophageal wall dose-surface data with spatial information improves the predictive power of our established NTCP model. For 149 NSCLC patients treated with highly conformal radiation therapy esophageal wall dose-surface histograms (DSHs) and polar dose-surface maps (DSMs) were generated. DSMs were used to generate new DSHs and dose-length-histograms that incorporate spatial information of the dose-surface distribution. From these histograms dose parameters were derived and univariate logistic regression analysis showed that they correlated significantly with AET. Following our previous work, new multivariable NTCP models were developed using the most significant dose histogram parameters based on univariate analysis (19 in total). However, the 19 new models incorporating esophageal wall dose-surface data with spatial information did not show improved predictive performance (area under the curve, AUC range 0.79-0.84) over the established multivariable NTCP model based on conventional dose-volume data (AUC  =  0.84). For prediction of AET, based on the proposed multivariable statistical approach, spatial information of the esophageal wall dose distribution is of no added value and it is sufficient to only consider MED as a predictive dosimetric parameter.

Magnetic domain wall conduits for single cell applications.

PubMed

Donolato, M; Torti, A; Kostesha, N; Deryabina, M; Sogne, E; Vavassori, P; Hansen, M F; Bertacco, R

2011-09-07

The ability to trap, manipulate and release single cells on a surface is important both for fundamental studies of cellular processes and for the development of novel lab-on-chip miniaturized tools for biological and medical applications. In this paper we demonstrate how magnetic domain walls generated in micro- and nano-structures fabricated on a chip surface can be used to handle single yeast cells labeled with magnetic beads. In detail, first we show that the proposed approach maintains the microorganism viable, as proven by monitoring the division of labeled yeast cells trapped by domain walls over 16 hours. Moreover, we demonstrate the controlled transport and release of individual yeast cells via displacement and annihilation of individual domain walls in micro- and nano-sized magnetic structures. These results pave the way to the implementation of magnetic devices based on domain walls technology in lab-on-chip systems devoted to accurate individual cell trapping and manipulation.

Enzymes and other agents that enhance cell wall extensibility

NASA Technical Reports Server (NTRS)

Cosgrove, D. J.

1999-01-01

Polysaccharides and proteins are secreted to the inner surface of the growing cell wall, where they assemble into a network that is mechanically strong, yet remains extensible until the cells cease growth. This review focuses on the agents that directly or indirectly enhance the extensibility properties of growing walls. The properties of expansins, endoglucanases, and xyloglucan transglycosylases are reviewed and their postulated roles in modulating wall extensibility are evaluated. A summary model for wall extension is presented, in which expansin is a primary agent of wall extension, whereas endoglucanases, xyloglucan endotransglycosylase, and other enzymes that alter wall structure act secondarily to modulate expansin action.

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

PubMed Central

Ashkenazy, Haim; Abadi, Shiran; Martz, Eric; Chay, Ofer; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir

2016-01-01

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. PMID:27166375

Hypothesis on interactions of macromolecules based on molecular vibration patterns in cells and tissues.

PubMed

Jaross, Werner

2018-01-01

The molecular vibration patterns of structure-forming macromolecules in the living cell create very specific electromagnetic frequency patterns which might be used for information on spatial position in the three-dimensional structure as well as the chemical characteristics. Chemical change of a molecule results in a change of the vibration pattern and thus in a change of the emitted electromagnetic frequency pattern. These patterns have to be received by proteins responsible for the necessary interactions and functions. Proteins can function as resonators for frequencies in the range of 1013-1015 Hz. The individual frequency pattern is defined by the amino acid sequence and the polarity of every amino acid caused by their functional groups. If the arriving electromagnetic signal pattern and the emitted pattern of the absorbing protein are matched in relevant parts and in opposite phase, photon energy in the characteristic frequencies can be transferred resulting in a conformational change of that molecule and respectively in an increase of its specific activity. The electromagnetic radiation is very weak. The possibilities to overcome intracellular distances are shown. The motor-driven directed transport of macromolecules starts in the Golgi apparatus. The relevance of molecular interactions based on this signaling for the induction and navigation in the intracellular transport is discussed.

Role of tumor–host interactions in interstitial diffusion of macromolecules: Cranial vs. subcutaneous tumors

PubMed Central

Pluen, Alain; Boucher, Yves; Ramanujan, Saroja; McKee, Trevor D.; Gohongi, Takeshi; di Tomaso, Emmanuelle; Brown, Edward B.; Izumi, Yotaro; Campbell, Robert B.; Berk, David A.; Jain, Rakesh K.

2001-01-01

The large size of many novel therapeutics impairs their transport through the tumor extracellular matrix and thus limits their therapeutic effectiveness. We propose that extracellular matrix composition, structure, and distribution determine the transport properties in tumors. Furthermore, because the characteristics of the extracellular matrix largely depend on the tumor–host interactions, we postulate that diffusion of macromolecules will vary with tumor type as well as anatomical location. Diffusion coefficients of macromolecules and liposomes in tumors growing in cranial windows (CWs) and dorsal chambers (DCs) were measured by fluorescence recovery after photobleaching. For the same tumor types, diffusion of large molecules was significantly faster in CW than in DC tumors. The greater diffusional hindrance in DC tumors was correlated with higher levels of collagen type I and its organization into fibrils. For molecules with diameters comparable to the interfibrillar space the diffusion was 5- to 10-fold slower in DC than in CW tumors. The slower diffusion in DC tumors was associated with a higher density of host stromal cells that synthesize and organize collagen type I. Our results point to the necessity of developing site-specific drug carriers to improve the delivery of molecular medicine to solid tumors. PMID:11274375

Critical considerations for developing nucleic acid macromolecule based drug products.

PubMed

Muralidhara, Bilikallahalli K; Baid, Rinku; Bishop, Steve M; Huang, Min; Wang, Wei; Nema, Sandeep

2016-03-01

Protein expression therapy using nucleic acid macromolecules (NAMs) as a new paradigm in medicine has recently gained immense therapeutic potential. With the advancement of nonviral delivery it has been possible to target NAMs against cancer, immunodeficiency and infectious diseases. Owing to the complex and fragile structure of NAMs, however, development of a suitable, stable formulation for a reasonable product shelf-life and efficacious delivery is indeed challenging to achieve. This review provides a synopsis of challenges in the formulation and stability of DNA/m-RNA based medicines and probable mitigation strategies including a brief summary of delivery options to the target cells. Nucleic acid based drugs at various stages of ongoing clinical trials are compiled. Copyright © 2016. Published by Elsevier Ltd.

The mecillinam resistome reveals a role for peptidoglycan endopeptidases in stimulating cell wall synthesis in Escherichia coli.

PubMed

Lai, Ghee Chuan; Cho, Hongbaek; Bernhardt, Thomas G

2017-07-01

Bacterial cells are typically surrounded by an net-like macromolecule called the cell wall constructed from the heteropolymer peptidoglycan (PG). Biogenesis of this matrix is the target of penicillin and related beta-lactams. These drugs inhibit the transpeptidase activity of PG synthases called penicillin-binding proteins (PBPs), preventing the crosslinking of nascent wall material into the existing network. The beta-lactam mecillinam specifically targets the PBP2 enzyme in the cell elongation machinery of Escherichia coli. Low-throughput selections for mecillinam resistance have historically been useful in defining mechanisms involved in cell wall biogenesis and the killing activity of beta-lactam antibiotics. Here, we used transposon-sequencing (Tn-Seq) as a high-throughput method to identify nearly all mecillinam resistance loci in the E. coli genome, providing a comprehensive resource for uncovering new mechanisms underlying PG assembly and drug resistance. Induction of the stringent response or the Rcs envelope stress response has been previously implicated in mecillinam resistance. We therefore also performed the Tn-Seq analysis in mutants defective for these responses in addition to wild-type cells. Thus, the utility of the dataset was greatly enhanced by determining the stress response dependence of each resistance locus in the resistome. Reasoning that stress response-independent resistance loci are those most likely to identify direct modulators of cell wall biogenesis, we focused our downstream analysis on this subset of the resistome. Characterization of one of these alleles led to the surprising discovery that the overproduction of endopeptidase enzymes that cleave crosslinks in the cell wall promotes mecillinam resistance by stimulating PG synthesis by a subset of PBPs. Our analysis of this activation mechanism suggests that, contrary to the prevailing view in the field, PG synthases and PG cleaving enzymes need not function in multi-enzyme complexes

Surface debris of canal walls after post space preparation in endodontically treated teeth: a scanning electron microscopic study.

PubMed

Serafino, Cinzia; Gallina, Giuseppe; Cumbo, Enzo; Ferrari, Marco

2004-03-01

To evaluate surface cleanliness of root canal walls along post space after endodontic treatment using 2 different irrigant regimens, obturation techniques, and post space preparation for adhesive bonding. Forty teeth, divided into 4 groups, were instrumented, using Ni-Ti rotary files, irrigated with NaOCl or NaOCl+EDTA and obturated with cold lateral condensation (CLC) or warm vertical condensation (WVC) of gutta-percha. After post space preparation, etching, and washing procedure, canal walls were observed using a scanning electron microscope (SEM). Amount of debris, smear layer, sealer/gutta-percha remnants, and visibility of open tubules were rated. Higher amounts of rough debris, large sealer/gutta-percha remnants, thick smear layer, and no visibility of tubule orifices were recorded in all the groups at apical level of post space. At middle and coronal levels areas of clean dentin, alternating with areas covered by thin smear layer, smaller debris, gutta-percha remnants, and orifices of tubules partially or totally occluded by plugs were frequently observed. After endodontic treatment, obturation, and post space preparation SEM analysis of canal walls along post space shows large areas (covered by smear layer, debris, and sealer/gutta-percha remnants) not available for adhesive bonding and resin cementation of fiber posts.

Equilibrium Wall Model Implementation in a Nodal Finite Element Flow Solver JENRE for Large Eddy Simulations

DTIC Science & Technology

2017-11-13

condition is applied to the inviscid and viscous fluxes on the wall to satisfy the surface physical condition, but a non -zero surface tangential...velocity profiles and turbulence quantities predicted by the current wall-model implementation agree well with available experimental data and...implementations. The volume and surface integrals based on the non -zero surface velocity in a cell adjacent to the wall show a good agreement with those

Synthesis and evaluation of macromolecule-bound derivatives of a peptidyl-1-beta-D-arabinofuranosylcytosine prodrug.

PubMed

Balajthy, Zoltan

2008-04-01

Macromolecule-bound Val-Leu-Lys-ara-C (1) prodrugs were synthesized with spacers (-HN-(CH(2))(x)-CO-; x =1,3,5) between the dextran carrier (T-70) and 1, in order to achieve a sustained-release drug delivery system dextran-NH-(CH(2))(x:1,3,5)-CO-Val-Leu-Lys-ara-C (5, 6 and 7). The conjugation increased the stability of 1 in aqueous buffer solutions by three times (t((1/2)) 53.0 h, pH 7.4). The length of spacer also regulated the rate of hydrolysis of the prodrugs in serum. The shortest spacer (-HN-(CH(2))-CO-, (2)) in 5 provided the best protection of 1 against the hydrolyzing ability of proteinase- alpha(2)-macroglobulin complexes, increasing its half-life approximately 30-fold. The conjugation procedure resulted in a growth arrest ability for macromolecular-bound prodrugs 5, 6 and 7 against L1210 with IC(50) of 0.01 microM in vitro, which is significantly lower than that of other ara-C-macromolecule conjugates. 5 and 6 arrested cell growth in a broader range of concentration, between 1 x 10(-5)-1.0 microM, than ara-C could.

Molecular surface mesh generation by filtering electron density map.

PubMed

Giard, Joachim; Macq, Benoît

2010-01-01

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

Catalytic Activity of a Binary Informational Macromolecule

NASA Technical Reports Server (NTRS)

Reader, John S.; Joyce, Gerald F.

2003-01-01

RNA molecules are thought to have played a prominent role in the early history of life on Earth based on their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, due to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unie'. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyze the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalyzed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

SURFACE MODIFICATION OF SILICA- AND CELLULOSE-BASED MICROFILTRATION MEMBRANES WITH FUNCTIONAL POLYAMINO ACIDS FOR HEAVY METAL SORPTION

EPA Science Inventory

Functionalized membranes represent a field with multiple applications. Examination of specific metal-macromolecule interactions on these surfaces presents an excellent method for characterizion of these materials. These interactions may also be exploited for heavy metal sorptio...

The effects of temperature on the surface resistivity of polyvinyl alcohol (PVA) thin films doped with silver nanoparticles and multi-walled carbon-nanotubes for optoelectronic and sensor applications

NASA Astrophysics Data System (ADS)

Polius, Jemilia R.

This thesis reports measurements of the temperature-dependent surface resistivity of multi-wall carbon nanotube doped polyvinyl alcohol (PVA) thin films. In the temperature range from 22°C to 40°C in a humidity controlled environment, it was found that the surface resistivity decreased initially but raised as the temperature continued to increase. I report surface resistivity measurements as a function of temperature of both multiwall and single-wall carbon nanotube doped PVA thin films, with comparison of the similarities and differences between the two types of film types. This research was conducted using the combined instrumentation of the KEITHLEY Model 6517 Electrometer and the KEITHLEY Model 8009 resistivity test fixture using both commercial and in-house produced organic thin films.

Film Self-Assembly of Oppositely Charged Macromolecules Triggered by Electrochemistry through a Morphogenic Approach.

PubMed

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.

Application of Polypyrrole Multi-Walled Carbon Nanotube Composite Layer for Detection of Mercury, Lead and Iron Ions Using Surface Plasmon Resonance Technique

PubMed Central

Sadrolhosseini, Amir Reza; Noor, A. S. M.; Bahrami, Afarin; Lim, H. N.; Talib, Zainal Abidin; Mahdi, Mohd. Adzir

2014-01-01

Polypyrrole multi-walled carbon nanotube composite layers were used to modify the gold layer to measure heavy metal ions using the surface plasmon resonance technique. The new sensor was fabricated to detect trace amounts of mercury (Hg), lead (Pb), and iron (Fe) ions. In the present research, the sensitivity of a polypyrrole multi-walled carbon nanotube composite layer and a polypyrrole layer were compared. The application of polypyrrole multi-walled carbon nanotubes enhanced the sensitivity and accuracy of the sensor for detecting ions in an aqueous solution due to the binding of mercury, lead, and iron ions to the sensing layer. The Hg ion bonded to the sensing layer more strongly than did the Pb and Fe ions. The limitation of the sensor was calculated to be about 0.1 ppm, which produced an angle shift in the region of 0.3° to 0.6°. PMID:24733263

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

PubMed

Hagiwara, Yohsuke; Tateno, Masaru

2010-10-20

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

A rapid live-cell ELISA for characterizing antibodies against cell surface antigens of Chlamydomonas reinhardtii and its use in isolating algae from natural environments with related cell wall components.

PubMed

Jiang, Wenzhi; Cossey, Sarah; Rosenberg, Julian N; Oyler, George A; Olson, Bradley J S C; Weeks, Donald P

2014-09-25

Cell walls are essential for most bacteria, archaea, fungi, algae and land plants to provide shape, structural integrity and protection from numerous biotic and abiotic environmental factors. In the case of eukaryotic algae, relatively little is known of the composition, structure or mechanisms of assembly of cell walls in individual species or between species and how these differences enable algae to inhabit a great diversity of environments. In this paper we describe the use of camelid antibody fragments (VHHs) and a streamlined ELISA assay as powerful new tools for obtaining mono-specific reagents for detecting individual algal cell wall components and for isolating algae that share a particular cell surface component. To develop new microalgal bioprospecting tools to aid in the search of environmental samples for algae that share similar cell wall and cell surface components, we have produced single-chain camelid antibodies raised against cell surface components of the single-cell alga, Chlamydomonas reinhardtii. We have cloned the variable-region domains (VHHs) from the camelid heavy-chain-only antibodies and overproduced tagged versions of these monoclonal-like antibodies in E. coli. Using these VHHs, we have developed an accurate, facile, low cost ELISA that uses live cells as a source of antigens in their native conformation and that requires less than 90 minutes to perform. This ELISA technique was demonstrated to be as accurate as standard ELISAs that employ proteins from cell lysates and that generally require >24 hours to complete. Among the cloned VHHs, VHH B11, exhibited the highest affinity (EC50 < 1 nM) for the C. reinhardtii cell surface. The live-cell ELISA procedure was employed to detect algae sharing cell surface components with C. reinhardtii in water samples from natural environments. In addition, mCherry-tagged VHH B11 was used along with fluorescence activated cell sorting (FACS) to select individual axenic isolates of presumed wild

DNS and modeling of the interaction between turbulent premixed flames and walls

NASA Technical Reports Server (NTRS)

Poinsot, T. J.; Haworth, D. C.

1992-01-01

The interaction between turbulent premixed flames and walls is studied using a two-dimensional full Navier-Stokes solver with simple chemistry. The effects of wall distance on the local and global flame structure are investigated. Quenching distances and maximum wall heat fluxes during quenching are computed in laminar cases and are found to be comparable to experimental and analytical results. For turbulent cases, it is shown that quenching distances and maximum heat fluxes remain of the same order as for laminar flames. Based on simulation results, a 'law-of-the-wall' model is derived to describe the interaction between a turbulent premixed flame and a wall. This model is constructed to provide reasonable behavior of flame surface density near a wall under the assumption that flame-wall interaction takes place at scales smaller than the computational mesh. It can be implemented in conjunction with any of several recent flamelet models based on a modeled surface density equation, with no additional constraints on mesh size or time step.

Surface tension effects on the behavior of a cavity growing, collapsing, and rebounding near a rigid wall.

PubMed

Zhang, Zhen-yu; Zhang, Hui-sheng

2004-11-01

Surface tension effects on the behavior of a pure vapor cavity or a cavity containing some noncondensible contents, which is growing, collapsing, and rebounding axisymmetrically near a rigid wall, are investigated numerically by the boundary integral method for different values of dimensionless stand-off parameter gamma, buoyancy parameter delta, and surface tension parameter beta. It is found that at the late stage of the collapse, if the resultant action of the Bjerknes force and the buoyancy force is not small, surface tension will not have significant effects on bubble behavior except that the bubble collapse time is shortened and the liquid jet becomes wider. If the resultant action of the two force is small enough, surface tension will have significant and in some cases substantial effects on bubble behavior, such as changing the direction of the liquid jet, making a new liquid jet appear, in some cases preventing the bubble from rebound before jet impact, and in other cases causing the bubble to rebound or even recollapse before jet impact. The mechanism of surface tension effects on the collapsing behavior of a cavity has been analyzed. The mechanisms of some complicated phenomena induced by surface tension effects are illustrated by analysis of the computed velocity fields and pressure contours of the liquid flow outside the bubble at different stages of the bubble evolution.

Biosynthesis of plant cell wall polysaccharides.

PubMed

Gibeaut, D M; Carpita, N C

1994-09-01

The cell wall is the principal structural element of plant form. Cellulose, long crystals of several dozen glucan chains, forms the microfibrillar foundation of plant cell walls and is synthesized at the plasma membrane. Except for callose, all other noncellulosic components are secreted to the cell surface and form a porous matrix assembled around the cellulose microfibrils. These diverse noncellulosic polysaccharides and proteins are made in the endomembrane system. Many questions about the biosynthesis and modification within the Golgi apparatus and integration of cell components at the cell surface remain unanswered. The lability of synthetic complexes upon isolation is one reason for slow progress. However, with new methods of membrane isolation and analysis of products in vitro, recent advances have been made in purifying active synthases from plasma membrane and Golgi apparatus. Likely synthase polypeptides have been identified by affinity-labeling techniques, but we are just beginning to understand the unique features of the coordinated assembly of complex polysaccharides. Nevertheless, such progress renews hope that the first gene of a synthase for a wall polysaccharide from higher plants is within our grasp.

Efficient Intracellular siRNA Delivery by Ethyleneimine-Modified Amphiphilic Macromolecules

PubMed Central

Sparks, Sarah M.; Waite, Carolyn L.; Harmon, Alexander M.; Nusblat, Leora M.; Roth, Charles M.; Uhrich, Kathryn E.

2013-01-01

Summary New materials that can bind and deliver oligonucleotides such as short interfering RNA (siRNA) without toxicity are greatly needed to fulfill the promise of therapeutic gene silencing. Amphiphilic macromolecules (AMs) were functionalized with linear ethyleneimines to create cationic AMs capable of complexing with siRNA. Structurally, the parent AM is formed from a mucic acid backbone whose tetra-hydroxy groups are alkylated with 12-carbon aliphatic chains to form the hydrophobic component of the macromolecule. This alkylated mucic acid is then mono-functionalized with poly(ethylene glycol) (PEG) as a hydrophilic component. The resulting AM contains a free carboxylic acid within the hydrophobic domain. In this work, linear ethyleneimines were conjugated to the free carboxylic acid to produce an AM with one primary amine (1N) or one primary amine and four secondary amines (5N). Further, an AM with amine substitution both to the free carboxylic acid in the hydrophobic domain and also to the adjacent PEG was synthesized to produce a polymer with one primary amine and eight secondary amines (9N), four located on each side of the AM hydrophobic domain. All amine-functionalized AMs formed nanoscale micelles but only the 5N and 9N AMs had cationic zeta potentials, which increased with increasing number of amines. All AMs exhibited less inherent cytotoxicity than linear polyethyleneimine (L-PEI) at concentrations of 10 µM and above. By increasing the length of the cationic ethyleneimine chain and the total number of amines, successful siRNA complexation and cellular siRNA delivery was achieved in a malignant glioma cell line. In addition, siRNA-induced silencing of firefly luciferase was observed using complexes of siRNA with the 9N AM and comparable to L-PEI, yet showed better cell viability at higher concentrations (above 10 µM). This work highlights the promise of cationic AMs as safe and efficient synthetic vectors for siRNA delivery. Specifically, a novel

Direct visualization of the arterial wall water permeability barrier using CARS microscopy

PubMed Central

Lucotte, Bertrand M.; Powell, Chloe; Knutson, Jay R.; Combs, Christian A.; Malide, Daniela; Yu, Zu-Xi; Knepper, Mark; Patel, Keval D.; Pielach, Anna; Johnson, Errin; Borysova, Lyudmyla; Balaban, Robert S.

2017-01-01

The artery wall is equipped with a water permeation barrier that allows blood to flow at high pressure without significant water leak. The precise location of this barrier is unknown despite its importance in vascular function and its contribution to many vascular complications when it is compromised. Herein we map the water permeability in intact arteries, using coherent anti-Stokes Raman scattering (CARS) microscopy and isotopic perfusion experiments. Generation of the CARS signal is optimized for water imaging with broadband excitation. We identify the water permeation barrier as the endothelial basolateral membrane and show that the apical membrane is highly permeable. This is confirmed by the distribution of the AQP1 water channel within endothelial membranes. These results indicate that arterial pressure equilibrates within the endothelium and is transmitted to the supporting basement membrane and internal elastic lamina macromolecules with minimal deformation of the sensitive endothelial cell. Disruption of this pressure transmission could contribute to endothelial cell dysfunction in various pathologies. PMID:28373558

Exciton Scattering approach for conjugated macromolecules: from electronic spectra to electron-phonon coupling

NASA Astrophysics Data System (ADS)

Tretiak, Sergei

2014-03-01

The exciton scattering (ES) technique is a multiscale approach developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, the electronic excitations in the molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph. The exciton propagation on the linear segments is characterized by the exciton dispersion, whereas the exciton scattering on 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. All parameters can be extracted from quantum-chemical computations of small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within considered molecular family could be performed with negligible numerical effort. The exciton scattering properties of molecular vertices can be further described by tight-binding or equivalently lattice models. The on-site energies and hopping constants are obtained from the exciton dispersion and scattering matrices. Such tight-binding model approach is particularly useful to describe the exciton-phonon coupling, energetic disorder and incoherent energy transfer in large branched conjugated molecules. Overall the ES applications 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.

Turbulent flame-wall interaction: a DNS study

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

Chen, Jackie; Hawkes, Evatt R; Sankaran, Ramanan

2010-01-01

A turbulent flame-wall interaction (FWI) configuration is studied using three-dimensional direct numerical simulation (DNS) and detailed chemical kinetics. The simulations are used to investigate the effects of the wall turbulent boundary layer (i) on the structure of a hydrogen-air premixed flame, (ii) on its near-wall propagation characteristics and (iii) on the spatial and temporal patterns of the convective wall heat flux. Results show that the local flame thickness and propagation speed vary between the core flow and the boundary layer, resulting in a regime change from flamelet near the channel centreline to a thickened flame at the wall. This findingmore » has strong implications for the modelling of turbulent combustion using Reynolds-averaged Navier-Stokes or large-eddy simulation techniques. Moreover, the DNS results suggest that the near-wall coherent turbulent structures play an important role on the convective wall heat transfer by pushing the hot reactive zone towards the cold solid surface. At the wall, exothermic radical recombination reactions become important, and are responsible for approximately 70% of the overall heat release rate at the wall. Spectral analysis of the convective wall heat flux provides an unambiguous picture of its spatial and temporal patterns, previously unobserved, that is directly related to the spatial and temporal characteristic scalings of the coherent near-wall turbulent structures.« less

Formation of Micro-Scale Gas Pockets From Underwater Wall Orifices

NASA Astrophysics Data System (ADS)

Pereira, Francisco A.; Gharib, Morteza

2012-11-01

Our experiments examine the formation of micro-scale gas pockets from orifices on walls with hydrophilic and hydrophobic wetting properties. Bubble injection is operated in a liquid at rest at constant flow rate and in a quasi-static regime, and the mechanism of bubble growth is investigated through high speed recordings. The growth dynamics is studied in terms of orifice size, surface wetting properties and buoyancy sign. The bubble formation is characterized by an explosive growth, with a pressure wave that causes the bubble to take highly transient shapes in its very initial stages, before stabilizing as a sphere and growing at a relatively slow rate. In case of positive buoyancy, the bubble elongates with the formation of a neck before detaching from the wall. When buoyancy acts towards the wall, the bubble attaches to the wall and expands laterally with a moving contact line. In presence of hydrophobic surfaces, the bubble attaches immediately to the wall irrespective of buoyancy direction and takes a hemispherical shape, expanding radially along the surface. A force balance is outlined to explain the different figures. The work was performed by FAP while on leave from CNR-INSEAN, and is supported by the Office of Naval Research (ONR).

Flow Kills Conductivity of Single Wall Carbon Nanotubes (SWNT) Composites

NASA Astrophysics Data System (ADS)

Bhatt, Sanjiv; Macosko, Christopher

2006-03-01

Most composites of polymer and single wall carbon nanotubes (SWNT) reported in the literature are made by solvent casting or simple compression molding. Commercial utility of these composites requires use of precision injection molding. We have observed a unique behavior wherein the SWNT composites made by injection molding or by extrusion are insulators but upon heating become electrically conductive. This behavior appears to be the result of a relaxation phenomenon in the SWNT composite. During flow into an injection mold or through an extrusion die the well-dispersed SWNT in the polymer matrix tend to align such that they are not in contact with each other and are farther than the minimum required distance, 5 nm (1), to achieve electrical percolation through electron hopping. Upon heating the SWNT relax and either touch each other or are at a distance less than or equal to 5 nm from each other to create a percolating. [1] Du, F., Scogna, R, C., Zhou, W., Brand, Stijn, Fischer, J. E., and Winey, K. I., Macromolecules 2004, 37, 9048-9055.

Hydrodynamic Trapping of Swimming Bacteria by Convex Walls

NASA Astrophysics Data System (ADS)

Sipos, O.; Nagy, K.; Di Leonardo, R.; Galajda, P.

2015-06-01

Swimming bacteria display a remarkable tendency to move along flat surfaces for prolonged times. This behavior may have a biological importance but can also be exploited by using microfabricated structures to manipulate bacteria. The main physical mechanism behind the surface entrapment of swimming bacteria is, however, still an open question. By studying the swimming motion of Escherichia coli cells near microfabricated pillars of variable size, we show that cell entrapment is also present for convex walls of sufficiently low curvature. Entrapment is, however, markedly reduced below a characteristic radius. Using a simple hydrodynamic model, we predict that trapped cells swim at a finite angle with the wall and a precise relation exists between the swimming angle at a flat wall and the critical radius of curvature for entrapment. Both predictions are quantitatively verified by experimental data. Our results demonstrate that the main mechanism for wall entrapment is hydrodynamic in nature and show the possibility of inhibiting cell adhesion, and thus biofilm formation, using convex features of appropriate curvature.

A novel solution for LED wall lamp design and simulation

NASA Astrophysics Data System (ADS)

Ge, Rui; Hong, Weibin; Li, Kuangqi; Liang, Pengxiang; Zhao, Fuli

2014-11-01

The model of the wall washer lamp and the practical illumination application have been established with a new design of the lens to meet the uniform illumination demand for wall washer lamp based on the Lambertian light sources. Our secondary optical design of freeform surface lens to LED wall washer lamp based on the conservation law of energy and Snell's law can improve the lighting effects as a uniform illumination. With the relationship between the surface of the lens and the surface of the target, a great number of discrete points of the freeform profile curve were obtained through the iterative method. After importing the data into our modeling program, the optical entity was obtained. Finally, to verify the feasibility of the algorithm, the model was simulated by specialized software, with both the LED Lambertian point source and LED panel source model.

Molecular dynamics simulations of the orientation properties of cytochrome c on the surface of single-walled carbon nanotubes.

PubMed

Zhang, Bing; Xu, Jia; Mo, Shu-Fan; Yao, Jian-Xi; Dai, Song-Yuan

2016-12-01

Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.

Method and apparatus for detecting irregularities on or in the wall of a vessel

DOEpatents

Bowling, Michael Keith

2000-09-12

A method of detecting irregularities on or in the wall of a vessel by detecting localized spatial temperature differentials on the wall surface, comprising scanning the vessel surface with a thermal imaging camera and recording the position of the or each region for which the thermal image from the camera is indicative of such a temperature differential across the region. The spatial temperature differential may be formed by bacterial growth on the vessel surface; alternatively, it may be the result of defects in the vessel wall such as thin regions or pin holes or cracks. The detection of leaks through the vessel wall may be enhanced by applying a pressure differential or a temperature differential across the vessel wall; the testing for leaks may be performed with the vessel full or empty, and from the inside or the outside.

SGS Closure Methodology for Surface-layer Rough-wall Turbulence.

NASA Astrophysics Data System (ADS)

Brasseur, James G.; Juneja, Anurag

1998-11-01

As reported in another abstract, necessary under-resolution and anisotropy of integral scales near the surface in LES of rough-wall boundary layers cause errors in the statistical structure of the modeled subgrid-scale (SGS) acceleration using eddy viscosity and similarity closures. The essential difficulty is an overly strong coupling between the modeled SGS stress tensor and predicted resolved velocity u^r. Specific to this problem, we propose a class of SGS closures in which subgrid scale velocities u^s1 between an explicit filter scale Δ and the grid scale δ are estimated from the solution to a separate prognostic equation, and the SGS stress tensor is formed using u^s1 as a surrogate for subgrid velocity u^s. The method is currently under development for pseudo-spectral LES where a filter at scales δ < Δ is explicit. The exact evolution equation for u^s1 contains dynamical interactions between u^r and u^s1 which can be calculated directly, and a term which is modeled to capture energy flux from the s1 scales without altering u^s1 structure. Three levels of closure for SGS stress are possible at different levels of accuracy and computational expense. The cheapest model has been tested with DNS and LES of anisotropic buoyancy-driven turbulence. Preliminary results show major improvement in the structure of the predicted SGS acceleration with much of the spurious coupling between u^r and SGS stress removed. Performance, predictions and cost of the three levels of closure are under analysis.

Locomotion in a liquid crystal near a wall

NASA Astrophysics Data System (ADS)

Powers, Thomas; Krieger, Madison; Spagnolie, Saverio

2015-11-01

Recent observations of bacteria swimming in nematic liquid crystal solution motivate the theoretical study of how swimming speed depends on liquid crystal properties. We consider the Taylor sheet near a wall, in which propulsion is achieved by the propagation of traveling waves along the length of the swimmer. Using the lubrication approximation, we determine how swimming speed depends on the Ericksen number, which is the ratio of elastic to viscous stresses. We also study the effect of anchoring strength, at the surface of the swimmer and the surface of the wall. Supported by NSF-CBET 1437195.

Protective interior wall and attaching means for a fusion reactor vacuum vessel

DOEpatents

Phelps, R.D.; Upham, G.A.; Anderson, P.M.

1985-03-01

The wall basically consists of an array of small rectangular plates attached to the existing walls with threaded fasteners. The protective wall effectively conceals and protects all mounting hardware beneath the plate array, while providing a substantial surface area that will absorb plasma energy.

Permeation enhancing polymers in oral delivery of hydrophilic macromolecules: thiomer/GSH systems.

PubMed

Bernkop-Schnürch, A; Kast, C E; Guggi, D

2003-12-05

Thiolated polymers (= thiomers) in combination with reduced glutathione (GSH) were shown to improve the uptake of hydrophilic macromolecules from the GI tract. The mechanism responsible for this permeation enhancing effect seems to be based on the thiol groups of the polymer. These groups inhibit protein tyrosine phosphatase, being involved in the closing process of tight junctions, via a GSH-mediated mechanism. The strong permeation enhancing effect of various thiomer/GSH systems such as poly(acrylic acid)-cysteine/GSH or chitosan-4-thio-butylamidine (chitosan-TBA)/GSH could be shown via permeation studies on freshly excised intestinal mucosa in Ussing-type chambers. Furthermore, the efficacy of the system was also shown in vivo. By utilizing poly(acrylic acid)-cysteine/GSH as carrier matrix, an absolute oral bioavailability for low molecular weight heparin of 19.9 +/- 9.3% and a pharmacological efficacy--calculated on the basis of the areas under the reduction in serum glucose levels of the oral formulation versus subcutaneous (s.c.) injection-for orally given insulin of 7% could be achieved. The incorporation of salmon calcitonin in chitosan-TBA/GSH led on the other hand to a pharmacological efficacy based on the areas under the reduction in plasma calcium levels of the oral thiomer formulation versus intravenous (i.v.) injection of 1.3%. Because of this high efficacy (i), the possibility to combine thiomer/GSH systems with additional low molecular weight permeation enhancers acting in other ways (ii) and minimal toxicological risks as these polymers are not absorbed from the GI tract (iii), thiolated polymers represent a promising novel tool for the oral administration of hydrophilic macromolecules.

Application of fluorescently labeled tracer technique for detection of natural active macromolecules in Chinese medicine.

PubMed

Zeng, Qiao-Hui; Zhang, Xue-Wu; Xu, Kai-Peng; Jiang, Jian-Guo

2014-02-01

Active substances in traditional Chinese Medicine (TCM) contain not only a variety of small molecules, but also many other macromolecules (TCMMs), such as proteins, peptides and polysaccharides. Active TCMM can achieve good therapeutic effects by regulating the body's overall function with lower side effects. This review summarized the literatures published in recent years on the application of fluorescently labeled tracer technique for detection of natural active macromolecules in TCM. Classified by fluorescent markers, applications of fluorescein, rhodamine, and quantum dots (QDs) in TCMM active tracer are reviewed, and the methods and principles of TCMM fluorescent marker are illustrated. Studies on active TCMMs and their action mechanism are quite difficult due to a multitarget, multicomponent, and multipath system of TCM. However, the development of fluorescently labeled active tracer technique (FLATT) provides this research with new tools. Traditional fluorescent markers have many deficiencies, such as easily quenched, short luminous cycle, and intrinsic toxicity. Relatively, FLATT has many obvious advantages, and its application in TCMM is still at the early stage. In order to improve the overall level of fluorescence labeling in TCMM active tracer, the improvement on FLATT's detection sensitivity and biological affinity is urgent and critical to allow study of these interesting molecules.

Quantitative elasticity measurement of urinary bladder wall using laser-induced surface acoustic waves.

PubMed

Li, Chunhui; Guan, Guangying; Zhang, Fan; Song, Shaozhen; Wang, Ruikang K; Huang, Zhihong; Nabi, Ghulam

2014-12-01

The maintenance of urinary bladder elasticity is essential to its functions, including the storage and voiding phases of the micturition cycle. The bladder stiffness can be changed by various pathophysiological conditions. Quantitative measurement of bladder elasticity is an essential step toward understanding various urinary bladder disease processes and improving patient care. As a nondestructive, and noncontact method, laser-induced surface acoustic waves (SAWs) can accurately characterize the elastic properties of different layers of organs such as the urinary bladder. This initial investigation evaluates the feasibility of a noncontact, all-optical method of generating and measuring the elasticity of the urinary bladder. Quantitative elasticity measurements of ex vivo porcine urinary bladder were made using the laser-induced SAW technique. A pulsed laser was used to excite SAWs that propagated on the bladder wall surface. A dedicated phase-sensitive optical coherence tomography (PhS-OCT) system remotely recorded the SAWs, from which the elasticity properties of different layers of the bladder were estimated. During the experiments, series of measurements were performed under five precisely controlled bladder volumes using water to estimate changes in the elasticity in relation to various urinary bladder contents. The results, validated by optical coherence elastography, show that the laser-induced SAW technique combined with PhS-OCT can be a feasible method of quantitative estimation of biomechanical properties.

Explosives screening on a vehicle surface

DOEpatents

Parmeter, John E.; Brusseau, Charles A.; Davis, Jerry D.; Linker, Kevin L.; Hannum, David W.

2005-02-01

A system for detecting particles on the outer surface of a vehicle has a housing capable of being placed in a test position adjacent to, but not in contact with, a portion of the outer surface of the vehicle. An elongate sealing member is fastened to the housing along a perimeter surrounding the wall, and the elongate sealing member has a contact surface facing away from the wall to contact the outer surface of the vehicle to define a test volume when the wall is in the test position. A gas flow system has at least one gas inlet extending through the wall for providing a gas stream against the surface of the vehicle within the test volume. This gas stream, which preferably is air, dislodges particles from the surface of the vehicle covered by the housing. The gas stream exits the test volume through a gas outlet and particles in the stream are detected.

Structural elucidation of Eucalyptus lignin and its dynamic changes in the cell walls during an integrated process of ionic liquids and successive alkali treatments.

PubMed

Li, Han-Yin; Wang, Chen-Zhou; Chen, Xue; Cao, Xue-Fei; Sun, Shao-Ni; Sun, Run-Cang

2016-12-01

An integrated process based on ionic liquids ([Bmim]Cl and [Bmim]OAc) pretreatment and successive alkali post-treatments (0.5, 2.0, and 4.0% NaOH at 90°C for 2h) was performed to isolate lignins from Eucalyptus. The structural features and spatial distribution of lignin in the Eucalyptus cell wall were investigated thoroughly. Results revealed that the ionic liquids pretreatment promoted the isolation of alkaline lignin from the pretreated samples without obvious structural changes. Additionally, the integrated process resulted in syringyl-rich lignin macromolecules with more β-O-4' linkages and less phenolic hydroxyl groups. Confocal Raman microscopy analysis showed that the dissolution behavior of lignin was varied in the morphologically distinct regions during the successive alkali treatments, and lignin dissolved was mainly stemmed from the secondary wall regions. These results provided some useful information for understanding the mechanisms of delignification during the integrated process and enhancing the potential utilizations of lignin in future biorefineries. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intimal and medial contributions to the hydraulic resistance of the arterial wall at different pressures: a combined computational and experimental study.

PubMed

Chooi, K Y; Comerford, A; Sherwin, S J; Weinberg, P D

2016-06-01

The hydraulic resistances of the intima and media determine water flux and the advection of macromolecules into and across the arterial wall. Despite several experimental and computational studies, these transport processes and their dependence on transmural pressure remain incompletely understood. Here, we use a combination of experimental and computational methods to ascertain how the hydraulic permeability of the rat abdominal aorta depends on these two layers and how it is affected by structural rearrangement of the media under pressure. Ex vivo experiments determined the conductance of the whole wall, the thickness of the media and the geometry of medial smooth muscle cells (SMCs) and extracellular matrix (ECM). Numerical methods were used to compute water flux through the media. Intimal values were obtained by subtraction. A mechanism was identified that modulates pressure-induced changes in medial transport properties: compaction of the ECM leading to spatial reorganization of SMCs. This is summarized in an empirical constitutive law for permeability and volumetric strain. It led to the physiologically interesting observation that, as a consequence of the changes in medial microstructure, the relative contributions of the intima and media to the hydraulic resistance of the wall depend on the applied pressure; medial resistance dominated at pressures above approximately 93 mmHg in this vessel. © 2016 The Authors.

High performance discharges in the Lithium Tokamak eXperiment with liquid lithium walls

DOE PAGES

Schmitt, J. C.; Bell, R. E.; Boyle, D. P.; ...

2015-05-15

The first-ever successful operation of a tokamak with a large area (40% of the total plasma surface area) liquid lithium wall has been achieved in the Lithium Tokamak eXperiment (LTX). These results were obtained with a new, electron beam-based lithium evaporation system, which can deposit a lithium coating on the limiting wall of LTX in a five-minute period. Preliminary analyses of diamagnetic and other data for discharges operated with a liquid lithium wall indicate that confinement times increased by 10 x compared to discharges with helium-dispersed solid lithium coatings. Ohmic energy confinement times with fresh lithium walls, solid and liquid,more » exceed several relevant empirical scaling expressions. Spectroscopic analysis of the discharges indicates that oxygen levels in the discharges limited on liquid lithium walls were significantly reduced compared to discharges limited on solid lithium walls. Finally, Tokamak operations with a full liquid lithium wall (85% of the total plasma surface area) have recently started.« less

Mechanosensation Dynamically Coordinates Polar Growth and Cell Wall Assembly to Promote Cell Survival.

PubMed

Davì, Valeria; Tanimoto, Hirokazu; Ershov, Dmitry; Haupt, Armin; De Belly, Henry; Le Borgne, Rémi; Couturier, Etienne; Boudaoud, Arezki; Minc, Nicolas

2018-04-23

How growing cells cope with size expansion while ensuring mechanical integrity is not known. In walled cells, such as those of microbes and plants, growth and viability are both supported by a thin and rigid encasing cell wall (CW). We deciphered the dynamic mechanisms controlling wall surface assembly during cell growth, using a sub-resolution microscopy approach to monitor CW thickness in live rod-shaped fission yeast cells. We found that polar cell growth yielded wall thinning and that thickness negatively influenced growth. Thickness at growing tips exhibited a fluctuating behavior with thickening phases followed by thinning phases, indicative of a delayed feedback promoting thickness homeostasis. This feedback was mediated by mechanosensing through the CW integrity pathway, which probes strain in the wall to adjust synthase localization and activity to surface growth. Mutants defective in thickness homeostasis lysed by rupturing the wall, demonstrating its pivotal role for walled cell survival. Copyright © 2018 Elsevier Inc. All rights reserved.

30 years of battling the cell wall.

PubMed

Latgé, J P

2017-01-01

In Aspergillus fumigatus, like in other pathogenic fungi, the cell wall is essential for fungal growth as well as for resisting environmental stresses such as phagocytic killing. Most of the chemical analyses undertaken on the cell wall of A. fumigatus are focused on the mycelial cell wall because it is the vegetative stage of the fungus. However, the cell walls of the mycelium and conidium (which is the infective propagule) are different especially at the level of the surface layer, which plays a significant role in the interaction between A. fumigatus conidia and phagocytic cells of the immune system. In spite of the essential function of the cell wall in fungal life, progresses have been extremely slow in the understanding of biosynthesis as well in the identification of the key host responses against the cell wall components. A major difficulty is the fact that the composition and structural organization of the cell wall is not immutably set and is constantly reshuffled depending on the environmental conditions. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Nonlinear vibration of double-walled boron nitride and carbon nanopeapods under multi-physical fields with consideration of surface stress effects

NASA Astrophysics Data System (ADS)

Ghorbanpour Arani, A.; Sabzeali, M.; BabaAkbar Zarei, H.

2017-12-01

In this study, the nonlinear thermo-electro vibrations of double-walled boron nitride nanopeapods (DWBNNPPs) and double-walled carbon nanopeapods (DWCNPPs) under magnetic field embedded in an elastic medium is investigated. DWBNNPPs are made of piezoelectric and smart materials therefore, electric field is effective on them; meanwhile, DWCNPPs are made of carbon thus, magnetic field can be useful to control them. The Pasternak model is used to simulate the effects of elastic medium which surrounds the system. Nanotubes are modeled with assumption of the Euler-Bernoulli beam (EBB) theory and the surface effects are considered to achieve accurate response of the system. Moreover, interaction between two layers is modeled by van der Waals (vdW) forces. The equations of motion are derived using the energy method and the Hamilton principle. Then the governing equations are solved by using Galerkin's method and incremental harmonic balance method (IHBM). The influences of various parameters such as the magnetic field, different types of DWCNPPs and DWBNNPPs, elastic medium, existence of fullerene and surface effect on the vibration behavior of the system are investigated. The results demonstrate that DWBNNPPs have more influence on the frequency of the system than DWCNPPs. In addition, the presence of fullerene in nanotubes has a negative impact on the frequency behavior of revisionthe system.

PREFACE: Domain wall dynamics in nanostructures Domain wall dynamics in nanostructures

NASA Astrophysics Data System (ADS)

Marrows, C. H.; Meier, G.

2012-01-01

Domain structures in magnetic materials are ubiquitous and have been studied for decades. The walls that separate them are topological defects in the magnetic order parameter and have a wide variety of complex forms. In general, their investigation is difficult in bulk materials since only the domain structure on the surface of a specimen is visible. Cutting the sample to reveal the interior causes a rearrangement of the domains into a new form. As with many other areas of magnetism, the study of domain wall physics has been revitalised by the advent of nanotechnology. The ability to fabricate nanoscale structures has permitted the formation of simplified and controlled domain patterns; the development of advanced microscopy methods has permitted them to be imaged and then modelled; subjecting them to ultrashort field and current pulses has permitted their dynamics to be explored. The latest results from all of these advances are described in this special issue. Not only has this led to results of great scientific beauty, but also to concepts of great applicability to future information technologies. In this issue the reader will find the latest results for these domain wall dynamics and the high-speed processes of topological structures such as domain walls and magnetic vortices. These dynamics can be driven by the application of magnetic fields, or by flowing currents through spintronic devices using the novel physics of spin-transfer torque. This complexity has been studied using a wide variety of experimental techniques at the edge of the spatial and temporal resolution currently available, and can be described using sophisticated analytical theory and computational modelling. As a result, the dynamics can be engineered to give rise to finely controlled memory and logic devices with new functionality. Moreover, the field is moving to study not only the conventional transition metal ferromagnets, but also complex heterostructures, novel magnets and even other

The geometry of slip surfaces in the hanging-wall of the Sierra Madre fault, La-Canada, California

NASA Astrophysics Data System (ADS)

Dor, O.; Sammis, C. G.; Ben-Zion, Y.

2009-12-01

Fault-slip data from the granitic hanging-wall of the Sierra Madre fault near La-Canada, California, show a steeply dipping conjugate set of cm- to decimeter scale slip surfaces (115 data samples) with moderate to strong inclinations of slip vectors. These off-fault damage elements may be associated with Mohr-Coulomb slip in the stress field of a propagating earthquake rupture. At the microscale, we identified two dominant fracture orientations. The first appears both near and far from the fault and is compatible with Andersonian failure on the main fault. The second appears only within meters from the fault and may be associated with the formation of the slip surfaces. Characterization of damage fabric in the microscale suggests that in-situ failure of grains under tension with minimal strain immediately above the fault plane may be associated with an opening mode of rupture. We conclude that the architecture of the slip surfaces was developed during slip events over a finite displacement history with fairly stable faulting conditions, and that with continuing displacement, as the rock mass approached the surface, a dynamic opening mode could have led to the shattering of grains in the immediate vicinity of the slip zone.

Vesicular thick-walled swollen hyphae in pulmonary zygomycosis.

PubMed

Kimura, Masatomo; Ito, Hiroyuki

2009-03-01

An autopsy case of pulmonary zygomycosis in a patient with rheumatoid arthritis on immunosuppressive therapy is presented herein. There was a pulmonary cavitated infarct caused by mycotic thrombosis. Thin-walled narrow hyphae and vesicular thick-walled swollen hyphae were found on the pleural surface and in the necrotic tissue at the periphery of the cavity. Findings of such shaped fungal elements may cause erroneous histopathological diagnosis because pauciseptate broad thin-walled hyphae are usually the only detectable fungal elements in zygomycosis tissue. Although immunohistochemistry confirmed these unusual elements to be zygomycetous in the present case, it is important for the differential diagnosis to be aware that zygomycetes can form thin narrow hyphae and vesicular thick-walled swollen hyphae.

Nanostructures and dynamics of macromolecules bound to attractive filler surfaces

NASA Astrophysics Data System (ADS)

Koga, Tad; Barkley, Deborah; Jiang, Naisheng; Endoh, Maya; Masui, Tomomi; Kishimoto, Hiroyuki; Nagao, Michihiro; Satija, Sushil; Taniguchi, Takashi

We report in-situ nanostructures and dynamics of polybutadiene (PB) chains bound to carbon black (CB) fillers (the so-called ``bound polymer layer (BPL)'') in a good solvent. The BPL on the CB fillers were extracted by solvent leaching of a CB-filled PB compound and subsequently dispersed in deuterated toluene to label the BPL for small-angle neutron scattering and neutron spin echo techniques. Intriguingly, the results demonstrate that the BPL is composed of two regions regardless of molecular weights of PB: the inner unswollen region of ~ 0.5 nm thick and outer swollen region where the polymer chains display a parabolic profile with a diffuse tail. This two-layer formation on the filler surface is similar to that reported for polymer chains adsorbed on planar substrates from melts. In addition, the results show that the dynamics of the swollen bound chains can be explained by the so-called ``breathing mode'' and is generalized with the thickness of the swollen BPL. Furthermore, we will discuss how the breathing collective dynamics is affected by the presence of polymer chains in a matrix solution. We acknowledge the financial support from NSF Grant No. CMMI-1332499.

Impact of the radiotherapy technique on the correlation between dose-volume histograms of the bladder wall defined on MRI imaging and dose-volume/surface histograms in prostate cancer patients

NASA Astrophysics Data System (ADS)

Maggio, Angelo; Carillo, Viviana; Cozzarini, Cesare; Perna, Lucia; Rancati, Tiziana; Valdagni, Riccardo; Gabriele, Pietro; Fiorino, Claudio

2013-04-01

The aim of this study was to evaluate the correlation between the ‘true’ absolute and relative dose-volume histograms (DVHs) of the bladder wall, dose-wall histogram (DWH) defined on MRI imaging and other surrogates of bladder dosimetry in prostate cancer patients, planned both with 3D-conformal and intensity-modulated radiation therapy (IMRT) techniques. For 17 prostate cancer patients, previously treated with radical intent, CT and MRI scans were acquired and matched. The contours of bladder walls were drawn by using MRI images. External bladder surfaces were then used to generate artificial bladder walls by performing automatic contractions of 5, 7 and 10 mm. For each patient a 3D conformal radiotherapy (3DCRT) and an IMRT treatment plan was generated with a prescription dose of 77.4 Gy (1.8 Gy/fr) and DVH of the whole bladder of the artificial walls (DVH-5/10) and dose-surface histograms (DSHs) were calculated and compared against the DWH in absolute and relative value, for both treatment planning techniques. A specific software (VODCA v. 4.4.0, MSS Inc.) was used for calculating the dose-volume/surface histogram. Correlation was quantified for selected dose-volume/surface parameters by the Spearman correlation coefficient. The agreement between %DWH and DVH5, DVH7 and DVH10 was found to be very good (maximum average deviations below 2%, SD < 5%): DVH5 showed the best agreement. The correlation was slightly better for absolute (R = 0.80-0.94) compared to relative (R = 0.66-0.92) histograms. The DSH was also found to be highly correlated with the DWH, although slightly higher deviations were generally found. The DVH was not a good surrogate of the DWH (R < 0.7 for most of parameters). When comparing the two treatment techniques, more pronounced differences between relative histograms were seen for IMRT with respect to 3DCRT (p < 0.0001).

Microfiberoptic fluorescence photobleaching reveals size-dependent macromolecule diffusion in extracellular space deep in brain.

PubMed

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.

Computer-controlled wall servicing robot

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

Lefkowitz, S.

1995-03-01

After four years of cooperative research, Pentek has unveiled a new robot with the capability to automatically deliver a variety of cleaning, painting, inspection, and surveillance devices to large vertical surfaces. The completely computer-controlled robot can position a working tool on a 50-foot tall by 50-foot wide vertical surface with a repeatability of 1/16 inch. The working end can literally {open_quotes}fly{close_quotes} across the face of a wall at speed of 60 per minute, and can handle working loads of 350 pounds. The robot was originally developed to decontaminate the walls of reactor fueling cavities at commercial nuclear power plants duringmore » fuel outages. If these cavities are left to dry after reactor refueling, contamination present in the residue could later become airborne and move throughout the containment building. Decontaminating the cavity during the refueling outage reduces the need for restrictive personal protective equipment during plant operations to limit the dose rates.« less

On the theory of compliant wall drag reduction in turbulent boundary layers

NASA Technical Reports Server (NTRS)

Ash, R. L.

1974-01-01

A theoretical model has been developed which can explain how the motion of a compliant wall reduces turbulent skin friction drag. Available experimental evidence at low speeds has been used to infer that a compliant surface selectively removes energy from the upper frequency range of the energy containing eddies and through resulting surface motions can produce locally negative Reynolds stresses at the wall. The theory establishes a preliminary amplitude and frequency criterion as the basis for designing effective drag reducing compliant surfaces.

Cellulose and lignin colocalization at the plant cell wall surface limits microbial hydrolysis of Populus biomass

DOE PAGES

Dumitrache, Alexandru; Tolbert, Allison; Natzke, Jace; ...

2017-04-20

Biorefining of plant feedstocks into fuels and specialty chemicals, using biological conversion, requires the solubilization of lignocellulosics into simpler oligomeric compounds. However, non-pretreated woody biomass has shown high resistance to hydrolysis by cellulolytic microbes or purified cellulases. We investigate the limited solubilization of Populus deltoides by the cellulolytic thermophile Clostridium thermocellum in the absence of solute inhibitors. Compared to control samples, fermented poplar revealed that the hydrolysis of carbohydrates in secondary cell walls ceased prematurely as lignin presence increased at the surface. In quantitative fluorescence colocalization analysis by confocal laser scanning microscopy, the Manders’ coefficient of fractional overlap between ligninmore » and cellulose signals increased from an average of 0.67 to a near-maximum 0.92 in fermented tissue. Chemical imaging by time-of-flight secondary ion mass spectrometry revealed a 49% decline in surface cellulose and a compensatory 30% and 11% increase in surface S- and G- lignin, respectively. Although 72% of the initial glucan was still present in the lignocellulose matrix of this feedstock, subsequent treatments with cell-free purified cellulases did not significantly restore hydrolysis. This confirmed that biomass surfaces had become non-productive for the C. thermocellum hydrolytic exoproteome. This study provides direct evidence for an explicit definition of feedstock recalcitrance, whereby depletion of surface carbohydrate increases lignin exposure which leads to inhibition of enzyme activity, while the bulk residual biomass retains significant undigested carbohydrate content. The analysis presented here establishes a novel method for the quantitation of lignocellulose recalcitrance.« less

Cellulose and lignin colocalization at the plant cell wall surface limits microbial hydrolysis of Populus biomass

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

Dumitrache, Alexandru; Tolbert, Allison; Natzke, Jace

Biorefining of plant feedstocks into fuels and specialty chemicals, using biological conversion, requires the solubilization of lignocellulosics into simpler oligomeric compounds. However, non-pretreated woody biomass has shown high resistance to hydrolysis by cellulolytic microbes or purified cellulases. We investigate the limited solubilization of Populus deltoides by the cellulolytic thermophile Clostridium thermocellum in the absence of solute inhibitors. Compared to control samples, fermented poplar revealed that the hydrolysis of carbohydrates in secondary cell walls ceased prematurely as lignin presence increased at the surface. In quantitative fluorescence colocalization analysis by confocal laser scanning microscopy, the Manders’ coefficient of fractional overlap between ligninmore » and cellulose signals increased from an average of 0.67 to a near-maximum 0.92 in fermented tissue. Chemical imaging by time-of-flight secondary ion mass spectrometry revealed a 49% decline in surface cellulose and a compensatory 30% and 11% increase in surface S- and G- lignin, respectively. Although 72% of the initial glucan was still present in the lignocellulose matrix of this feedstock, subsequent treatments with cell-free purified cellulases did not significantly restore hydrolysis. This confirmed that biomass surfaces had become non-productive for the C. thermocellum hydrolytic exoproteome. This study provides direct evidence for an explicit definition of feedstock recalcitrance, whereby depletion of surface carbohydrate increases lignin exposure which leads to inhibition of enzyme activity, while the bulk residual biomass retains significant undigested carbohydrate content. The analysis presented here establishes a novel method for the quantitation of lignocellulose recalcitrance.« less

Three-component borehole wall-locking seismic detector

DOEpatents

Owen, Thomas E.

1994-01-01

A seismic detector for boreholes is described that has an accelerometer sensor block for sensing vibrations in geologic formations of the earth. The density of the seismic detector is approximately matched to the density of the formations in which the detector is utilized. A simple compass is used to orient the seismic detector. A large surface area shoe having a radius approximately equal to the radius of the borehole in which the seismic detector is located may be pushed against the side of the borehole by actuating cylinders contained in the seismic detector. Hydraulic drive of the cylinders is provided external to the detector. By using the large surface area wall-locking shoe, force holding the seismic detector in place is distributed over a larger area of the borehole wall thereby eliminating concentrated stresses. Borehole wall-locking forces up to ten times the weight of the seismic detector can be applied thereby ensuring maximum detection frequency response up to 2,000 hertz using accelerometer sensors in a triaxial array within the seismic detector.

A self-consistent view on plasma-neutral interaction near a wall: plasma acceleration by momentum removal and heating by cold walls

NASA Astrophysics Data System (ADS)

van Rooij, Gerard; den Harder, Niek; Minea, Teofil; Shumack, Amy; de Blank, H.; Plasma Physics Team

2014-10-01

In plasma physics, material walls are generally regarded as perfect sinks for charged particles and their energy. A special case arises when the wall efficiently reflects the neutralized plasma particles (with a significant portion of their kinetic energy) and at the same time the upstream plasma is of sufficiently high density to yield strong neutral-ion coupling (i.e. reflected energy and momentum will not escape from the plasma). Under these conditions, plasma-surface interaction will feedback to the upstream plasma and a self-consistent view on the coupling between plasma and neutrals is required for correct prediction of plasma conditions and plasma-surface interaction. Here, an analytical and numerical study of the fluid equations is combined with experiments (in hydrogen and argon) to construct such a self-consistent view. It shows how plasma momentum removal builds up upstream pressure and causes plasma acceleration towards the wall. It also shows how energy reflection causes plasma heating, which recycles part of the reflected power to the wall and induces additional flow acceleration due to local sound speed increase. The findings are relevant as generic textbook example and are at play in the boundary plasma of fusion devices.

Freeze-thaw and high-voltage discharge allow macromolecule uptake into ileal brush-border vesicles

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

Donowitz, M.; Emmer, E.; McCullen, J.

1987-06-01

High-voltage discharge or one cycle of freeze-thawing are shown to transiently permeabilize rabbit ileal brush-border membrane vesicles to macromolecules. Uptake of the radiolabeled macromolecule dextran, mol wt 70,000, used as a marker for vesicle permeability, was determined by a rapid filtration technique, with uptake defined as substrate associated with the vesicle and releasable after incubation of vesicles with 0.1% saponin. Dextran added immediately after electric shock (2000 V) or at the beginning of one cycle of freeze-thawing was taken up approximately eightfold compared with control. ATP also was taken up into freeze-thawed vesicles, whereas there was no significant uptake intomore » control vesicles. The increase in vesicle permeability was reversible, based on Na-dependent D-glucose uptake being decreased when studied 5 but not 15 min after electric shock, and was not significantly decreased after completion of one cycle of freeze-thawing. In addition, adenosine 3',5'-cyclic monophosphate and Ca/sup 2 +/-calmodulin-dependent protein kinase activity were similar in control vesicles and vesicles exposed to high-voltage discharge or freeze-thawing. Also, vesicles freeze-thawed with (/sup 32/P)ATP demonstrated increased phosphorylation compared with nonfrozen vesicles, while freeze-thawing did not alter vesicle protein as judged by Coomassie blue staining. These techniques should allow intestinal membrane vesicles to be used for studies of intracellular control of transport processes, for instance, studies of protein kinase regulation of transport.« less

Measurements of wall shear stress in a planar turbulent Couette flow with porous walls

NASA Astrophysics Data System (ADS)

Beuther, Paul

2013-11-01

Measurements of drag on a moving web in a multi-span festoon show a stronger than expected dependency on the porosity of the web. The experiments suggest a wall shear stress 3-4 times larger than non-porous webs or historical Couette flow data for solid walls. Previous DNS studies by Jimenez et al. (JFM Vol 442) of boundary layers with passive porous surfaces predict a much smaller increase in wall shear stress for a porous wall of only 40%. Other DNS studies by Quadrio et al. (JFM Vol 576) of porous walls with periodic transpiration do show a large increase in drag under certain periodic conditions of modest amplitude. Although those results are aligned in magnitude with this study, the exact reason for the observed high drag for porous webs in this present study is not understood because there was no external disturbance applied to the web. It can be hypothesized that natural flutter of the web results in a similar mechanism shown in the periodic DNS study, but when the natural flutter was reduced by increasing web tension, there was only a small decrease of the drag. A key difference in this study is that because of the multiple parallel spans in a festoon, any transpiration in one layer must act in the opposite manner on the adjacent span.

Molecular imprinting at walls of silica nanotubes for TNT recognition.

PubMed

Xie, Chenggen; Liu, Bianhua; Wang, Zhenyang; Gao, Daming; Guan, Guijian; Zhang, Zhongping

2008-01-15

This paper reports the molecular imprinting at the walls of highly uniform silica nanotubes for the recognition of 2,4,6-trinitrotoluene (TNT). It has been demonstrated that TNT templates were efficiently imprinted into the matrix of silica through the strong acid-base pairing interaction between TNT and 3-aminopropyltriethoxysilane (APTS). TNT-imprinted silica nanotubes were synthesized by the gelation reaction between APTS and tetraethylorthosilicate (TEOS), selectively occurring at the porous walls of APTS-modified alumina membranes. The removal of the original TNT templates leaves the imprinted cavities with covalently anchored amine groups at the cavity walls. A high density of recognition sites with molecular selectivity to the TNT analyte was created at the wall of silica nanotubes. Furthermore, most of these recognition sites are situated at the inside and outside surfaces of tubular walls and in the proximity of the two surfaces due to the ultrathin wall thickness of only 15 nm, providing a better site accessibility and lower mass-transfer resistance. Therefore, greater capacity and faster kinetics of uptaking target species were achieved. The silica nanotube reported herein is an ideal form of material for imprinting various organic or biological molecules toward applications in chemical/biological sensors and bioassay.

Comprehensive evaluation of Streptococcus sanguinis cell wall-anchored proteins in early infective endocarditis.

PubMed

Turner, Lauren Senty; Kanamoto, Taisei; Unoki, Takeshi; Munro, Cindy L; Wu, Hui; Kitten, Todd

2009-11-01

Streptococcus sanguinis is a member of the viridans group of streptococci and a leading cause of the life-threatening endovascular disease infective endocarditis. Initial contact with the cardiac infection site is likely mediated by S. sanguinis surface proteins. In an attempt to identify the proteins required for this crucial step in pathogenesis, we searched for surface-exposed, cell wall-anchored proteins encoded by S. sanguinis and then used a targeted signature-tagged mutagenesis (STM) approach to evaluate their contributions to virulence. Thirty-three predicted cell wall-anchored proteins were identified-a number much larger than those found in related species. The requirement of each cell wall-anchored protein for infective endocarditis was assessed in the rabbit model. It was found that no single cell wall-anchored protein was essential for the development of early infective endocarditis. STM screening was also employed for the evaluation of three predicted sortase transpeptidase enzymes, which mediate the cell surface presentation of cell wall-anchored proteins. The sortase A mutant exhibited a modest (approximately 2-fold) reduction in competitiveness, while the other two sortase mutants were indistinguishable from the parental strain. The combined results suggest that while cell wall-anchored proteins may play a role in S. sanguinis infective endocarditis, strategies designed to interfere with individual cell wall-anchored proteins or sortases would not be effective for disease prevention.

Flame front propagation in a channel with porous walls

NASA Astrophysics Data System (ADS)

Golovastov, S. V.; Bivol, G. Yu

2016-11-01

Propagation of the detonation front in hydrogen-air mixture was investigated in rectangular cross-section channels with sound-absorbing boundaries. The front of luminescence was detected in a channel with acoustically absorbing walls as opposed to a channel with solid walls. Flame dynamics was recorded using a high-speed camera. The flame was observed to have a V-shaped profile in the acoustically absorbing section. The possible reason for the formation of the V-shaped flame front is friction under the surface due to open pores. In these shear flows, the kinetic energy of the flow on the surface can be easily converted into heat. A relatively small disturbance may eventually lead to significant local stretching of the flame front surface. Trajectories of the flame front along the axis and the boundary are presented for solid and porous surfaces.

Structural investigation of nonpolar sulfur cross-linked macromolecules in petroleum

NASA Astrophysics Data System (ADS)

Adam, P.; Schmid, J. C.; Mycke, B.; Strazielle, C.; Connan, J.; Huc, A.; Riva, A.; Albrecht, P.

1993-07-01

A novel hexane-soluble nonpolar macromolecular fraction (NPMF) has been found to occur in substantial amounts (up to 32%) in sulfur-rich crude oils and a rock extract. It is highly aliphatic and has a molecular weight culminating at several thousand mass units, as proven by spectroscopic and molecular weight studies. C-S bond hydrogenolysis of NPMF with Raney nickel as a catalyst yields high proportions of aliphatic hydrocarbons in which long linear, acyclic polyisoprenoid and carotenoid chains usually predominate (except in one case) over polycyclic structures, such as steroids and hopanoids. Hence, NPMF consists mainly of macromolecules composed of low molecular weight hydrocarbon subunits cross-linked with sulfide bridges. Use of deuterated Raney nickel indicated in one case (Rozel Point oil) that the long chains and some hopanoids are multiattached to the macromolecular network, whereas other structural subunits, such as steroids or gammacerane, are essentially monoattached. Detailed structural determinations of the hydrocarbon "building blocks" of NPMF give information on their origin and the mode of formation of these macromolecules in the subsurface. Indeed, most of the building blocks can be related to algal (e.g., long linear chains, steroids, β-carotene, and related carotenoids) or bacterial (e.g., acyclic and monocyclic carotenoids, long-chain acyclic isoprenoids) precursors which essentially exist in living organisms as monounsaturated or polyunsaturated species or are easily transformed into such species by diagenetic processes (e.g., steroids). It appears that these alkenes or polyenes become selectively trapped into a macromolecular network by reaction with inorganic sulfur species produced by bacteria in a kind of natural, low-temperature, vulcanization process. This process could start at early diagenesis already in the water column or eventually continue in the bottom sediment. Although its exact nature is yet unknown, it seems likely that the

A Near-Wall Reynolds-Stress Closure Without Wall Normals

NASA Technical Reports Server (NTRS)

Yuan, S. P.; So, R. M. C.

1997-01-01

Turbulent wall-bounded complex flows are commonly encountered in engineering practice and are of considerable interest in a variety of industrial applications. The presence of a wall significantly affects turbulence characteristics. In addition to the wall effects, turbulent wall-bounded flows become more complicated by the presence of additional body forces (e.g. centrifugal force and Coriolis force) and complex geometry. Most near-wall Reynolds stress models are developed from a high-Reynolds-number model which assumes turbulence is homogenous (or quasi-homogenous). Near-wall modifications are proposed to include wall effects in near-wall regions. In this process, wall normals are introduced. Good predictions could be obtained by Reynolds stress models with wall normals. However, ambiguity arises when the models are applied in flows with multiple walls. Many models have been proposed to model turbulent flows. Among them, Reynolds stress models, in which turbulent stresses are obtained by solving the Reynolds stress transport equations, have been proved to be the most successful ones. To apply the Reynolds stress models to wall-bounded flows, near-wall corrections accounting for the wall effects are needed, and the resulting models are called near-wall Reynolds stress models. In most of the existing near-wall models, the near-wall corrections invoke wall normals. These wall-dependent near-wall models are difficult to implement for turbulent flows with complex geometry and may give inaccurate predictions due to the ambiguity of wall normals at corners connecting multiple walls. The objective of this study is to develop a more general and flexible near-wall Reynolds stress model without using any wall-dependent variable for wall-bounded turbulent flows. With the aid of near-wall asymptotic analysis and results of direct numerical simulation, a new near-wall Reynolds stress model (NNWRS) is formulated based on Speziale et al.'s high-Reynolds-stress model with wall

Local wall heat flux/temperature meter for convective flow and method of utilizing same

DOEpatents

Boyd, Ronald D.; Ekhlassi, Ali; Cofie, Penrose

2004-11-30

According to one embodiment of the invention, a method includes providing a conduit having a fluid flowing therethrough, disposing a plurality of temperature measurement devices inside a wall of the conduit, positioning at least some of the temperature measurement devices proximate an inside surface of the wall of the conduit, positioning at least some of the temperature measurement devices at different radial positions at the same circumferential location within the wall, measuring a plurality of temperatures of the wall with respective ones of the temperature measurement devices to obtain a three-dimensional temperature topology of the wall, determining the temperature dependent thermal conductivity of the conduit, and determining a multi-dimensional thermal characteristic of the inside surface of the wall of the conduit based on extrapolation of the three-dimensional temperature topology and the temperature dependent thermal conductivities.

Local wall heat flux/temperature meter for convective flow and method of utilizing same

NASA Technical Reports Server (NTRS)

Cofie, Penrose (Inventor); Ekhlassi, Ali (Inventor); Boyd, Ronald D. (Inventor)

2004-01-01

According to one embodiment of the invention, a method includes providing a conduit having a fluid flowing therethrough, disposing a plurality of temperature measurement devices inside a wall of the conduit, positioning at least some of the temperature measurement devices proximate an inside surface of the wall of the conduit, positioning at least some of the temperature measurement devices at different radial positions at the same circumferential location within the wall, measuring a plurality of temperatures of the wall with respective ones of the temperature measurement devices to obtain a three-dimensional temperature topology of the wall, determining the temperature dependent thermal conductivity of the conduit, and determining a multi-dimensional thermal characteristic of the inside surface of the wall of the conduit based on extrapolation of the three-dimensional temperature topology and the temperature dependent thermal conductivities.

Enhancing oil removal from water by immobilizing multi-wall carbon nanotubes on the surface of polyurethane foam.

PubMed

Keshavarz, Alireza; Zilouei, Hamid; Abdolmaleki, Amir; Asadinezhad, Ahmad

2015-07-01

A surface modification method was carried out to enhance the light crude oil sorption capacity of polyurethane foam (PUF) through immobilization of multi-walled carbon nanotube (MWCNT) on the foam surface at various concentrations. The developed sorbent was characterized using scanning electron microscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis, and tensile elongation test. The results obtained from thermogravimetric and tensile elongation tests showed the improvement of thermal and mechanical resistance of surface-modified foam. The experimental data also revealed that the immobilization of MWCNT on PUF surface enhanced the sorption capacity of light crude oil and reduced water sorption. The highest oil removal capacity was obtained for 1 wt% MWCNT on PUF surface which was 21.44% enhancement in light crude oil sorption compared to the blank PUF. The reusability of surface modified PUF was determined through four cycles of chemical regeneration using petroleum ether. The adsorption of light crude oil with 30 g initial mass showed that 85.45% of the initial oil sorption capacity of this modified sorbent was remained after four regeneration cycles. Equilibrium isotherms for adsorption of oil were analyzed by the Freundlich, Langmuir, Temkin, and Redlich-Peterson models through linear and non-linear regression methods. Results of equilibrium revealed that Langmuir isotherm is the best fitting model and non-linear method is a more accurate way to predict the parameters involved in the isotherms. The overall findings suggested the promising potentials of the developed sorbent in order to be efficiently used in large-scale oil spill cleanup. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ballistic Limit Equation for Single Wall Titanium

NASA Technical Reports Server (NTRS)

Ratliff, J. M.; Christiansen, Eric L.; Bryant, C.

2009-01-01

Hypervelocity impact tests and hydrocode simulations were used to determine the ballistic limit equation (BLE) for perforation of a titanium wall, as a function of wall thickness. Two titanium alloys were considered, and separate BLEs were derived for each. Tested wall thicknesses ranged from 0.5mm to 2.0mm. The single-wall damage equation of Cour-Palais [ref. 1] was used to analyze the Ti wall's shielding effectiveness. It was concluded that the Cour-Palais single-wall equation produced a non-conservative prediction of the ballistic limit for the Ti shield. The inaccurate prediction was not a particularly surprising result; the Cour-Palais single-wall BLE contains shield material properties as parameters, but it was formulated only from tests of different aluminum alloys. Single-wall Ti shield tests were run (thicknesses of 2.0 mm, 1.5 mm, 1.0 mm, and 0.5 mm) on Ti 15-3-3-3 material custom cut from rod stock. Hypervelocity impact (HVI) tests were used to establish the failure threshold empirically, using the additional constraint that the damage scales with impact energy, as was indicated by hydrocode simulations. The criterion for shield failure was defined as no detached spall from the shield back surface during HVI. Based on the test results, which confirmed an approximately energy-dependent shield effectiveness, the Cour-Palais equation was modified.

Microfluidics with fluid walls.

PubMed

Walsh, Edmond J; Feuerborn, Alexander; Wheeler, James H R; Tan, Ann Na; Durham, William M; Foster, Kevin R; Cook, Peter R

2017-10-10

Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method - Freestyle Fluidics - that overcomes many key limitations. In this method, liquids are confined by fluid (not solid) walls. Aqueous circuits with any 2D shape are printed in seconds on plastic or glass Petri dishes; then, interfacial forces pin liquids to substrates, and overlaying an immiscible liquid prevents evaporation. Confining fluid walls are pliant and resilient; they self-heal when liquids are pipetted through them. We drive flow through a wide range of circuits passively by manipulating surface tension and hydrostatic pressure, and actively using external pumps. Finally, we validate the technology with two challenging applications - triggering an inflammatory response in human cells and chemotaxis in bacterial biofilms. This approach provides a powerful and versatile alternative to traditional microfluidics.The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.

Application of flow field-flow fractionation for the characterization of macromolecules of biological interest: a review

PubMed Central

Qureshi, Rashid Nazir

2010-01-01

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 of application fields. In food analysis, FlFFF is applied to determine the molecular size distribution of starches and modified celluloses, or to study protein aggregation during food processing. In industrial analysis, it is applied for the characterization of polysaccharides that are used as thickeners and dispersing agents. In pharmaceutical and biomedical laboratories, FlFFF is used to monitor the refolding of recombinant proteins, to detect aggregates of antibodies, or to determine the size distribution of drug carrier particles. In environmental studies, FlFFF is used to characterize natural colloids in water streams, and especially to study trace metal distributions over colloidal particles. In this review, first a short discussion of the state of the art in instrumentation is given. Developments in the coupling of FlFFF to various detection modes are then highlighted. Finally, application studies are discussed and ordered according to the type of (bio) macromolecules or bioparticles that are fractionated. PMID:20957473

Silicon carbide at nanoscale: Finite single-walled to "infinite" multi-walled tubes

NASA Astrophysics Data System (ADS)

Adhikari, Kapil

A systematic ab initio study of silicon carbide (SiC) nanostructures, especially finite single-walled, infinite double- and multi-walled nanotubes and nanocones is presented. Electronic and structural properties of all these nanostructures have been calculated using hybrid density functionals (B3LYP and PBE0) as implemented in the GAUSSIAN 03/09 suite of software. The unusual dependence of band gap of silicon carbide nanotubes (SiCNT) has been explained as a direct consequence of curvature effect on the ionicity of the bonds. The study of fullerene hemisphere capped, finite SiC nanotubes indicates that the carbon-capped SiC nanotubes are energetically more preferred than silicon-capped finite or hydrogen terminated infinite nanotubes. Capping a nanotube by fullerene hemisphere reduces its band gap. SiC nanocones have also been investigated as possible cap structures of nanotubes. Electronic properties of the nanocones are found to be strongly dependent upon their tip and edge structures, with possible interesting applications in surface science. Three types of double-walled SiCNTs (n, n)@(m, m) (3 ≤ n ≤ 6 ; 7 ≤ m ≤ 12) have been studied using the finite cluster approximation. The stabilities of these nanotubes are of the same order as those of the single-walled SiC nanotubes and it should be experimentally possible to synthesize both single-walled and double-walled SiC nanotubes. The binding energy per atom or the cohesive energy of the double-walled nanotubes depends not only on the number of atoms but also on the coupling of the constituent single-walled nanotubes and their types. A study of binding energies, Mulliken charges, density of states and HOMO-LUMO gaps has been performed for all nanotubes from (n, n)@(n+3,n+3) to (n, n)@(n+6, n+6) (n=3-6). Evolution of band gaps of the SiCNTs with increase in the number of walls has also been investigated. The nature of interaction between transition metal atoms and silicon carbide nanotubes with different

Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155

PubMed Central

2010-01-01

Background The usually non-pathogenic soil bacterium Mycobacterium smegmatis is commonly used as a model mycobacterial organism because it is fast growing and shares many features with pathogenic mycobacteria. Proteomic studies of M. smegmatis can shed light on mechanisms of mycobacterial growth, complex lipid metabolism, interactions with the bacterial environment and provide a tractable system for antimycobacterial drug development. The cell wall proteins are particularly interesting in this respect. The aim of this study was to construct a reference protein map for these proteins in M. smegmatis. Results A proteomic analysis approach, based on one dimensional polyacrylamide gel electrophoresis and LC-MS/MS, was used to identify and characterize the cell wall associated proteins of M. smegmatis. An enzymatic cell surface shaving method was used to determine the surface-exposed proteins. As a result, a total of 390 cell wall proteins and 63 surface-exposed proteins were identified. Further analysis of the 390 cell wall proteins provided the theoretical molecular mass and pI distributions and determined that 26 proteins are shared with the surface-exposed proteome. Detailed information about functional classification, signal peptides and number of transmembrane domains are given next to discussing the identified transcriptional regulators, transport proteins and the proteins involved in lipid metabolism and cell division. Conclusion In short, a comprehensive profile of the M. smegmatis cell wall subproteome is reported. The current research may help the identification of some valuable vaccine and drug target candidates and provide foundation for the future design of preventive, diagnostic, and therapeutic strategies against mycobacterial diseases. PMID:20412585

Elasticity of the living abdominal wall in laparoscopic surgery.

PubMed

Song, Chengli; Alijani, Afshin; Frank, Tim; Hanna, George; Cuschieri, Alfred

2006-01-01

Laparoscopic surgery requires inflation of the abdominal cavity and this offers a unique opportunity to measure the mechanical properties of the living abdominal wall. We used a motion analysis system to study the abdominal wall motion of 18 patients undergoing laparoscopic surgery, and found that the mean Young's modulus was 27.7+/-4.5 and 21.0+/-3.7 kPa for male and female, respectively. During inflation, the abdominal wall changed from a cylinder to a dome shape. The average expansion in the abdominal wall surface was 20%, and a working space of 1.27 x 10(-3)m(3) was created by expansion, reshaping of the abdominal wall and diaphragmatic movement. For the first time, the elasticity of human abdominal wall was obtained from the patients undergoing laparoscopic surgery, and a 3D simulation model of human abdominal wall has been developed to analyse the motion pattern in laparoscopic surgery. Based on this study, a mechanical abdominal wall lift and a surgical simulator for safe/ergonomic port placements are under development.

Effect of Novel Quercetin Titanium Dioxide-Decorated Multi-Walled Carbon Nanotubes Nanocomposite on Bacillus subtilis Biofilm Development

PubMed Central

Raie, Diana S.; Mhatre, Eisha; El-Desouki, Doaa S.; Labena, Ahmed; El-Ghannam, Gamal; Farahat, Laila A.; Youssef, Tareq; Fritzsche, Wolfgang; Kovács, Ákos T.

2018-01-01

The present work was targeted to design a surface against cell seeding and adhering of bacteria, Bacillus subtilis. A multi-walled carbon nanotube/titanium dioxide nano-power was produced via simple mixing of carbon nanotube and titanium dioxide nanoparticles during the sol-gel process followed by heat treatment. Successfully, quercetin was immobilized on the nanocomposite via physical adsorption to form a quercetin/multi-walled carbon nanotube/titanium dioxide nanocomposite. The adhesion of bacteria on the coated-slides was verified after 24 h using confocal laser-scanning microscopy. Results indicated that the quercetin/multi-walled carbon nanotube/titanium dioxide nanocomposite had more negativity and higher recovery by glass surfaces than its counterpart. Moreover, coating surfaces with the quercetin-modified nanocomposite lowered both hydrophilicity and surface-attached bacteria compared to surfaces coated with the multi-walled carbon nanotubes/titanium dioxide nanocomposite. PMID:29346268

A dynamic subgrid-scale parameterization of the effective wall stress in atmospheric boundary layer flows over multiscale, fractal-like surfaces

NASA Astrophysics Data System (ADS)

Anderson, William; Meneveau, Charles

2010-05-01

A dynamic subgrid-scale (SGS) parameterization for hydrodynamic surface roughness is developed for large-eddy simulation (LES) of atmospheric boundary layer (ABL) flow over multiscale, fractal-like surfaces. The model consists of two parts. First, a baseline model represents surface roughness at horizontal length-scales that can be resolved in the LES. This model takes the form of a force using a prescribed drag coefficient. This approach is tested in LES of flow over cubes, wavy surfaces, and ellipsoidal roughness elements for which there are detailed experimental data available. Secondly, a dynamic roughness model is built, accounting for SGS surface details of finer resolution than the LES grid width. The SGS boundary condition is based on the logarithmic law of the wall, where the unresolved roughness of the surface is modeled as the product of local root-mean-square (RMS) of the unresolved surface height and an unknown dimensionless model coefficient. This coefficient is evaluated dynamically by comparing the plane-average hydrodynamic drag at two resolutions (grid- and test-filter scale, Germano et al., 1991). The new model is tested on surfaces generated through superposition of random-phase Fourier modes with prescribed, power-law surface-height spectra. The results show that the method yields convergent results and correct trends. Limitations and further challenges are highlighted. Supported by the US National Science Foundation (EAR-0609690).

RADIOAUTOGRAPHIC STUDY OF CELL WALL DEPOSITION IN GROWING PLANT CELLS

PubMed Central

Ray, Peter M.

1967-01-01

Segments cut from growing oat coleoptiles and pea stems were fed glucose-3H in presence and absence of the growth hormone indoleacetic acid (IAA). By means of electron microscope radioautography it was demonstrated that new cell wall material is deposited both at the wall surface (apposition) and within the preexisting wall structure (internally). Quantitative profiles for the distribution of incorporation with position through the thickness of the wall were obtained for the thick outer wall of epidermal cells. With both oat coleoptile and pea stem epidermal outer walls, it was found that a larger proportion of the newly synthesized wall material appeared to become incorporated within the wall in the presence of IAA. Extraction experiments on coleoptile tissue showed that activity that had been incorporated into the cell wall interior represented noncellulosic constituents, mainly hemicelluloses, whereas cellulose was deposited largely or entirely by apposition. It seems possible that internal incorporation of hemicelluloses plays a role in the cell wall expansion process that is involved in cell growth. PMID:6064369

Location on chitin in the cyst wall of Entamoeba invadens with colloidal gold tracers.

PubMed

Arroyo-Begovich, A; Cárabez-Trejo, A

1982-04-01

Chitin was located in the cyst wall of Entamoeba invadens with colloidal gold-linked wheat germ agglutinin. Cysts stained differentially from trophozoites when encysting cultures were treated with the gold tracer; cysts acquired a wine-red coloration while, in general trophozoites remained unstained. Observation of cells with the electron microscope revealed that the tracer particles were bound specifically to the walls of the surface of the cyst when cells were exposed in suspension, and to the cyst wall cross-section, when cells were exposed to the tracer in thin section, indicating that chitin fibers were distributed on the surface as well as throughout the matrix of the cyst wall.

X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.

PubMed

Büttner, Felix Michael; Renner-Schneck, Michaela; Stehle, Thilo

2015-02-01

The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding. Copyright © 2015 Elsevier GmbH. All rights reserved.

Weathering of radiocaesium contamination on urban streets, walls and roofs.

PubMed

Andersson, K G; Roed, J; Fogh, C L

2002-01-01

Recent investigations in Russia have emphasised the significance of dose contributions from contamination on urban streets and roof pavings, and, typically to a lesser extent, walls in the urban environment. The crucial factor determining the magnitude of these contributions is the retention of the contamination by the different types of urban surface. Since the Chernobyl accident, a series of long-term field studies has been carried out on urban streets, walls and roofs, to examine the weathering processes of 137Cs on the various surface types. The derived time-functions are applied to estimate resultant long-term doses to inhabitants of an urban centre. The paper highlights the effect on caesium retention of surface material characteristics.

[Hydroxyproline: Rich glycoproteins of the plant and cell wall]. Annual technical progress report, 1993

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

Varner, J.E.

1993-06-01

Since xylem tissue includes the main cell types which are lignified, we are interested in gene expression of glycine-rich proteins and proline-rich proteins, and other proteins which are involved in secondary cell wall thickening during xylogenesis. Since the main feature of xylogenesis is the deposition of additional wall components, study of the mechanism of xylogenesis will greatly advance our knowledge of the synthesis and assembly of wall macromolecules. We are using the in vitro xylogenesis system from isolated Zinnia mesophyll cells to isolate genes which are specifically expressed during xylogenesis. We have used subtractive hybridization methods to isolate a numbermore » of cDNA clones for differentially regulated genes from the cells after hormonal induction. So far, we have partially characterized 18 different cDNA clones from 239 positive clones. These differentially regulated genes can be divided into three sets according to the characteristics of gene expression in the induction medium and the control medium. The first set is induced in both the induction medium and the control medium without hormones. The second set is induced mainly in the induction medium and in the control medium with the addition of NAA alone. Two of thesegenes are exclusively induced by auxin. The third set of genes is induced mainly in the induction medium. Since these genes are not induced by either auxin or cytokinin alone, they may be directly involved in the process of xylogenesis. Our experiments on the localization of H{sub 2}O{sub 2} production reinforce the earlier ideas of others that H{sub 2}O{sub 2} is involved in normal lignification.« less

Vertical regolith shield wall construction for lunar base applications

NASA Technical Reports Server (NTRS)

Kaplicky, Jan; Nixon, David; Wernick, Jane

1992-01-01

Lunar bases located on the lunar surface will require permanent protection from radiation and launch ejecta. This paper outlines a method of providing physical protection using lunar regolith that is constructed in situ as a modular vertical wall using specially devised methods of containment and construction. Deployable compartments, reinforced with corner struts, are elevated and filled by a moving gantry. The compartments interlock to form a stable wall. Different wall heights, thicknesses, and plan configurations are achieved by varying the geometry of the individual compartments, which are made from woven carbon fibers. Conventional terrestrial structural engineering techniques can be modified and used to establish the structural integrity and performance of the wall assembly.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

PubMed

Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

2006-07-01

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

ENHANCEMENT OF A SUNSPOT LIGHT WALL WITH EXTERNAL DISTURBANCES

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

Yang, Shuhong; Zhang, Jun; Erdélyi, Robert, E-mail: shuhongyang@nao.cas.cn

Based on the Interface Region Imaging Spectrograph observations, we study the response of a solar sunspot light wall to external disturbances. A flare occurrence near the light wall caused material to erupt from the lower solar atmosphere into the corona. Some material falls back to the solar surface and hits the light bridge (i.e., the base of the light wall), then sudden brightenings appear at the wall base followed by the rise of wall top, leading to an increase of the wall height. Once the brightness of the wall base fades, the height of the light wall begins to decrease.more » Five hours later, another nearby flare takes place, and a bright channel is formed that extends from the flare toward the light bridge. Although no obvious material flow along the bright channel is found, some ejected material is conjectured to reach the light bridge. Subsequently, the wall base brightens and the wall height begins to increase again. Once more, when the brightness of the wall base decays, the wall top fluctuates to lower heights. We suggest, based on the observed cases, that the interaction of falling material and ejected flare material with the light wall results in the brightenings of wall base and causes the height of the light wall to increase. Our results reveal that the light wall can be not only powered by the linkage of p -mode from below the photosphere, but may also be enhanced by external disturbances, such as falling material.« less

Terahertz analysis of stratified wall plaster at buildings of cultural importance across Europe

NASA Astrophysics Data System (ADS)

Walker, Gillian C.; Jackson, J. Bianca; Giovannacci, David; Bowen, John W.; Delandes, Bruno; Labaune, Julien; Mourou, Gerard; Menu, Michel; Detalle, Vincent

2013-05-01

Terahertz (THz) radiation is being developed as a tool for the analysis of cultural heritage, and due to recent advances in technology is now available commercially in systems which can be deployed for field analysis. The radiation is capable of penetrating up to one centimetre of wall plaster and is delivered in ultrafast pulses which are reflected from layers within this region. The technique is non-contact, non-invasive and non-destructive. While sub-surface radar is able to penetrate over a metre of wall plaster, producing details of internal structures, infrared and ultraviolet techniques produce information about the surface layers of wall plaster. THz radiation is able to provide information about the interim region of up to approximately one centimetre into the wall surface. Data from Chartres Cathedral, France, Riga Dome Cathedral, Latvia, and Chartreuse du Val de Bénédiction, France is presented each with different research questions. The presence of sub-surface paint layers was expected from documentary evidence, dating to the 13th Century, at Chartres Cathedral. In contrast, at the Riga Dome Cathedral surface painting had been obscured as recently as 1941 during the Russian occupation of Latvia using white lead-based paint. In the 13th Century, wall paintings at the Chapel of the Frescos, Chartreuse du Val de Benediction in Villeneuve les Avignon were constructed using sinopia under-painting on plaster covering uneven stonework.. This paper compares and contrasts the ability of THz radiation to provide information about sub-surface features in churches and Cathedrals across Europe by analysing depth based profiles gained from the reflected signal.

Rate measurements of the hydrolysis of complex organic macromolecules in cold aqueous solutions: implications for prebiotic chemistry on the early Earth and Titan.

PubMed

Neish, C D; Somogyi, A; Imanaka, H; Lunine, J I; Smith, M A

2008-04-01

Organic macromolecules ("complex tholins") were synthesized from a 0.95 N(2)/0.05 CH(4) atmosphere in a high-voltage AC flow discharge reactor. When placed in liquid water, specific water soluble compounds in the macromolecules demonstrated Arrhenius type first order kinetics between 273 and 313 K and produced oxygenated organic species with activation energies in the range of approximately 60+/-10 kJ mol(-1). These reactions displayed half lives between 0.3 and 17 days at 273 K. Oxygen incorporation into such materials--a necessary step toward the formation of biological molecules--is therefore fast compared to processes that occur on geologic timescales, which include the freezing of impact melt pools and possible cryovolcanic sites on Saturn's organic-rich moon Titan.

Rate Measurements of the Hydrolysis of Complex Organic Macromolecules in Cold Aqueous Solutions: Implications for Prebiotic Chemistry on the Early Earth and Titan

NASA Astrophysics Data System (ADS)

Neish, C. D.; Somogyi, Á.; Imanaka, H .; Lunine, J. I.; Smith, M. A.

2008-04-01

Organic macromolecules (``complex tholins'') were synthesized from a 0.95 N2 / 0.05 CH4 atmosphere in a high-voltage AC flow discharge reactor. When placed in liquid water, specific water soluble compounds in the macromolecules demonstrated Arrhenius type first order kinetics between 273 and 313 K and produced oxygenated organic species with activation energies in the range of ~60 +/- 10 kJ mol-1. These reactions displayed half lives between 0.3 and 17 days at 273 K. Oxygen incorporation into such materials-a necessary step toward the formation of biological molecules-is therefore fast compared to processes that occur on geologic timescales, which include the freezing of impact melt pools and possible cryovolcanic sites on Saturn's organic-rich moon Titan.

Preparation of magnetic core mesoporous shell microspheres with C18-modified interior pore-walls for fast extraction and analysis of phthalates in water samples.

PubMed

Li, Zhongbo; Huang, Danni; Fu, Chinfai; Wei, Biwen; Yu, Wenjia; Deng, Chunhui; Zhang, Xiangmin

2011-09-16

In this study, core-shell magnetic mesoporous microspheres with C18-functionalized interior pore-walls were synthesized through coating Fe(3)O(4) microspheres with a mesoporous inorganic-organic hybrid layer with a n-octadecyltriethoxysilane (C18TES) and tetraethyl orthosilicate (TEOS) as the silica source and cetyltrimethylammonia bromide (CTAB) as a template. The obtained C18-functionalized Fe(3)O(4)@mSiO(2) microspheres possess numerous C18 groups anchored in the interior pore-walls, large surface area (274.7 m(2)/g, high magnetization (40.8 emu/g) and superparamagnetism, uniform mesopores (4.1 nm), which makes them ideal absorbents for simple, fast, and efficient extraction and enrichment of hydrophobic organic compounds in water samples. Several kinds of phthalates were used as the model hydrophobic organic compounds to systematically evaluate the performance of the C18-functionalized Fe(3)O(4)@mSiO(2) microspheres in extracting hydrophobic molecules by using a gas chromatography-mass spectrometry. Various parameters, including eluting solvent, the amounts of absorbents, extraction time and elution time were optimized. Hydrophobic extraction was performed in the interior pore of magnetic mesoporous microspheres, and the materials had the anti-interference ability to macromolecular proteins, which was also investigated in the work. Under the optimized conditions, C18-functionalized Fe(3)O(4)@mSiO(2) microspheres were successfully used to analyze the real water samples. The results indicated that this novel method was fast, convenient and efficient for the target compounds and could avoid being interfered by macromolecules. Copyright © 2011 Elsevier B.V. All rights reserved.

Charge effects on the hindered transport of macromolecules across the endothelial surface glycocalyx layer.

PubMed

Sugihara-Seki, Masako; Akinaga, Takeshi; O-Tani, Hideyuki

2012-01-01

A fluid mechanical and electrostatic model for the transport of solute molecules across the vascular endothelial surface glycocalyx layer (EGL) was developed to study the charge effect on the diffusive and convective transport of the solutes. The solute was assumed to be a spherical particle with a constant surface charge density, and the EGL was represented as an array of periodically arranged circular cylinders of like charge, with a constant surface charge density. By combining the fluid mechanical analyses for the flow around a solute suspended in an electrolyte solution and the electrostatic analyses for the free energy of the interaction between the solute and cylinders based on a mean field theory, we estimated the transport coefficients of the solute across the EGL. Both of diffusive and convective transports are reduced compared to those for an uncharged system, due to the stronger exclusion of the solute that results from the repulsive electrostatic interaction. The model prediction for the reflection coefficient for serum albumin agreed well with experimental observations if the charge density in the EGL is ranged from approximately -10 to -30 mEq/l.

Recording Rapidly Changing Cylinder-wall Temperatures

NASA Technical Reports Server (NTRS)

Meier, Adolph

1942-01-01

The present report deals with the design and testing of a measuring plug suggested by H. Pfriem for recording quasi-stationary cylinder wall temperatures. The new device is a resistance thermometer, the temperature-susceptible part of which consists of a gold coating applied by evaporation under high vacuum and electrolytically strengthened. After overcoming initial difficulties, calibration of plugs up to and beyond 400 degrees C was possible. The measurements were made on high-speed internal combustion engines. The increasing effect of carbon deposit at the wall surface with increasing operating period is indicated by means of charts.

Near-wall turbulence alteration through thin streamwise riblets

NASA Technical Reports Server (NTRS)

Wilkinson, Stephen P.; Lazos, Barry S.

1987-01-01

The possibility of improving the level of drag reduction associated with near-wall riblets is considered. The methodology involves the use of a hot-wire anemometer to study various surface geometries on small, easily constructed models. These models consist of small, adjacent rectangular channels on the wall aligned in the streamwise direction. The VITA technique is modified and applied to thin-element-array and smooth flat-plate data and the results are indicated schematically.

Comprehensive Evaluation of Streptococcus sanguinis Cell Wall-Anchored Proteins in Early Infective Endocarditis▿ †

PubMed Central

Turner, Lauren Senty; Kanamoto, Taisei; Unoki, Takeshi; Munro, Cindy L.; Wu, Hui; Kitten, Todd

2009-01-01

Streptococcus sanguinis is a member of the viridans group of streptococci and a leading cause of the life-threatening endovascular disease infective endocarditis. Initial contact with the cardiac infection site is likely mediated by S. sanguinis surface proteins. In an attempt to identify the proteins required for this crucial step in pathogenesis, we searched for surface-exposed, cell wall-anchored proteins encoded by S. sanguinis and then used a targeted signature-tagged mutagenesis (STM) approach to evaluate their contributions to virulence. Thirty-three predicted cell wall-anchored proteins were identified—a number much larger than those found in related species. The requirement of each cell wall-anchored protein for infective endocarditis was assessed in the rabbit model. It was found that no single cell wall-anchored protein was essential for the development of early infective endocarditis. STM screening was also employed for the evaluation of three predicted sortase transpeptidase enzymes, which mediate the cell surface presentation of cell wall-anchored proteins. The sortase A mutant exhibited a modest (∼2-fold) reduction in competitiveness, while the other two sortase mutants were indistinguishable from the parental strain. The combined results suggest that while cell wall-anchored proteins may play a role in S. sanguinis infective endocarditis, strategies designed to interfere with individual cell wall-anchored proteins or sortases would not be effective for disease prevention. PMID:19703977

Investigation of wall-bounded turbulence over regularly distributed roughness

NASA Astrophysics Data System (ADS)

Placidi, Marco; Ganapathisubramani, Bharathram

2012-11-01

The effects of regularly distributed roughness elements on the structure of a turbulent boundary layer are examined by performing a series of Planar (high resolution l+ ~ 30) and Stereoscopic Particle Image Velocimetry (PIV) experiments in a wind tunnel. An adequate description of how to best characterise a rough wall, especially one where the density of roughness elements is sparse, is yet to be developed. In this study, rough surfaces consisting of regularly and uniformly distributed LEGO® blocks are used. Twelve different patterns are adopted in order to systematically examine the effects of frontal solidity (λf, frontal area of the roughness elements per unit wall-parallel area) and plan solidity (λp, plan area of roughness elements per unit wall-parallel area), on the turbulence structure. The Karman number, Reτ , is approximately 4000 across the different cases. Spanwise 3D vector fields at two different wall-normal locations (top of the canopy and within the log-region) are also compared to examine the spanwise homogeneity of the flow across different surfaces. In the talk, a detailed analysis of mean and rms velocity profiles, Reynolds stresses, and quadrant decomposition for the different patterns will be presented.

Hygrothermal behavior for a clay brick wall

NASA Astrophysics Data System (ADS)

Allam, R.; Issaadi, N.; Belarbi, R.; El-Meligy, M.; Altahrany, A.

2018-06-01

In Egypt, the clay brick is the common building materials which are used. By studying clay brick walls behavior for the heat and moisture transfer, the efficient use of the clay brick can be reached. So, this research studies the hygrothermal transfer in this material by measuring the hygrothermal properties and performing experimental tests for a constructed clay brick wall. We present the model for the hygrothermal transfer in the clay brick which takes the temperature and the vapor pressure as driving potentials. In addition, this research compares the presented model with previous models. By constructing the clay brick wall between two climates chambers with different boundary conditions, we can validate the numerical model and analyze the hygrothermal transfer in the wall. The temperature and relative humidity profiles within the material are measured experimentally and determined numerically. The numerical and experimental results have a good convergence with 3.5% difference. The surface boundary conditions, the ground effect, the infiltration from the closed chambers and the material heterogeneity affects the results. Thermal transfer of the clay brick walls reaches the steady state very rapidly than the moisture transfer. That means the effect of using only the external brick wall in the building in hot climate without increase the thermal resistance for the wall, will add more energy losses in the clay brick walls buildings. Also, the behavior of the wall at the heat and mass transfer calls the three-dimensional analysis for the whole building to reach the real behavior.

Hygrothermal behavior for a clay brick wall

NASA Astrophysics Data System (ADS)

Allam, R.; Issaadi, N.; Belarbi, R.; El-Meligy, M.; Altahrany, A.

2018-01-01

In Egypt, the clay brick is the common building materials which are used. By studying clay brick walls behavior for the heat and moisture transfer, the efficient use of the clay brick can be reached. So, this research studies the hygrothermal transfer in this material by measuring the hygrothermal properties and performing experimental tests for a constructed clay brick wall. We present the model for the hygrothermal transfer in the clay brick which takes the temperature and the vapor pressure as driving potentials. In addition, this research compares the presented model with previous models. By constructing the clay brick wall between two climates chambers with different boundary conditions, we can validate the numerical model and analyze the hygrothermal transfer in the wall. The temperature and relative humidity profiles within the material are measured experimentally and determined numerically. The numerical and experimental results have a good convergence with 3.5% difference. The surface boundary conditions, the ground effect, the infiltration from the closed chambers and the material heterogeneity affects the results. Thermal transfer of the clay brick walls reaches the steady state very rapidly than the moisture transfer. That means the effect of using only the external brick wall in the building in hot climate without increase the thermal resistance for the wall, will add more energy losses in the clay brick walls buildings. Also, the behavior of the wall at the heat and mass transfer calls the three-dimensional analysis for the whole building to reach the real behavior.

Turbine airfoil with a compliant outer wall

DOEpatents

Campbell, Christian X [Oviedo, FL; Morrison, Jay A [Oviedo, FL

2012-04-03

A turbine airfoil usable in a turbine engine with a cooling system and a compliant dual wall configuration configured to enable thermal expansion between inner and outer layers while eliminating stress formation in the outer layer is disclosed. The compliant dual wall configuration may be formed a dual wall formed from inner and outer layers separated by a support structure. The outer layer may be a compliant layer configured such that the outer layer may thermally expand and thereby reduce the stress within the outer layer. The outer layer may be formed from a nonplanar surface configured to thermally expand. In another embodiment, the outer layer may be planar and include a plurality of slots enabling unrestricted thermal expansion in a direction aligned with the outer layer.

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

NASA Technical Reports Server (NTRS)

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.

First wall structural analysis of the aqueous self-cooled blanket concept

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

O'Brien, D.A.; Steiner, D.; Embrechts, M.J.

1986-11-01

A recently proposed blanket concept using water coolant with dissolved lithium compounds for breeding employs water cooled first walls. Water cooled first walls for blankets have also been proposed for some solid breeder blankets. Design options for water cooled first walls are examined in this paper. Four geometries and three materials are analyzed for water coolant at 300/sup 0/C and 13.8 MPa (2000 psi). Maximum neutron wall loads (with surface heat loads being 25% of neutron wall load) are determined for each geometry and material combination. Of the materials studied, only vanadium alloy is found to be capable of withstandingmore » high wall loads (>10MW/m/sup 2/ neutron and >2.5 MW/m/sup 2/ heat).« less

Relationship of wood surface energy to surface composition

Treesearch

Feipeng P. Liu; Timothy G. Rials; John Simonsen

1998-01-01

The wood cell wall is composed of cellulose, lignin, hemicelluloses, and extractives. Thus, the surface energy of the wood material must be some combination of the surface energies of these components. The influence of extractives on wood surface chemistry can be important in diverse industrial applications, such as coating, pulping, and wood-based composites. In this...

Stellate macroporous silica nanospheres in bio-macromolecules encapsulation and delivery

NASA Astrophysics Data System (ADS)

Chi, Hao-Hsin

This project focused on using mesoporous silica as a solid support to encapsulate enzymes for operating a highly economic, and recyclable biomass processing system. The main objective is to turn non-food biomass sources into food products. Enzymes are macromolecules with the structural backbone of proteins or ribonucleic acid sequences (RNAs) which work as catalysts in living organisms. Enzymes have the advantage of being the least contaminating catalyst due to normal catalyst might generate toxic by-product, and preferable to organic and inorganic catalysts, especially when used for product related to human used, which require biocompatibility of final product. However, there are several disadvantages in enzyme utilization. Their fabrication is time-consuming and requires elaborated molecular biology processes. Most of the enzymes need well-defined reaction conditions to be functional and operate at high yield. Unfortunately, although they are reusable as normal catalysts, it proves difficult to extract or reuse the enzymes from a reaction. Also, enzyme molecules are easily degradable and demand proper storage. To overcome some of the disadvantages, especially regarding stability to degradation, recovery, and reusability, immobilization of enzyme on solid support has become a thriving methodology. In recent years, mesoporous silica nanomaterials(MSN) have been at the forefront of enzyme immobilization given their extensive surface area, which provides capability to increase enzyme loading and for their demonstrate ability to protect enzyme from degradation, thus enabling high recyclability. Mesoporous silica is biocompatible and has already been used for several applications included. Catalysis, drug delivery, and Bio-imaging. Previously published research utilized mesoporous silica to deliver drugs, DNAs, RNAs or encapsulate single enzyme. The objective of this research is completed to develop a new porous silica platform that is unique in its porosity structure

Hydrodynamic chromatography of macromolecules using polymer monolithic columns.

PubMed

Edam, Rob; Eeltink, Sebastiaan; Vanhoutte, Dominique J D; Kok, Wim Th; Schoenmakers, Peter J

2011-12-02

The selectivity window of size-based separations of macromolecules was tailored by tuning the macropore size of polymer monolithic columns. Monolithic materials with pore sizes ranging between 75 nm and 1.2 μm were prepared in situ in large I.D. columns. The dominant separation mechanism was hydrodynamic chromatography in the flow-through pores. The calibration curves for synthetic polymers matched with the elution behavior by HDC separations in packed columns with 'analyte-to-pore' aspect ratios (λ) up to 0.2. For large-macropore monoliths, a deviation in retention behavior was observed for small polystyrene polymers (M(r)<20 kDa), which may be explained by a combined HDC-SEC mechanism for λ<0.02. The availability of monoliths with very narrow pore sizes allowed investigation of separations at high λ values. For high-molecular weight polymers (M(r)>300,000 Da) confined in narrow channels, the separation strongly depended on flow rate. Flow-rate dependent elution behavior was evaluated by calculation of Deborah numbers and confirmed to be outside the scope of classic shear deformation or slalom chromatography. Shear-induced forces acting on the periphery of coiled polymers in solution may be responsible for flow-rate dependent elution. Copyright © 2011 Elsevier B.V. All rights reserved.

Function of terahertz spectra in monitoring the decomposing process of biological macromolecules and in investigating the causes of photoinhibition.

PubMed

Qu, Yuangang; Zhang, Shuai; Lian, Yuji; Kuang, Tingyun

2017-03-01

Chlorophyll a and β-carotene play an important role in harvesting light energy, which is used to drive photosynthesis in plants. In this study, terahertz (THz) and visible range spectra of chlorophyll a and β-carotene and their changes under light treatment were investigated. The results show that the all THz transmission and absorption spectra of chlorophyll a and β-carotene changed upon light treatment, with the maximum changes at 15 min of illumination indicating the greatest changes of the collective vibrational mode of chlorophyll a and β-carotene. The absorption spectra of chlorophyll a in the visible light region decreased upon light treatment, signifying the degradation of chlorophyll a molecules. It can be inferred from these results that the THz spectra are very sensitive in monitoring the changes of the collective vibrational mode, despite the absence of changes in molecular configuration. The THz spectra can therefore be used to monitor the decomposing process of biological macromolecules; however, visible absorption spectra can only be used to monitor the breakdown extent of biological macromolecules.

Pulmonary vascular clearance of harmful endogenous macromolecules in a porcine model of acute liver failure.

PubMed

Nedredal, Geir I; Elvevold, Kjetil; Chedid, Marcio F; Ytrebø, Lars M; Rose, Christopher F; Sen, Sambit; Smedsrød, Bård; Jalan, Rajiv; Revhaug, Arthur

2016-01-01

Pulmonary complications are common in acute liver failure (ALF). The role of the lungs in the uptake of harmful soluble endogenous macromolecules was evaluated in a porcine model of ALF induced by hepatic devascularization (n = 8) vs. controls (n = 8). In additional experiments, pulmonary uptake was investigated in healthy pigs. Fluorochrome-labeled modified albumin (MA) was applied to investigate the cellular uptake. As compared to controls, the ALF group displayed a 4-fold net increased lung uptake of hyaluronan, and 5-fold net increased uptake of both tissue plasminogen activator and lysosomal enzymes. Anatomical distribution experiments in healthy animals revealed that radiolabeled MA uptake (taken up by the same receptor as hyaluronan) was 53% by the liver, and 24% by the lungs. The lung uptake of LPS was 14% whereas 60% remained in the blood. Both fluorescence and electron microscopy revealed initial uptake of MA by pulmonary endothelial cells (PECs) with later translocation to pulmonary intravascular macrophages (PIMs). Moreover, the presence of PIMs was evident 10 min after injection. Systemic inflammatory markers such as leukopenia and increased serum TNF-α levels were evident after 20 min in the MA and LPS groups. Significant lung uptake of harmful soluble macromolecules compensated for the defect liver scavenger function in the ALF-group. Infusion of MA induced increased TNF-α serum levels and leukopenia, similar to the effect of the known inflammatory mediator LPS. These observations suggest a potential mechanism that may contribute to lung damage secondary to liver disease.

THESEUS 1, FERONIA and relatives: a family of cell wall-sensing receptor kinases?

PubMed

Cheung, Alice Y; Wu, Hen-Ming

2011-12-01

The plant cell wall provides form and integrity to the cell as well as a dynamic interface between a cell and its environment. Therefore mechanisms capable of policing changes in the cell wall, signaling cellular responses including those that would feedback regulate cell wall properties are expected to play important roles in facilitating growth and ensuring survival. Discoveries in the last few years that the Arabidopsis THESEUS 1 receptor-like kinase (RLK) may function as a sensor for cell wall defects to regulate growth and that its relatives FERONIA and ANXURs regulate pollen tube integrity imply strongly that they play key roles in cell wall-related processes. Furthermore, FERONIA acts as a cell surface regulator for RAC/ROP GTPases and activates production of reactive oxygen species which are, respectively, important molecular switches and mediators for diverse processes. These findings position the THESEUS 1/FERONIA family RLKs as surface regulators and potential cell wall sensors capable of broadly and profoundly impacting cellular pathways in response to diverse signals. Copyright © 2011 Elsevier Ltd. All rights reserved.

Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately

PubMed Central

2017-01-01

Förster resonance energy transfer (FRET) measurements from a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the structure and dynamics of DA labeled macromolecules. Accurate descriptions of FRET measurements by molecular models are complicated because the fluorophores are usually coupled to the macromolecule via flexible long linkers allowing for diffusional exchange between multiple states with different fluorescence properties caused by distinct environmental quenching, dye mobilities, and variable DA distances. It is often assumed for the analysis of fluorescence intensity decays that DA distances and D quenching are uncorrelated (homogeneous quenching by FRET) and that the exchange between distinct fluorophore states is slow (quasistatic). This allows us to introduce the FRET-induced donor decay, εD(t), a function solely depending on the species fraction distribution of the rate constants of energy transfer by FRET, for a convenient joint analysis of fluorescence decays of FRET and reference samples by integrated graphical and analytical procedures. Additionally, we developed a simulation toolkit to model dye diffusion, fluorescence quenching by the protein surface, and FRET. A benchmark study with simulated fluorescence decays of 500 protein structures demonstrates that the quasistatic homogeneous model works very well and recovers for single conformations the average DA distances with an accuracy of < 2%. For more complex cases, where proteins adopt multiple conformations with significantly different dye environments (heterogeneous case), we introduce a general analysis framework and evaluate its power in resolving heterogeneities in DA distances. The developed fast simulation methods, relying on Brownian dynamics of a coarse-grained dye in its sterically accessible volume, allow us to incorporate structural information in the decay analysis for heterogeneous cases by relating dye states

Pore-wall roughness as a fractal surface and theoretical simulation of mercury intrusion/retraction in porous media

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

Tsakiroglou, C.D.; Payatakes, A.C.

The mercury intrusion/retraction curves of many types of porous materials (e.g., sandstones) have sections of finite slope in the region of high and very high pressure. This feature is attributed to the existence of microroughness on the pore walls. In the present work pore-wall roughness features are added to a three-dimensional primary network of chambers-and-throats using ideas of fractal geometry. The roughness of the throats is modeled with a finite number of self-similar triangular prisms of progressively smaller sizes. The roughness of the chambers is modeled in a similar way using right circular cones instead of prisms. Three parameters sufficemore » for the complete characterization of the model of fractal roughness, namely, the number of features per unit length, the common angle of sharpness, and the number of layers (which is taken to be the same for throats and chambers). Analytical relations that give the surface area, pore volume, and mercury saturation of the pore network as functions of the fractal roughness parameters are developed for monolayer and multilayer arrangements. The chamber-and-throat network with fractal pore-wall roughness is used to develop an extended version of the computer-aided simulator of mercury porosimetry that has been reported in previous publications. This new simulator is used to investigate the effects of the roughness features on the form of mercury intrusion/retraction curves. It turns out that the fractal model of the porewall roughness gives an adequate representation of real porous media, and capillary pressure curves which are similar to the experimental ones for many typical porous materials such as sandstones. The method is demonstrated with the analysis of a Greek sandstone.« less

In vitro platelet activation, aggregation and platelet-granulocyte complex formation induced by surface modified single-walled carbon nanotubes.

PubMed

Fent, János; Bihari, Péter; Vippola, Minnamari; Sarlin, Essi; Lakatos, Susan

2015-08-01

Surface modification of single-walled carbon nanotubes (SWCNTs) such as carboxylation, amidation, hydroxylation and pegylation is used to reduce the nanotube toxicity and render them more suitable for biomedical applications than their pristine counterparts. Toxicity can be manifested in platelet activation as it has been shown for SWCNTs. However, the effect of various surface modifications on the platelet activating potential of SWCNTs has not been tested yet. In vitro platelet activation (CD62P) as well as the platelet-granulocyte complex formation (CD15/CD41 double positivity) in human whole blood were measured by flow cytometry in the presence of 0.1mg/ml of pristine or various surface modified SWCNTs. The effect of various SWCNTs was tested by whole blood impedance aggregometry, too. All tested SWCNTs but the hydroxylated ones activate platelets and promote platelet-granulocyte complex formation in vitro. Carboxylated, pegylated and pristine SWCNTs induce whole blood aggregation as well. Although pegylation is preferred from biomedical point of view, among the samples tested by us pegylated SWCNTs induced far the most prominent activation and a well detectable aggregation of platelets in whole blood. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimization of crystallization conditions for biological macromolecules.

PubMed

McPherson, Alexander; Cudney, Bob

2014-11-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Optimization of crystallization conditions for biological macromolecules

PubMed Central

McPherson, Alexander; Cudney, Bob

2014-01-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success. PMID:25372810

Wall characterization for through-the-wall radar applications

NASA Astrophysics Data System (ADS)

Greneker, Gene; Rausch, E. O.

2008-04-01

There has been continuing interest in the penetration of multilayer building materials, such as wood walls with air gaps and concrete hollow core block, using through-the-wall (TTW) radar systems. TTW operational techniques and signal propagation paths vary depending on how the TTW system is intended to be operated. For example, the operator of a TTW radar may be required to place the radar against the intervening wall of interest while collecting data. Other operational doctrines allow the radar to be operated in a stand-off mode from the wall. The stand-off distances can vary from feet to hundreds of feet, depending on the type of radar being used. When a signal is propagated through a multilayer wall with air gaps between the material and the wall construction uses materials of radically different dielectric constants, attenuation may not be the only effect that the probing signal experiences passing through the wall. This paper presents measurements of a hollow core concrete block wall and the measurement of a standard wall constructed of siding and wallboard. Both types of walls are typically found in most U.S. homes. These limited measurements demonstrate that the type of wall being penetrated by a wideband signal can modify the probing signal.

Effect of a surface-to-gap temperature discontinuity on the heat transfer to reusable surface insulation tile gaps. [of the space shuttle

NASA Technical Reports Server (NTRS)

Throckmorton, D. A.

1976-01-01

An experimental investigation is presented that was performed to determine the effect of a surface-to-gap wall temperature discontinuity on the heat transfer within space shuttle, reusable surface insulation, tile gaps submerged in a thick turbulent boundary layer. Heat-transfer measurements were obtained on a flat-plate, single-gap model submerged in a turbulent tunnel wall boundary layer at a nominal free-stream Mach number of 10.3 and free-stream Reynolds numbers per meter of 1.5 million, 3.3 million and 7.8 million. Surface-to-gap wall temperature discontinuities of varying degree were created by heating the surface of the model upstream of the instrumented gap. The sweep angle of the gap was varied between 0 deg and 60 deg; gap width and depth were held constant. A surface-to-gap wall temperature discontinuity (surface temperature greater than gap wall temperature) results in increased heat transfer to the near-surface portion of the gap, as compared with the heat transfer under isothermal conditions, while decreasing the heat transfer to the deeper portions of the gap. The nondimensionalized heat transfer to the near-surface portion of the gap is shown to decrease with increasing Reynolds number; in the deeper portion of the gap, the heat transfer increases with Reynolds number.

The Impact of a Deepwater Wave on a Wall with Finite Vertical Extent

NASA Astrophysics Data System (ADS)

Wang, An; Duncan, James H.

2016-11-01

The impact of a dispersively focused 2D plunging breaker (average wave frequency 1.15 Hz) on a 2D wall that is 45 cm high and 30 cm thick is studied experimentally. The temporal evolution of the water surface profile upstream of the wall is measured with a cinematic LIF technique using frame rates up to 4,500 Hz. Impact pressures on the wall are measured simultaneously at sample rates up to 900 kHz. The wall is located horizontally 6.41 m from the wave maker in all cases and the submergence of the bottom surface of the wall is varied. It is found that the impact behavior varies dramatically with the wall submergence. When the bottom is submerged by 13.3 cm, a flip-through impact occurs. In this case, the impact evolves without wave breaking and a vertical jet is formed. When the wall is submerged by less than 4.5 cm, small-amplitude components in the wave packet interact with the bottom of the wall before the main crest arrives. Ripples reflected during this interaction modify the behavior of the incoming breaker significantly. When the bottom of the wall is located sufficiently high above the mean water level, the first interaction occurs when the undisturbed wave crest collides with the wall. The highest pressures are observed in this case. The support of the Office of Naval Research is gratefully acknowledged.

A Near-Wall Reynolds-Stress Closure without Wall Normals

NASA Technical Reports Server (NTRS)

Yuan, S. P.; So, R. M. C.

1997-01-01

With the aid of near-wall asymptotic analysis and results of direct numerical simulation, a new near-wall Reynolds stress model (NNWRS) is formulated based on the SSG high-Reynolds-stress model with wall-independent near-wall corrections. Only one damping function is used for flows with a wide range of Reynolds numbers to ensure that the near-wall modifications diminish away from the walls. The model is able to reproduce complicated flow phenomena induced by complex geometry, such as flow recirculation, reattachment and boundary-layer redevelopment in backward-facing step flow and secondary flow in three-dimensional square duct flow. In simple flows, including fully developed channel/pipe flow, Couette flow and boundary-layer flow, the wall effects are dominant, and the NNWRS model predicts less degree of turbulent anisotropy in the near-wall region compared with a wall-dependent near-wall Reynolds Stress model (NWRS) developed by So and colleagues. The comparison of the predictions given by the two models rectifies the misconception that the overshooting of skin friction coefficient in backward-facing step flow prevalent in those near-wall, models with wall normal is caused by he use of wall normal.

Energy transmission through a double-wall curved stiffened panel using Green's theorem

NASA Astrophysics Data System (ADS)

Ghosh, Subha; Bhattacharya, Partha

2015-04-01

It is a common practice in aerospace and automobile industries to use double wall panels as fuselage skins or in window panels to improve acoustic insulation. However, the scientific community is yet to develop a reliable prediction method for a suitable vibro-acoustic model for sound transmission through a curved double-wall panel. In this quest, the present work tries to delve into the modeling of energy transmission through a double-wall curved panel. Subsequently the radiation of sound power into the free field from the curved panel in the low to mid frequency range is also studied. In the developed model to simulate a stiffened aircraft fuselage configuration, the outer wall is provided with longitudinal stiffeners. A modal expansion theory based on Green's theorem is implemented to model the energy transmission through an acoustically coupled double-wall curved panel. An elemental radiator approach is implemented to calculate the radiated energy from the curved surface in to the free field. The developed model is first validated with various numerical models available. It has been observed in the present study that the radius of curvature of the surface has a prominent effect on the behavior of radiated sound power into the free field. Effect of the thickness of the air gap between the two curved surfaces on the sound power radiation has also been noted.

Enzymatic cell wall degradation of Chlorella vulgaris and other microalgae for biofuels production.

PubMed

Gerken, Henri G; Donohoe, Bryon; Knoshaug, Eric P

2013-01-01

Cell walls of microalgae consist of a polysaccharide and glycoprotein matrix providing the cells with a formidable defense against its environment. We characterized enzymes that can digest the cell wall and weaken this defense for the purpose of protoplasting or lipid extraction. A growth inhibition screen demonstrated that chitinase, lysozyme, pectinase, sulfatase, β-glucuronidase, and laminarinase had the broadest effect across the various Chlorella strains tested and also inhibited Nannochloropsis and Nannochloris strains. Chlorella is typically most sensitive to chitinases and lysozymes, both enzymes that degrade polymers containing N-acetylglucosamine. Using a fluorescent DNA stain, we developed rapid methodology to quantify changes in permeability in response to enzyme digestion and found that treatment with lysozyme in conjunction with other enzymes has a drastic effect on cell permeability. Transmission electron microscopy of enzymatically treated Chlorella vulgaris indicates that lysozyme degrades the outer surface of the cell wall and removes hair-like fibers protruding from the surface, which differs from the activity of chitinase. This action on the outer surface of the cell causes visible protuberances on the cell surface and presumably leads to the increased settling rate when cells are treated with lysozyme. We demonstrate radical ultrastructural changes to the cell wall in response to treatment with various enzyme combinations which, in some cases, causes a greater than twofold increase in the thickness of the cell wall. The enzymes characterized in this study should prove useful in the engineering and extraction of oils from microalgae.

The Surface Reactivities of Single-Walled Carbon Nanotubes and Their Related Toxicities

NASA Astrophysics Data System (ADS)

Ren, Lei

After 20 years of extensive exploration, people are more and more convinced on the great potentials of single-walled carbon nanotubes (SWCNTs) in the applications of many different areas. On the other hand, the properties and toxicities have also been closely watched for the safe utilization. In this dissertation I focus on the surface properties of SWCNTs and their related toxicities. In chapter 2, we revealed the generation of peroxyl radical by the unmodified SWCNT and the poly(ethylene glycol) functionalized SWCNT in aqueous solution with capillary electrophoresis (CE) and a reactive oxygen species (ROS) indicator, 2,7-dichlorodihydrofluorescein (H2DCF). According to the results, we identified peroxyl radical, ROO• as the major ROS in our system. Peroxyl radical could be produced from the adsorption of oxygen on the SWCNT surface. In chapter 3, we studied oxidation of several biologically relevant reducing agents in the presence of SWCNTs in aqueous solutions. H2DCF and several small antioxidants (vitamin C, Trolox, and cysteine), and a high-molecular-weight ROS scavenger (bovine serum albumin (BSA)) were selected as reductants. We revealed that the unmodified or carboxylated SWCNT played duplex roles by acting as both oxidants and catalysts in the reaction. In chapter 4, we confirmed that SWCNTs bind to horseradish peroxidase (HRP) at a site proximate to the enzyme's activity center and participating in the ET process, enhancing the activity of (HRP) in the solution-based redox reaction. The capability of SWCNT in receiving electrons and the direct attachment of HRP to the surface of SWCNT strongly affected the enzyme activity due to the direct involvement of SWCNT in ET. In chapter 5, the toxicity of SWCNTs coated with different concentrations of BSA to a human fibroblast cell line was explored. The result indicates that the toxicity of SWCNTs decrease with the higher coating degree as assumed. Then we choose mitochondrion to study the interactions between

Isotropic thin-walled pressure vessel experiment

NASA Technical Reports Server (NTRS)

Denton, Nancy L.; Hillsman, Vernon S.

1992-01-01

The objectives are: (1) to investigate the stress and strain distributions on the surface of a thin walled cylinder subject to internal pressure and/or axial load; and (2) to relate stress and strain distributions to material properties and cylinder geometry. The experiment, supplies, and procedure are presented.

Automatic lumen and outer wall segmentation of the carotid artery using deformable three-dimensional models in MR angiography and vessel wall images.

PubMed

van 't Klooster, Ronald; de Koning, Patrick J H; Dehnavi, Reza Alizadeh; Tamsma, Jouke T; de Roos, Albert; Reiber, Johan H C; van der Geest, Rob J

2012-01-01

To develop and validate an automated segmentation technique for the detection of the lumen and outer wall boundaries in MR vessel wall studies of the common carotid artery. A new segmentation method was developed using a three-dimensional (3D) deformable vessel model requiring only one single user interaction by combining 3D MR angiography (MRA) and 2D vessel wall images. This vessel model is a 3D cylindrical Non-Uniform Rational B-Spline (NURBS) surface which can be deformed to fit the underlying image data. Image data of 45 subjects was used to validate the method by comparing manual and automatic segmentations. Vessel wall thickness and volume measurements obtained by both methods were compared. Substantial agreement was observed between manual and automatic segmentation; over 85% of the vessel wall contours were segmented successfully. The interclass correlation was 0.690 for the vessel wall thickness and 0.793 for the vessel wall volume. Compared with manual image analysis, the automated method demonstrated improved interobserver agreement and inter-scan reproducibility. Additionally, the proposed automated image analysis approach was substantially faster. This new automated method can reduce analysis time and enhance reproducibility of the quantification of vessel wall dimensions in clinical studies. Copyright © 2011 Wiley Periodicals, Inc.

Cell wall proteome of pathogenic fungi.

PubMed

Karkowska-Kuleta, Justyna; Kozik, Andrzej

2015-01-01

A fast development of a wide variety of proteomic techniques supported by mass spectrometry coupled with high performance liquid chromatography has been observed in recent years. It significantly contributes to the progress in research on the cell wall, very important part of the cells of pathogenic fungi. This complicated structure composed of different polysaccharides, proteins, lipids and melanin, plays a key role in interactions with the host during infection. Changes in the set of the surface-exposed proteins under different environmental conditions provide an effective way for pathogens to respond, adapt and survive in the new niches of infection. This work summarizes the current state of knowledge on proteins, studied both qualitatively and quantitatively, and found within the cell wall of fungal pathogens for humans, including Candida albicans, Candida glabrata, Aspergillus fumigatus, Cryptococcus neoformans and other medically important fungi. The described proteomic studies involved the isolation and fractionation of particular sets of proteins of interest with various techniques, often based on differences in their linkages to the polysaccharide scaffold. Furthermore, the proteinaceous contents of extracellular vesicles ("virulence bags") of C. albicans, C. neoformans, Histoplasma capsulatum and Paracoccidioides brasiliensis are compared, because their production can partially explain the problem of non-classical protein secretion by fungi. The role assigned to surface-exposed proteins in pathogenesis of fungal infections is enormously high, thus justifying the need for further investigation of cell wall proteomes.

Detection of honeycomb cell walls from measurement data based on Harris corner detection algorithm

NASA Astrophysics Data System (ADS)

Qin, Yan; Dong, Zhigang; Kang, Renke; Yang, Jie; Ayinde, Babajide O.

2018-06-01

A honeycomb core is a discontinuous material with a thin-wall structure—a characteristic that makes accurate surface measurement difficult. This paper presents a cell wall detection method based on the Harris corner detection algorithm using laser measurement data. The vertexes of honeycomb cores are recognized with two different methods: one method is the reduction of data density, and the other is the optimization of the threshold of the Harris corner detection algorithm. Each cell wall is then identified in accordance with the neighboring relationships of its vertexes. Experiments were carried out for different types and surface shapes of honeycomb cores, where the proposed method was proved effective in dealing with noise due to burrs and/or deformation of cell walls.

Construction and test of flexible walls for the throat of the ILR high-speed wind tunnel

NASA Technical Reports Server (NTRS)

Igeta, Y.

1983-01-01

Aerodynamic tests in wind tunnels are jeopardized by the lateral limitations of the throat. This influence expands with increasing size of the model in proportion to the cross-section of the throat. Wall interference of this type can be avoided by giving the wall the form of a stream surface that would be identical to the one observed during free flight. To solve this problem, flexible walls that can adapt to every contour of surface flow are needed.

Macromolecule simulation and CH4 adsorption mechanism of coal vitrinite

NASA Astrophysics Data System (ADS)

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

Poster – 41: External marker block placement on the breast or chest wall for left-sided deep inspiration breath-hold radiotherapy

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

Conroy, Leigh; Guebert, Alexandra; Smith, Wendy

Purpose: We investigate DIBH breast radiotherapy using the Real-time Position Management (RPM) system with the marker-block placed on the target breast or chest wall. Methods: We measured surface dose for three different RPM marker-blocks using EBT3 Gafchromic film at 0° and 30° incidence. A registration study was performed to determine the breast surface position that best correlates with overall internal chest wall position. Surface and chest wall contours from MV images of the medial tangent field were extracted for 15 patients. Surface contours were divided into three potential marker-block positions on the breast: Superior, Middle, and Inferior. Translational registration wasmore » used to align the partial contours to the first-fraction contour. Each resultant transformation matrix was applied to the chest wall contour, and the minimum distance between the reference chest wall contour and the transformed chest wall contour was evaluated for each pixel. Results: The measured surface dose for the 2-dot, 6-dot, and 4-dot marker-blocks at 0° incidence were 74%, 71%, and 77% of dose to dmax respectively. At 30° beam incidence this increased to 76%, 72%, and 81%. The best external surface position was patient and fraction dependent, with no consistent best choice. Conclusions: The increase in surface dose directly under the RPM block is approximately equivalent to 3 mm of bolus. No marker-block position on the breast surface was found to be more representative of overall chest wall motion; therefore block positional stability and reproducibility can be used to determine optimal placement on the breast or chest wall.« less

Channel-Forming Bacterial Toxins in Biosensing and Macromolecule Delivery

PubMed Central

Gurnev, Philip A.; Nestorovich, Ekaterina M.

2014-01-01

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. PMID:25153255

Thermal repellent properties of surface coating using silica

NASA Astrophysics Data System (ADS)

Lee, Y. Y.; Halim, M. S.; Aminudin, E.; Guntor, N. A.

2017-11-01

Extensive land development in urban areas is completely altering the surface profile of human living environment. As cities growing rapidly, impervious building and paved surfaces are replacing the natural landscape. In the developing countries with tropical climate, large masses of building elements, such as brick wall and concrete members, absorb and store large amount of heat, which in turn radiate back to the surrounding air during the night time. This bubble of heat is known as urban heat island (UHI). The use of high albedo urban surfaces is an inexpensive measure that can reduce surrounded temperature. Thus, the main focus of this study is to investigate the ability of silica, SiO2, with high albedo value, to be used as a thermal-repelled surface coating for brick wall. Three different silica coatings were used, namely silicone resin, silicone wax and rain repellent and one exterior commercial paint (jota shield paint) that commercially available in the market were applied on small-scale brick wall models. An uncoated sample also had been fabricated as a control sample for comparison. These models were placed at the outdoor space for solar exposure. Outdoor environment measurement was carried out where the ambient temperature, surface temperature, relative humidity and UV reflectance were recorded. The effect of different type of surface coating on temperature variation of the surface brick wall and the thermal performance of coatings as potential of heat reduction for brick wall have been studied. Based on the results, model with silicone resin achieved the lowest surface temperature which indicated that SiO2 can be potentially used to reduce heat absorption on the brick wall and further retains indoor passive thermal comfortability.

Turbulent boundary layer on a convex, curved surface

NASA Technical Reports Server (NTRS)

Gillis, J. C.; Johnston, J. P.; Kays, W. M.; Moffat, R. J.

1980-01-01

The effects of strong convex curvature on boundary layer turbulence were investigated. The data gathered on the behavior of Reynolds stress suggested the formulation of a simple turbulence model. Three sets of data were taken on two separate facilities. Both rigs had flow from a flat surface, over a convex surface with 90 deg of turning, and then onto a flat recovery surface. The geometry was adjusted so that, for both rigs, the pressure gradient along the test surface was zero - thus avoiding any effects of streamwise acceleration on the wall layers. Results show that after a sudden introduction of curvature, the shear stress in the outer part of the boundary layer is sharply diminished and is even slightly negative near the edge. The wall shear also drops off quickly downstream. In contrast, when the surface suddenly becomes flat again, the wall shear and shear stress profiles recover very slowly towards flat wall conditions.

A significant reduction of ice adhesion on nanostructured surfaces that consist of an array of single-walled carbon nanotubes: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Bao, Luyao; Huang, Zhaoyuan; Priezjev, Nikolai V.; Chen, Shaoqiang; Luo, Kai; Hu, Haibao

2018-04-01

It is well recognized that excessive ice accumulation at low-temperature conditions can cause significant damage to civil infrastructure. The passive anti-icing surfaces provide a promising solution to suppress ice nucleation and enhance ice removal. However, despite extensive efforts, it remains a challenge to design anti-icing surfaces with low ice adhesion. Using all-atom molecular dynamics (MD) simulations, we show that surfaces with single-walled carbon nanotube array (CNTA) significantly reduce ice adhesion due to the extremely low solid areal fraction. It was found that the CNTA surface exhibits up to a 45% decrease in the ice adhesion strength in comparison with the atomically smooth graphene surface. The details of the ice detachment from the CNTA surface were examined for different water-carbon interaction energies and temperatures of the ice cube. Remarkably, the results of MD simulations demonstrate that the ice detaching strength depends linearly on the ratio of the ice-surface interaction energy and the ice temperature. These results open the possibility for designing novel robust surfaces with low ice adhesion for passive anti-icing applications.

Modelling Unsteady Wall Pressures Beneath Turbulent Boundary Layers

NASA Technical Reports Server (NTRS)

Ahn, B-K.; Graham, W. R.; Rizzi, S. A.

2004-01-01

As a structural entity of turbulence, hairpin vortices are believed to play a major role in developing and sustaining the turbulence process in the near wall region of turbulent boundary layers and may be regarded as the simplest conceptual model that can account for the essential features of the wall pressure fluctuations. In this work we focus on fully developed typical hairpin vortices and estimate the associated surface pressure distributions and their corresponding spectra. On the basis of the attached eddy model, we develop a representation of the overall surface pressure spectra in terms of the eddy size distribution. Instantaneous wavenumber spectra and spatial correlations are readily derivable from this representation. The model is validated by comparison of predicted wavenumber spectra and cross-correlations with existing emperical models and experimental data.

Wall effects in continuous microfluidic magneto-affinity cell separation.

PubMed

Wu, Liqun; Zhang, Yong; Palaniapan, Moorthi; Roy, Partha

2010-05-01

Continuous microfluidic magneto-affinity cell separator combines unique microscale flow phenomenon with advantageous nanobead properties, to isolate cells with high specificity. Owing to the comparable size of the cell-bead complexes and the microchannels, the walls of the microchannel exert a strong influence on the separation of cells by this method. We present a theoretical and experimental study that provides a quantitative description of hydrodynamic wall interactions and wall rolling velocity of cells. A transient convection model describes the transport of cells in two-phase microfluidic flow under the influence of an external magnetic field. Transport of cells along the microchannel walls is also considered via an additional equation. Results show the variation of cell flux in the fluid phases and the wall as a function of a dimensionless parameter arising in the equations. Our results suggest that conditions may be optimized to maximize cell separation while minimizing contact with the wall surfaces. Experimentally measured cell rolling velocities on the wall indicate the presence of other near-wall forces in addition to fluid shear forces. Separation of a human colon carcinoma cell line from a mixture of red blood cells, with folic acid conjugated 1 microm and 200 nm beads, is reported.

Reflection of a shock wave from a thermally accommodating wall - Molecular simulation.

NASA Technical Reports Server (NTRS)

Deiwert, G. S.

1973-01-01

Reflection of a plane shock wave from a wall has been simulated on a microscopic scale using a direct simulation Monte Carlo technique of the type developed by Bird. A monatomic gas model representing argon was used to describe the fluid medium and a simple one-parameter accommodation coefficient model was used to describe the gas-surface interaction. The influence of surface accommodation was studied parametrically by varying the accommodation coefficient from zero to one. Results are presented showing the temporal variations of flow field density, and mass, momentum, and energy fluxes to the wall during the shock wave reflection process. The energy flux was used to determine the wall temperature history. Comparisons with experiment are found to be satisfactory where data are available.

Helicity-dependent single-walled carbon nanotube alignment on graphite for helical angle and handedness recognition

PubMed Central

Chen, Yabin; Shen, Ziyong; Xu, Ziwei; Hu, Yue; Xu, Haitao; Wang, Sheng; Guo, Xiaolei; Zhang, Yanfeng; Peng, Lianmao; Ding, Feng; Liu, Zhongfan; Zhang, Jin

2013-01-01

Aligned single-walled carbon nanotube arrays provide a great potential for the carbon-based nanodevices and circuit integration. Aligning single-walled carbon nanotubes with selected helicities and identifying their helical structures remain a daunting issue. The widely used gas-directed and surface-directed growth modes generally suffer the drawbacks of mixed and unknown helicities of the aligned single-walled carbon nanotubes. Here we develop a rational approach to anchor the single-walled carbon nanotubes on graphite surfaces, on which the orientation of each single-walled carbon nanotube sensitively depends on its helical angle and handedness. This approach can be exploited to conveniently measure both the helical angle and handedness of the single-walled carbon nanotube simultaneously at a low cost. In addition, by combining with the resonant Raman spectroscopy, the (n,m) index of anchored single-walled carbon nanotube can be further determined from the (d,θ) plot, and the assigned (n,m) values by this approach are validated by both the electronic transition energy Eii measurement and nanodevice application. PMID:23892334

Stereological estimation of cell wall density of DR12 tomato mutant using three-dimensional confocal imaging

PubMed Central

Legland, David; Guillon, Fabienne; Kiêu, Kiên; Bouchet, Brigitte; Devaux, Marie-Françoise

2010-01-01

Background and Aims The cellular structure of fleshy fruits is of interest to study fruit shape, size, mechanical behaviour or sensory texture. The cellular structure is usually not observed in the whole fruit but, instead, in a sample of limited size and volume. It is therefore difficult to extend measurements to the whole fruit and/or to a specific genotype, or to describe the cellular structure heterogeneity within the fruit. Methods An integrated method is presented to describe the cellular structure of the whole fruit from partial three-dimensional (3D) observations, involving the following steps: (1) fruit sampling, (2) 3D image acquisition and processing and (3) measurement and estimation of relevant 3D morphological parameters. This method was applied to characterize DR12 mutant and wild-type tomatoes (Solanum lycopersicum). Key Results The cellular structure was described using the total volume of the pericarp, the surface area of the cell walls and the ratio of cell-wall surface area to pericarp volume, referred to as the cell-wall surface density. The heterogeneity of cellular structure within the fruit was investigated by estimating variations in the cell-wall surface density with distance to the epidermis. Conclusions The DR12 mutant presents a greater pericarp volume and an increase of cell-wall surface density under the epidermis. PMID:19952012

The effect of variable size posterior wall acetabular fractures on contact characteristics of the hip joint.

PubMed

Olson, S A; Bay, B K; Pollak, A N; Sharkey, N A; Lee, T

1996-01-01

The indications for open reduction and internal fixation of posterior wall acetabular fractures associated with a clinically stable hip joint are unclear. In previous work a large posterior wall defect (27% articular surface area) resulted in significant alteration of load transmission across the hip; specifically, there was a transition from evenly distributed loading along the acetabular articular surface to loading concentrated mainly in the superior portion of the articular surface during simulated single leg stance. However, the majority of posterior wall fractures involve a smaller amount of the articular surface. Posterior wall acetabular fractures not associated with instability of the hip are commonly treated nonoperatively. This practice does not account for the size of the posterior wall fracture. To study the biomechanical consequences of variably sized articular defects, a laboratory experiment was conducted evaluating three progressively larger posterior wall defects of the acetabulum during simulated single leg stance using superlow Fuji prescale film (Itochu International, New York): (a) 1/3 articular surface width through a 50 degrees arc along the posterior wall of the acetabulum, (b) 2/3, and (c) 3/3 articular width defects through the same 50 degrees arc along the posterior wall of the acetabulum. In the intact acetabulum, 48% of the total articular contact was located in the superior acetabulum. Twenty-eight percent of articular contact was in the anterior wall region of the acetabulum and 24% in the posterior wall region. After the 1/3 width posterior wall defect, 64% of the articular contact was located in the superior acetabulum (p = 0.0011). The 2/3 width posterior wall defect resulted in 71% of articular contact area being located in the superior acetabulum (p = 0.0006). After the 3/3 width posterior wall defect, 77% of articular contact was located in the superior acetabulum, significantly greater than the intact condition (p < 0

Characteristic microwave background distortions from collapsing domain wall bubbles

NASA Technical Reports Server (NTRS)

Goetz, Guenter; Noetzold, Dirk

1990-01-01

The magnitude and angular pattern of distortions of the microwave background are analyzed by collapsing spherical domain walls. A characteristic pattern of redshift distortions of red or blue spikes surrounded by blue discs was found. The width and height of a spike is related to the diameter and magnitude of the disc. A measurement of the relations between these quantities thus can serve as an unambiguous indicator for a collapsing spherical domain wall. From the redshift distortion in the blue discs an upper bound was found on the surface energy density of the walls sigma is less than or approximately 8 MeV cubed.

Quantification of common carotid artery and descending aorta vessel wall thickness from MR vessel wall imaging using a fully automated processing pipeline.

PubMed

Gao, Shan; van 't Klooster, Ronald; Brandts, Anne; Roes, Stijntje D; Alizadeh Dehnavi, Reza; de Roos, Albert; Westenberg, Jos J M; van der Geest, Rob J

2017-01-01

To develop and evaluate a method that can fully automatically identify the vessel wall boundaries and quantify the wall thickness for both common carotid artery (CCA) and descending aorta (DAO) from axial magnetic resonance (MR) images. 3T MRI data acquired with T 1 -weighted gradient-echo black-blood imaging sequence from carotid (39 subjects) and aorta (39 subjects) were used to develop and test the algorithm. The vessel wall segmentation was achieved by respectively fitting a 3D cylindrical B-spline surface to the boundaries of lumen and outer wall. The tube-fitting was based on the edge detection performed on the signal intensity (SI) profile along the surface normal. To achieve a fully automated process, Hough Transform (HT) was developed to estimate the lumen centerline and radii for the target vessel. Using the outputs of HT, a tube model for lumen segmentation was initialized and deformed to fit the image data. Finally, lumen segmentation was dilated to initiate the adaptation procedure of outer wall tube. The algorithm was validated by determining: 1) its performance against manual tracing; 2) its interscan reproducibility in quantifying vessel wall thickness (VWT); 3) its capability of detecting VWT difference in hypertensive patients compared with healthy controls. Statistical analysis including Bland-Altman analysis, t-test, and sample size calculation were performed for the purpose of algorithm evaluation. The mean distance between the manual and automatically detected lumen/outer wall contours was 0.00 ± 0.23/0.09 ± 0.21 mm for CCA and 0.12 ± 0.24/0.14 ± 0.35 mm for DAO. No significant difference was observed between the interscan VWT assessment using automated segmentation for both CCA (P = 0.19) and DAO (P = 0.94). Both manual and automated segmentation detected significantly higher carotid (P = 0.016 and P = 0.005) and aortic (P < 0.001 and P = 0.021) wall thickness in the hypertensive patients. A reliable and reproducible pipeline for fully

Effect of Temperature on the Desorption of Lithium from Molybdenum(110) Surfaces: Implications for Fusion Reactor First Wall Materials

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

Chen, Mohan; Roszell, John; Scoullos, Emanuel V.

2016-03-30

Determining the strength of Li binding to Mo is critical to assessing the survivability of Li as a potential first wall material in fusion reactors. Here, we present the results of a joint experimental and theoretical investigation into how Li desorbs from Mo(110) surfaces, based on what can be deduced from temperature-programmed desorption measurements and density functional theory (DFT). Li desorption peaks measured at temperatures ranging from 711 K (1 monolayer, ML) to 1030 K (0.04 ML), with corresponding desorption onsets from 489 to 878 K, follow a trend similar to predicted Gibbs free energies for Li adsorption. Bader chargemore » analysis of DFT densities reveals that repulsive forces between neighboring positively charged Li atoms increase with coverage and thus reduce the bond strength between Mo and Li, thereby lowering the desorption temperature as the coverage increases. In addition, DFT predicts that Li desorbs at higher temperatures from a surface with vacancies than from a perfect surface, offering an explanation for the anomalously high desorption temperatures for the last Li to desorb from Mo(110). Analysis of simulated local densities of states indicates that the stronger binding to the defective surface is correlated with enhanced interaction between Li and Mo, involving the Li 2s electrons and not only the Mo 4d electrons as in the case of the pristine surface, but also the Mo 5s electrons in the case with surface vacancies. We suggest that steps and kinks present on the Mo(110) surface behave similarly and contribute to the high desorption temperatures. These findings imply that roughened Mo surfaces may strengthen Li film adhesion at higher temperatures.« less

Dynamics of active sites in biological macromolecules using a Green-function approach: An application to heme vibrational dynamics in myoglobin

NASA Astrophysics Data System (ADS)

Rai, Brajesh; Prohofsky, Earl

2003-03-01

Dynamics of functionally active regions of biological macromolecules can be studied using a Green-function technique. This approach uses the fact that in most cases one has a good set of force constants for active sites, and rather poorly defined force field parameters for other regions of the macromolecule. The Green-function method is applied to study the iron vibrational modes of the heme active site in myoglobin. In this approach, the heme active site is viewed as a system interacting with surrounding globin, which acts as an excitation bath. The normal modes of heme and globin are separately calculated using the best available force fields for the two entities. The iron vibrational spectrum of myoglobin is then obtained using the solutions of the heme and globin, and by considering physically meaningful interactions between the two units. The refinement of the Green-function calculations to the experimental data from an x-ray synchrotron-based Nuclear Resonance Vibrational Spectroscopy provides important insights into the character of iron normal modes of myoglobin.

Application of pulsed field gradient NMR techniques for investigating binding of flavor compounds to macromolecules.

PubMed

Jung, Da-Mi; De Ropp, Jeffrey S; Ebeler, Susan E

2002-07-17

Two diffusion-based NMR techniques are presented and used to investigate the binding of selected flavor compounds to macromolecules. A pulsed field gradient NMR (PFG-NMR) method was applied to measure the apparent diffusion coefficients of four alkanone compounds as they associated with bovine serum albumin (BSA). The change in the apparent diffusion coefficient as a function of the BSA/alkanone ratio was fitted to yield binding constants (K(a)()) and binding stoichiometry (n) for each alkanone. The results showed that the apparent diffusion coefficients of alkanones increased with a decrease in the BSA/alkanone ratios, and the measured values of K(a)() and n were comparable with those obtained with other methods and depended on the alkanone structure. A diffusion-based nuclear Overhauser effect (called diffusion NOE pumping) method was also applied to screen mixtures of flavor compounds and identify those that have a binding affinity to complex macromolecules. Using this technique benzaldehyde and vanillin were observed to bind with bovine serum albumin, whereas 2-phenylethanol was identified as a nonbinding or weakly binding ligand with BSA. The diffusion NOE pumping method was also applied to a hydro alcoholic solution of cacao bean tannin extracts to which a mixture of ethylbenzoate, benzaldehyde, and 2-phenylethanol was added. The diffusion NOE pumping technique clearly indicated that ethylbenzoate had a stronger binding affinity to the polymeric (-)-epicatechin units of the cacao bean tannin extracts than the other two flavor compounds. The results successfully demonstrate the potential applications of diffusion-based NMR techniques for studying flavors and nonvolatile food matrix interactions.

Medial frontal GABA is lower in older schizophrenia: a MEGA-PRESS with macromolecule suppression study.

PubMed

Rowland, L M; Krause, B W; Wijtenburg, S A; McMahon, R P; Chiappelli, J; Nugent, K L; Nisonger, S J; Korenic, S A; Kochunov, P; Hong, L E

2016-02-01

Gamma-butyric acid (GABA) dysfunction has been implicated in the pathophysiology of schizophrenia and its cognitive deficits. Proton magnetic resonance spectroscopy (MRS) was used to test the hypothesis that older participants with schizophrenia have lower anterior cingulate GABA levels compared with older control participants. One-hundred forty-five participants completed this study. For detection of GABA, spectra were acquired from the medial frontal/anterior cingulate cortex using a macromolecule-suppressed MEGA-PRESS sequence. Patients were evaluated for psychopathology and all participants completed neuropsychological tests of working memory, processing speed and functional capacity. GABA levels were significantly lower in the older participants with schizophrenia (n=31) compared with the older control (n=37) group (P=0.003) but not between the younger control (n=40) and schizophrenia (n=29) groups (P=0.994). Age strongly predicted GABA levels in the schizophrenia group accounting for 42% of the variance, but the effect of age was less in the control group accounting for 5.7% of the variance. GABA levels were specifically related to working memory but not processing speed performance, functional capacity, or positive or negative symptom severity. This is the largest MRS study of GABA in schizophrenia and the first to examine GABA without macromolecule contamination, a potentially significant issue in previous studies. GABA levels more rapidly declined with advancing age in the schizophrenia compared with the control group. Interventions targeted at halting the decline or increasing GABA levels may improve functional outcomes and quality of life as patients with schizophrenia age.

Medial Frontal GABA is Lower in Older Schizophrenia: A MEGA-PRESS with Macromolecule Suppression Study

PubMed Central

Rowland, Laura M; Krause, Benjamin W.; Wijtenburg, S. Andrea; McMahon, Robert P.; Chiappelli, Joshua; Nugent, Katie L.; Nisonger, Sarah J.; Korenic, Stephanie A.; Kochunov, Peter; Hong, L. Elliot

2015-01-01

Gamma-butyric acid (GABA) dysfunction has been implicated in the pathophysiology of schizophrenia and its cognitive deficits. Proton magnetic resonance spectroscopy (MRS) was used to test the hypothesis that older participants with schizophrenia have lower anterior cingulate GABA levels compared to older control participants. One-hundred and forty-five participants completed this study. For detection of GABA, spectra were acquired from the medial frontal/anterior cingulate cortex using a macromolecule-suppressed MEGA-PRESS sequence. Patients were evaluated for psychopathology and all participants completed neuropsychological tests of working memory, processing speed, and functional capacity. GABA levels were significantly lower in the older participants with schizophrenia(n=31) compared to the older control(n=37) group (p=0.003) but not between the younger control(n=40) and schizophrenia (n=29) groups (p=0.994). Age strongly predicted GABA levels in the schizophrenia group accounting for 42% of the variance, but the effect of age was less in the control group accounting for 5.7% of the variance. GABA levels were specifically related to working memory but not processing speed performance, functional capacity, or positive or negative symptom severity. This is the largest MRS study of GABA in schizophrenia and the first to examine GABA without macromolecule contamination, a potentially significant issue in previous studies. GABA levels more rapidly declined with advancing age in the schizophrenia compared to the control group. Interventions targeted at halting the decline or increasing GABA levels may improve functional outcomes and quality of life as patients with schizophrenia age. PMID:25824298

Distribution volumes of macromolecules in human ovarian and endometrial cancers--effects of extracellular matrix structure.

PubMed

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. Copyright © 2015 the American Physiological Society.

Attachment of Single-wall Carbon Nanotubes (SWNTs) on Platinum Surfaces by Self-Assembling Techniques

NASA Technical Reports Server (NTRS)

Rosario-Castro, Belinda I.; Cabrera, Carlos R.; Perez-Davis, Maria; Lebron, Marisabel; Meador, Michael

2003-01-01

Single-wall carbon nanotubes (SWNTs) are very interesting materials because of their morphology, electronic and mechanical properties. Its morphology (high length-to-diameter ratio) and electronic properties suggest potential application of SWNTs as anode material for lithium ion secondary batteries. The introduction of SWNTs on these types of sources systems will improve their performance, efficiency, and capacity to store energy. A purification method has been applied for the removal of iron and amorphous carbon from the nanotubes. Unpurified and purified SWNTs were characterized by transmission electron microscopy (TEM), and thermogravimetric analysis (TGA). In order to attach carbon nanotubes on platinum electrode surfaces, a self-assembled monolayer (SAM) of 4-aminothiophenol (4-ATP) was deposited over the electrodes. The amino-terminated SAM obtained was characterized by cyclic voltammetry, X-ray photoelectron spectroscopy (XPS), and Fourier-transforms infrared (FTIR) spectroscopy. Carbon nanotubes were deposited over the amino-terminated SAM by an amide bond formed between SAM amino groups and carboxylic acid groups at the open ends of the carbon nanotubes.This deposition was characterized using Raman spectroscopy and Scanning Electron microscopy (SEM).

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

PubMed

Zhang, Qing; Beard, Daniel A; Schlick, Tamar

2003-12-01

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK

Dispersive Stiffness of Dzyaloshinskii Domain Walls

NASA Astrophysics Data System (ADS)

Pellegren, J. P.; Lau, D.; Sokalski, V.

2017-07-01

It is well documented that subjecting perpendicular magnetic films that exhibit the interfacial Dzyaloshinskii-Moriya interaction to an in-plane magnetic field results in a domain wall (DW) energy σ , which is highly anisotropic with respect to the orientation of the DW in the film plane Θ . We demonstrate that this anisotropy has a profound impact on the elastic response of the DW as characterized by the surface stiffness σ ˜ (Θ )=σ (Θ )+σ''(Θ ) and evaluate its dependence on the length scale of deformation. The influence of stiffness on DW mobility in the creep regime is assessed, with analytic and numerical calculations showing trends in σ ˜ that better represent experimental measurements of domain wall velocity in magnetic thin films compared to σ alone. Our treatment provides experimental support for theoretical models of the mobility of anisotropic elastic manifolds and makes progress toward a more complete understanding of magnetic domain wall creep.

Great Wall of China

NASA Technical Reports Server (NTRS)

2001-01-01

This ASTER sub-image covers a 12 x 12 km area in northern Shanxi Province, China, and was acquired January 9, 2001. The low sun angle, and light snow cover highlight a section of the Great Wall, visible as a black line running diagonally through the image from lower left to upper right. The Great Wall is over 2000 years old and was built over a period of 1000 years. Stretching 4500 miles from Korea to the Gobi Desert it was first built to protect China from marauders from the north.

This image is located at 40.2 degrees north latitude and 112.8 degrees east longitude.

Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of International Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products. Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, Calif., is the U.S. Science team leader; Moshe Pniel of JPL is the project manager. ASTER is the only high resolution imaging sensor on Terra. The primary goal of the ASTER mission is to obtain high-resolution image data in 14 channels over the entire land surface, as well as black and white stereo images. With revisit time of between 4 and 16 days, ASTER will provide the capability for repeat coverage of changing areas on Earth's surface.

The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats, monitoring potentially active volcanoes, identifying crop stress, determining cloud morphology and physical properties, wetlands Evaluation, thermal pollution monitoring, coral reef degradation, surface temperature mapping of soils and geology, and

Effect of shape and size of lung and chest wall on stresses in the lung

NASA Technical Reports Server (NTRS)

Vawter, D. L.; Matthews, F. L.; West, J. B.

1975-01-01

To understand better the effect of shape and size of lung and chest wall on the distribution of stresses, strains, and surface pressures, we analyzed a theoretical model using the technique of finite elements. First we investigated the effects of changing the chest wall shape during expansion, and second we studied lungs of a variety of inherent shapes and sizes. We found that, in general, the distributions of alveolar size, mechanical stresses, and surface pressures in the lungs were dominated by the weight of the lung and that changing the shape of the lung or chest wall had relatively little effect. Only at high states of expansion where the lung was very stiff did changing the shape of the chest wall cause substantial changes. Altering the inherent shape of the lung generally had little effect but the topographical differences in stresses and surface pressures were approximately proportional to lung height. The results are generally consistent with those found in the dog by Hoppin et al (1969).

Quantifying near-wall coherent structures in turbulent convection

NASA Astrophysics Data System (ADS)

Gunasegarane, G. S.; A Puthenveettil, Baburaj; K Agrawal, Yogesh; Schmeling, Daniel; Bosbach, Johannes; Arakeri, Jaywant; IIT Madras-DLR-IISc Collaboration

2011-11-01

We present planforms of line plumes formed on horizontal surfaces in turbulent convection, along with the length of near- wall line plumes measured from these planforms, in a six decade range of Rayleigh numbers (105 < Ra <1011) and at three Prandtl numbers (Pr = 0 . 7 , 6 , 602). Using geometric constraints on the relations for the mean plume spacings, we obtain expressions for the total length of these near-wall plumes in turbulent convection. The plume length per unit area (Lp / A), made dimensionless by the near-wall length scale in turbulent convection (Zw) remains a constant for a given fluid. The Nusselt number is shown to be directly proportional to Lp H / A for a given fluid layer of height H. Increase in Pr has a weak influence in decreasing Lp / A . These expressions match the measurements, thereby showing that the assumption of laminar natural convection boundary layers in turbulent convection is consistent with the observed total length of line plumes. We then show that similar relationships are obtained based on the assumption that the line plumes are the outcome of the instability of laminar natural convection boundary layers on the horizontal surfaces.

Electronic method for autofluorography of macromolecules on two-D matrices

DOEpatents

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.

Wall shear stress fixed points in blood flow

NASA Astrophysics Data System (ADS)

Arzani, Amirhossein; Shadden, Shawn

2017-11-01

Patient-specific computational fluid dynamics produces large datasets, and wall shear stress (WSS) is one of the most important parameters due to its close connection with the biological processes at the wall. While some studies have investigated WSS vectorial features, the WSS fixed points have not received much attention. In this talk, we will discuss the importance of WSS fixed points from three viewpoints. First, we will review how WSS fixed points relate to the flow physics away from the wall. Second, we will discuss how certain types of WSS fixed points lead to high biochemical surface concentration in cardiovascular mass transport problems. Finally, we will introduce a new measure to track the exposure of endothelial cells to WSS fixed points.

Surface Functionalization of Exosomes Using Click Chemistry

PubMed Central

2015-01-01

A method for conjugation of ligands to the surface of exosomes was developed using click chemistry. Copper-catalyzed azide alkyne cycloaddition (click chemistry) is ideal for biocojugation of small molecules and macromolecules to the surface of exosomes, due to fast reaction times, high specificity, and compatibility in aqueous buffers. Exosomes cross-linked with alkyne groups using carbodiimide chemistry were conjugated to a model azide, azide-fluor 545. Conjugation had no effect on the size of exosomes, nor was there any change in the extent of exosome adherence/internalization with recipient cells, suggesting the reaction conditions were mild on exosome structure and function. We further investigated the extent of exosomal protein modification with alkyne groups. Using liposomes with surface alkyne groups of a similar size and concentration to exosomes, we estimated that approximately 1.5 alkyne groups were present for every 150 kDa of exosomal protein. PMID:25220352

Relating Nanoscale Accessibility within Plant Cell Walls to Improved Enzyme Hydrolysis Yields in Corn Stover Subjected to Diverse Pretreatments.

PubMed

Crowe, Jacob D; Zarger, Rachael A; Hodge, David B

2017-10-04

Simultaneous chemical modification and physical reorganization of plant cell walls via alkaline hydrogen peroxide or liquid hot water pretreatment can alter cell wall structural properties impacting nanoscale porosity. Nanoscale porosity was characterized using solute exclusion to assess accessible pore volumes, water retention value as a proxy for accessible water-cell walls surface area, and solute-induced cell wall swelling to measure cell wall rigidity. Key findings concluded that delignification by alkaline hydrogen peroxide pretreatment decreased cell wall rigidity and that the subsequent cell wall swelling resulted increased nanoscale porosity and improved enzyme binding and hydrolysis compared to limited swelling and increased accessible surface areas observed in liquid hot water pretreated biomass. The volume accessible to a 90 Å dextran probe within the cell wall was found to be correlated to both enzyme binding and glucose hydrolysis yields, indicating cell wall porosity is a key contributor to effective hydrolysis yields.

A method of eliminating hydrogen maser wall shift

NASA Technical Reports Server (NTRS)

Levine, M. W.; Vessot, R. F. C.

1972-01-01

Maser output frequency shift was prevented by storage bulb kept at temperature at which wall shift is zero and effects of bulb size, shape, and surface texture are eliminated. Servo system is shown, along with bidirectional counter.

Local and global gravitational aspects of domain wall space-times

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

Cvetic, M.; Griffies, S.; Soleng, H.H.

1993-09-15

Local and global gravitational effects induced by eternal vacuum domain walls are studied. We concentrate on thin walls between nonequal and nonpositive cosmological constants on each side of the wall. The assumption of homogeneity, isotropy, and geodesic completeness of the space-time intrinsic to the wall as described in the comoving coordinate system and the constraint that the same symmetries hold in hypersurfaces parallel to the wall yield a general [ital Ansatz] for the line element of space-time. We restrict the problem further by demanding that the wall's surface energy density, [sigma], is positive and by requiring that the infinitely thinmore » wall represents a thin-wall limit of kinklike scalar field configuration. These vacuum domain walls fall in three classes depending on the value of their [sigma]: (1) extreme walls with [sigma]=[sigma][sub ext] are planar, static walls corresponding to supersymmetric configurations, (2) nonextreme walls with [sigma]=[sigma][sub non][gt][sigma][sub ext] correspond to expanding bubbles with observers on either side of the wall being [ital inside] the bubble, and (3) ultraextreme walls with [sigma]=[sigma][sub ultra][lt][sigma][sub ext] represent the bubbles of false vacuum decay. On the sides with less negative cosmological constant, the extreme, nonextreme, and ultraextreme walls exhibit no, repulsive, and attractive effective gravitational forces,'' respectively. These gravitational forces'' are global effects not caused by local curvature. Since the nonextreme wall encloses observers on both sides, the supersymmetric system has the lowest gravitational mass accessible to outside observers. It is conjectured that similar positive mass protection occurs in all physical systems and that no finite negative mass object can exist inside the universe.« less

Physiologic upper limits of pore size of different blood capillary types and another perspective on the dual pore theory of microvascular permeability.

PubMed