WorldWideScience

Sample records for solution conformation studies

  1. Solution conformation of the response regulator proteins from Deinococcus radiodurans studied by SAXS

    Science.gov (United States)

    Li, Li-Qin; Liu, Ying; Liu, Peng; Dong, Yu-Hui

    2011-10-01

    In this paper the solution conformation of the response regulator proteins from Deinococcus radiodurans was studied by small-angle X-ray scattering (SAXS). The SAXS curves of Dr-rrA in solutions were obtained at Beamline 1W2A of Beijing Synchrotron Radiation Facility (BSRF). Two possible conformations of the response regulator proteins, compact and incompact conformations, have been represented by the known crystallographic structures. And theoretical solution scattering curves of the two possible conformations were calculated and fitted to the experimental scattering curve of Dr-rrA, respectively. The result indicates that the solution conformation of the response regulator proteins is inclined to the compact one, which is in agreement with the result of biochemical experiments.

  2. Solution and conformational properties of wheat beta-D-glucans studied by light scattering and viscometry.

    Science.gov (United States)

    Li, Wei; Cui, Steve W; Wang, Qi

    2006-02-01

    The solution properties of wheat beta-glucan were investigated by light scattering and viscometric methods. The hydrodynamic radius (R(h)), weight average molecular weight (M(w)), radius of gyration (R(g)), and the second virial coefficient (A(2)) of wheat beta-glucan were determined by both dynamic and static light scattering methods, whereas the critical concentrations (c) of the solution were derived from [eta] via viscometric method. The structure sensitive parameters, rho (1.52-1.62), the conformation parameter nu (0.62), and the Mark-Houwink-Sakurada exponents alpha (0.78) confirmed the random coil conformation of wheat beta-glucan in 0.5 M NaOH solution. The characteristic ratio (4.97) was obtained by the random flight model, and the statistical segment length (8.83 nm) was derived from the wormlike cylinder model. It was found that the wormlike cylinder model could explain the chain stiffness better than the random flight model, which suggested an extended random coil conformation of wheat beta-glucan in 0.5 M NaOH solution. The study also revealed that the structure feature of wheat beta-glucan; that is, the higher trisaccharide-to-tetrasaccharide ratio contributed to the stiffer chain conformation compared with other cereal beta-glucans.

  3. Conformational study of a single molecule of poly para phenylene ethynylenes in dilute solutions.

    Science.gov (United States)

    Maskey, Sabina; Pierce, Flint; Perahia, Dvora; Grest, Gary S

    2011-06-28

    The conformation of single molecules of dialkyl poly para phenylene ethynylenes (PPEs), electro-active polymers, is studied in solutions using molecular dynamics simulations. The conformation of conjugated polymers affects their electro-optical properties and therefore is critical to their current and potential uses, though only limited theoretical knowledge is available regarding the factors that control their configuration. The present study investigates the affects of molecular parameters including molecular weight of the polymer and chemical structure of the side chains of PPEs in different solvents on the conformation of the polymers. The PPEs are modeled atomistically where the solvents are modeled both implicitly and explicitly. The study finds that PPEs assume extended configuration which is affected by the length of the polymer backbone and the nature and length of substituting side chains. While the polymer remains extended, local dynamics is retained and no long range correlations are observed within the backbone. The results are compared with scattering experiments.

  4. Conformational Study of DNA Sugars: from the Gas Phase to Solution

    Science.gov (United States)

    Uriarte, Iciar; Vallejo-López, Montserrat; Cocinero, Emilio J.; Corzana, Francisco; Davis, Benjamin G.

    2017-06-01

    Sugars are versatile molecules that play a variety of roles in the organism. For example, they are important in energy storage processes or as structural scaffolds. Here, we focus on the monosaccharide present in DNA by addressing the conformational and puckering properties in the gas phase of α- and β-methyl-2-deoxy-ribofuranoside and α- and β-methyl-2-deoxy-ribopiranoside. Other sugars have been previously studied in the gas phase The work presented here stems from a combination of chemical synthesis, ultrafast vaporization methods, supersonic expansions, microwave spectroscopy (both chirped-pulsed and Balle-Flygare cavity-based spectrometers) and NMR spectroscopy. Previous studies in the gas phase had been performed on 2-deoxyribose, but only piranose forms were detected. However, thanks to the combination of these techniques, we have isolated and characterized for the first time the conformational landscape of the sugar present in DNA in its biologically relevant furanose form. Our gas phase study serves as a probe of the conformational preferences of these biomolecules under isolation conditions. Thanks to the NMR experiments, we can characterize the favored conformations in solution and extract the role of the solvent in the structure and puckering of the monosaccharides. E. J. Cocinero, A. Lesarri, P. Écija, F. J. Basterretxea, J.-U. Grabow, J. A. Fernández, F. Castaño, Angew. Chem. Int. Edit. 2012, 51, 3119. P. Écija, I. Uriarte, L. Spada, B. G. Davis, W. Caminati, F. J. Basterretxea, A. Lesarri, E. J. Cocinero, Chem. Commun. 2016, 52, 6241. I. Peña, E. J. Cocinero, C. Cabezas, A. Lesarri, S. Mata, P. Écija, A. M. Daly, Á. Cimas, C. Bermúdez, F. J. Basterretxea, S. Blanco, J. A. Fernández, J. C. López, F. Castaño, J. L. Alonso, Angew. Chem. Int. Edit. 2013, 52, 11840.

  5. Conformational disorder in phosphopeptides: solution studies by CD and NMR techniques

    Directory of Open Access Journals (Sweden)

    Leone Marilisa

    2014-01-01

    Full Text Available In the last few years intrinsically disordered proteins (IDPs have received great attention from the scientific community as they participate in several important biological processes and diseases. The intrinsic disorder and flexibility of IDPs grant them a number of advantages with respect to ordered proteins, such as conformational plasticity to bind several targets, a large interaction surface, involvement in high specificity/low affinity interactions, enhanced binding kinetics. It is assumed that post-translational modifications such as phosphorylation can stimulate structural rearrangement in IDPs and facilitate their binding to partners. To better understand at a structural level the multifaceted mechanisms that govern molecular recognition processes involving IDPs, we designed, synthesized by solid phase methods, and structurally characterized unstructured peptides. These molecules contain a putative disordered module, flanked at either the N- or C-terminal ends by a different phosphorylated amino acid (serine or threonine to mimick the effects of phosphorylation. The absence of an ordered state in the designed peptides was proved experimentally by CD and NMR conformational studies that were carried out under different solution conditions

  6. Conformations of gelatin in trivalent chromium salt solutions: Viscosity and dynamic light scattering study

    Science.gov (United States)

    Qiao, Congde; Zhang, Jianlong; Kong, Aiqun

    2017-02-01

    An investigation of the influences of pH, salt type, and salt concentration on the conformations of gelatin molecules in trivalent chromium salt solutions was performed by viscosity and dynamic light scattering (DLS) techniques. It was found that the viscosity behaviors as polyelectrolytes or polyampholytes depended on the charge distribution on the gelatin chains, which can be tuned by the value of pH of the gelatin solution. The intrinsic viscosity of gelatin in basic chromium sulfate aqueous solution at pH = 2.0 first decreased and then increased with increasing Cr(OH)SO4 concentration, while a monotonic decrease of the intrinsic viscosity of gelatin was observed in CrCl3 solution. However, the intrinsic viscosity of gelatin at pH = 5.0 was found to be increased first and then decreased with an increase in salt concentration in Cr(OH)SO4 solution, as well as in CrCl3 solution. We suggested that the observed viscosity behavior of gelatin in trivalent chromium salt solutions was attributed to the comprehensive effects of shielding, overcharging, and crosslinking (complexation) caused by the introduction of the different counterions. In addition, the average hydrodynamic radius ( R h ) of gelatin molecules in various salt solutions was determined by DLS. It was found that the change trend of R h with salt concentration was the same as the change of intrinsic viscosity. Based on the results of the viscosity and DLS, a possible mechanism for the conformational transition of gelatin chains with external conditions including pH, salt concentration, and salt type is proposed.

  7. The solution conformation of sialyl-alpha (2----6)-lactose studied by modern NMR techniques and Monte Carlo simulations.

    Science.gov (United States)

    Poppe, L; Stuike-Prill, R; Meyer, B; van Halbeek, H

    1992-03-01

    We present a comprehensive strategy for detailed characterization of the solution conformations of oligosaccharides by NMR spectroscopy and force-field calculations. Our experimental strategy generates a number of interglycosidic spatial constraints that is sufficiently large to allow us to determine glycosidic linkage conformations with a precision heretofore unachievable. In addition to the commonly used [1H,1H] NOE contacts between aliphatic protons, our constraints are: (a) homonuclear NOEs of hydroxyl protons in H2O to other protons in the oligosaccharide, (b) heteronuclear [1H,13C] NOEs, (c) isotope effects of O1H/O2H hydroxyl groups on 13C chemical shifts, and (d) long-range heteronuclear scalar couplings across glycosidic bonds. We have used this approach to study the trisaccharide sialyl-alpha (2----6)-lactose in aqueous solution. The experimentally determined geometrical constraints were compared to results obtained from force-field calculations based on Metropolis Monte Carlo simulations. The molecule was found to exist in 2 families of conformers. The preferred conformations of the alpha (2----6)-linkage of the trisaccharide are best described by an equilibrium of 2 conformers with phi angles at -60 degrees or 180 degrees and of the 3 staggered rotamers of the omega angle with a predominant gt conformer. Three intramolecular hydrogen bonds, involving the hydroxyl protons on C8 and C7 of the sialic acid residue and on C3 of the reducing-end glucose residue, contribute significantly to the conformational stability of the trisaccharide in aqueous solution.

  8. Conformation and arrangement of polyelectrolytes in semi-diluted solution. A study by small angle neutrons scattering; Conformation et arrangement des polyelectrolytes en solution semi-diluee. Etude par diffusion des neutrons aux petits angles

    Energy Technology Data Exchange (ETDEWEB)

    Spiteri, M.N.

    1997-03-25

    Polyelectrolytes have particular physical and chemical properties and can thus be used for instance for petroleum production. Some of their microscopic properties have been studied in this work. With the particular zero average contrast technique, the small angle neutron scattering allows to directly know the form factors in semi-diluted solutions of polyelectrolytes where the chains are mixed. Another measure leads to the crystal structure. The electrostatic screen effects when salt is added in aqueous solutions of completely charged PSSNa solutions (f=1) (sodium polystyrene sulfonate) are studied. It seems that the chains take a vermiform conformation. Their persistence length varies as I{sup -1/3} (I is the ionic force). The hydrophobicity effects in partially charged PSSNa solutions (f<1) are given too. They lead to a progressive collapse of the chains when their charge rates decrease. The screen and condensation effects when the charge rate f of the PSSNa (f>f(Manning)) varies in a polar solvent (DMSO) are studied. The vermiform chains have the same persistence length (for each f) which varies as I{sup -1/4}. Lastly, the f variation effects in the case of a weakly charged hydrophilic poly-ion (f

  9. Conformational isomerism and self-association of calixarene building blocks in non-polar solution studied by Fourier transform infrared spectrometry

    NARCIS (Netherlands)

    Lutz, Bert T.G.; Astarloa, Gonzalo; van der Maas, John H.; Janssen, R.G.; Janssen, Rob G.; Verboom, Willem; Reinhoudt, David

    1995-01-01

    In order to establish the conformational equilibrium of calix[6]arene derivatives, a series of phenolic building blocks differing in chain length (oligomers) have been studied in solution by Fourier transform infrared spectrometry (FT-IR). Different intramolecular OH ¿ X interactions have been

  10. Conformations of a dipolar solute in a Stockmayer solvent channel.

    Science.gov (United States)

    Yi, Taeil; Wang, Qian; Lichter, Seth

    2012-10-30

    A wide range of molecules, from inorganic to biological, self-assemble on surfaces. Previous studies have elucidated many features of solute reorganization on surfaces using coarse-grained modeling, implicit solvents, and constraints such as chemically bonding the solute to the surface. Using molecular dynamics simulations under various combinations of interaction parameters, solute fractions, and solute dipole moment, we study the redistribution of freely-rotating dipolar solute molecules solvated by a water-like Stockmayer solvent initially adhered to a face-centered cubic substrate. The balance of attractive and repulsive forces is essential for acquiring a particular stable conformation. Here we show that the adsorbed molecules redistribute into different conformations--wetting film, nonwetting, partial wetting, and pseudopartial wetting drops--depending on the parameter values. We observe that the pseudopartial wetting drop is transient and its rate of spreading fluctuates, slowing to nearly zero as it passes through particular conformations before reaching an equilibrium thin film. Strong attraction between solute molecules yields a droplet with a net dipole moment. A high solute fraction leads to a pancake-like conformation arising from a balance of surface tension and van der Waals forces. This study augments our understanding of the evolution of aggregates in biological systems and also the design of polymers for self-assembled monolayers for industrial applications.

  11. The solutions of time and space conformable fractional heat equations with conformable Fourier transform

    Directory of Open Access Journals (Sweden)

    Çenesiz Yücel

    2015-12-01

    Full Text Available In this paper our aim is to find the solutions of time and space fractional heat differential equations by using new definition of fractional derivative called conformable fractional derivative. Also based on conformable fractional derivative definition conformable Fourier Transform is defined. Fourier sine and Fourier cosine transform definitions are given and space fractional heat equation is solved by conformable Fourier transform.

  12. Conformation of poly(γ-glutamic acid) in aqueous solution.

    Science.gov (United States)

    Muroga, Yoshio; Nakaya, Asami; Inoue, Atsuki; Itoh, Daiki; Abiru, Masaya; Wada, Kaori; Takada, Masako; Ikake, Hiroki; Shimizu, Shigeru

    2016-04-01

    Local conformation and overall conformation of poly(γ-DL-glutamic acid) (PγDLGA) and poly(γ-L-glutamic acid) (PγLGA) in aqueous solution was studied as a function of degree of ionization ε by (1) H-NMR, circular dichroism, and potentiometric titration. It was clarified that their local conformation is represented by random coil over an entire ε range and their overall conformation is represented by expanded random-coil in a range of ε > ε(*) , where ε(*) is about 0.3, 0.35, 0.45, and 0.5 for added-salt concentration of 0.02M, 0.05M, 0.1M, and 0.2M, respectively. In a range of ε acidic media. © 2015 Wiley Periodicals, Inc.

  13. Weyl Conformal Gravity: Mannheim-Kazanas Solution

    CERN Document Server

    Bhattacharya, Amrita; Scalia, Massimo; Cattani, Carlo; Nandi, Kamal K

    2009-01-01

    In this paper, we first point out certain interesting features of the Mannheim-Kazanas solution of Weyl conformal gravity. Next, we adopt the viewpoint that physical effects in Weyl gravity should be determined by the combined effect of both the constants $\\gamma$ and k appearing in the solution, and not by $\\gamma$ alone. This idea is supported by the effect of tidal forces as well as by the required stability of circular orbits of massive particles. To deal with massless particles, we employ the Rindler-Ishak method for calculating the bending of light rays up to second order, which at once reveals the exact Schwarzschild terms as well as the combined effect of $\\gamma$ and k. The enhanced light bending in the attractive halo gravity then provides a positive lower bound for $\\gamma$. A certain reported discrepancy in the literature is also resolved. It turns out that even the first order light bending is modified by Weyl gravity. This is a new effect though too minuscule to be observed at present.

  14. C-metric solution for conformal gravity with a conformally coupled scalar field

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Kun, E-mail: mengkun@tjpu.edu.cn [School of Science, Tianjin Polytechnic University, Tianjin 300387 (China); Zhao, Liu, E-mail: lzhao@nankai.edu.cn [School of Physics, Nankai University, Tianjin 300071 (China)

    2017-02-15

    The C-metric solution of conformal gravity with a conformally coupled scalar field is presented. The solution belongs to the class of Petrov type D spacetimes and is conformal to the standard AdS C-metric appeared in vacuum Einstein gravity. For all parameter ranges, we identify some of the physically interesting static regions and the corresponding coordinate ranges. The solution may contain a black hole event horizon, an acceleration horizon, either of which may be cut by the conformal infinity or be hidden behind the conformal infinity. Since the model is conformally invariant, we also discussed the possible effects of the conformal gauge choices on the structure of the spacetime.

  15. Regular and conformal regular cores for static and rotating solutions

    Energy Technology Data Exchange (ETDEWEB)

    Azreg-Aïnou, Mustapha

    2014-03-07

    Using a new metric for generating rotating solutions, we derive in a general fashion the solution of an imperfect fluid and that of its conformal homolog. We discuss the conditions that the stress–energy tensors and invariant scalars be regular. On classical physical grounds, it is stressed that conformal fluids used as cores for static or rotating solutions are exempt from any malicious behavior in that they are finite and defined everywhere.

  16. Conformational analysis of Gly-Ala-NHMe in D2O and DMSO solutions: A two-dimensional infrared spectroscopy study

    DEFF Research Database (Denmark)

    Candelaresi, Marco; Ragnoni, Elena; Cappelli, Chiara

    2013-01-01

    A relevant number of experiments on short peptides has been performed in recent years. One of the major problems rises from the simultaneous presence of slightly different conformers at equilibrium in solution. In the present paper, the conformational characteristics of the Gly-l-Ala-Methyl amide...... dipeptide in D2O and DMSO solutions are investigated by nonlinear IR spectroscopy. The pump-probe scheme with ultrashort mid-infrared pulses, in the Amide I region, is used to determine the mutual orientation of the two C=O bonds and the dynamics due to solute-solvent interactions. The coupling between...... and molecular dynamics simulations are performed to identify the most stable geometries. By comparing the experimental and the theoretical data, we establish the prevalence of β-like polar conformers in both water and DMSO solvents. © 2013 American Chemical Society....

  17. De novo design, synthesis and solution conformational study of two didehydroundecapeptides: effect of nature and number of amino acids interspersed between ΔPhe residues.

    Science.gov (United States)

    Dutta, Madhvi Gupta; Mathur, Puniti; Chauhan, Virander S

    2011-12-01

    De novo design of peptides and proteins has recently surfaced as an approach for investigating protein structure and function. This approach vitally tests our knowledge of protein folding and function, while also laying the groundwork for the fabrication of proteins with properties not precedented in nature. The success relies heavily on the ability to design relatively short peptides that can espouse stable secondary structures. To this end, substitution with α,β-didehydroamino acids, especially α,β-didehydrophenylalanine (Δ(z)Phe), comes in use for spawning well-defined structural motifs. Introduction of ΔPhe induces β-bends in small and 3(10)-helices in longer peptide sequences. The present work aims to investigate the effect of nature and the number of amino acids interspersed between two ΔPhe residues in two model undecapeptides, Ac-Gly-Ala-ΔPhe-Ile-Val-ΔPhe-Ile-Val-ΔPhe-Ala-Gly-NH(2) (I) and Boc-Val-ΔPhe-Phe-Ala-Phe-ΔPhe-Phe-Leu-Ala-ΔPhe-Gly-OMe (II). Peptide I was synthesized using solid-phase chemistry and characterized using circular dichroism spectroscopy. Peptide II was synthesized using solution-phase chemistry and characterized using circular dichroism and nuclear magnetic resonance spectroscopy. Peptide I was designed to examine the effect of incorporating β-strand-favoring residues like valine and isoleucine as spacers between two ΔPhe residues on the final conformation of the resulting peptide. Circular dichroism studies on this peptide have shown the existence of a 3(10)-helical conformation. Peptide II possesses three amino acids as spacers between ΔPhe residues and has been reported to adopt a mixed 3(10)/α-helical conformation using circular dichroism and nuclear magnetic resonance spectroscopy studies. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.

  18. Conformal block study and bounding OPE in conformal field theories

    CERN Document Server

    Yvernay, Pierre

    2015-01-01

    During the past few years, the re-emergence of conformal bootstrap as a numerical tool to solve conformal field theory allowed more precise estimation of several presumed conformal field theory among which we could cite the 3D Ising model. This work intends to provide insight on conformal blocks which are elementary objects in the conformal bootstrap approach. These are considered in Euclidian space where we study fields of all equal dimension. This study allows us to improve bounds derived in \\cite{OPEconv}.

  19. Conformations and Conformational Processes of Hexahydrobenzazocines by NMR and DFT Studies.

    Science.gov (United States)

    Musielak, Bogdan; Holak, Tad A; Rys, Barbara

    2015-09-18

    Conformational processes that occur in hexahydrobenzazocines have been studied with the (1)H and (13)C dynamic nuclear magnetic resonance (DNMR) spectroscopy. The coalescence effects are assigned to two different conformational processes: the ring-inversion of the ground-state conformations and the interconversion between two different conformers. The barriers for these processes are in the range of 42-52 and 42-43 kJ mol(-1), respectively. Molecular modeling on the density functional theory (DFT) level and the gauge invariant atomic orbitals (GIAO)-DFT calculations of isotropic shieldings and coupling constants for the set of low-energy conformations were compared with the experimental NMR data. The ground-state of all compounds in solution is the boat-chair (BC) conformation. The BC form adopts two different conformations because the nitrogen atom can be in the boat or chair parts of the BC structure. These two conformers are engaged in the interconversion process.

  20. Small angle x-ray studies reveal that Aspergillus niger glucoamylase has a defined extended conformation and can form dimers in solution

    DEFF Research Database (Denmark)

    Jørgensen, Anders Dysted; Nøhr, Jane; Kastrup, Jette Sandholm

    2008-01-01

    The industrially important glucoamylase 1 is an exo-acting glycosidase with substrate preference for alpha-1,4 and alpha-1,6 linkages at non-reducing ends of starch. It consists of a starch binding and a catalytic domain interspersed by a highly glycosylated polypeptide linker. The linker function...... is poorly understood and structurally undescribed, and data regarding domain organization and intramolecular functional cooperativity are conflicting or non-comprehensive. Here, we report a combined small angle x-ray scattering and calorimetry study of Aspergillus niger glucoamylase 1, glucoamylase 2, which...... lacks a starch binding domain, and an engineered low-glycosylated variant of glucoamylase 1 with a short linker. Low resolution solution structures show that the linker adopts a compact structure rendering a well defined extended overall conformation to glucoamylase. We demonstrate that binding...

  1. Conformal transistor arrays based on solution-processed organic crystals.

    Science.gov (United States)

    Zhao, Xiaoli; Zhang, Bing; Tang, Qingxin; Ding, Xueyan; Wang, Shuya; Zhou, Yuying; Tong, Yanhong; Liu, Yichun

    2017-11-13

    Conformal transistor array based on solution-processed organic crystals, which can provide sensory and scanning features for monitoring, biofeedback, and tracking of physiological function, presents one of the most promising technologies for future large-scale low-cost wearable and implantable electronics. However, it is still a huge challenge for the integration of solution-processed organic crystals into conformal FETs owing to a generally existing swelling phenomenon of the elastic materials and the lack of the corresponding device fabrication technology. Here, we present a promising route to fabricate a conformal field-effect transistor (FET) array based on solution-processed TIPS-pentacene single-crystal micro/nanowire array. By simply drop-casting the organic solution on an anti-solvent photolithography-compatible electrode with bottom-contact coplanar configuration, the transistor array can be formed and can conform onto uneven objects. Excellent electrical properties with device yield as high as 100%, field-effect mobility up to 0.79 cm 2 V -1 s -1 , low threshold voltage, and good device uniformity are demonstrated. The results open up the capability of solution-processed organic crystals for conformal electronics, suggesting their substantial promise for next-generation wearable and implantable electronics.

  2. Multiple Conformations of E. Coli Hsp90 in Solution: Insights Into the Conformational Dynamics of Hsp90

    Energy Technology Data Exchange (ETDEWEB)

    Krukenberg, K.A.; Forster, F.; Rice, L.M.; Sali, A.; Agard, D.A.

    2009-05-20

    Hsp90, an essential eukaryotic chaperone, depends upon its intrinsic ATPase activity for function. Crystal structures of the bacterial Hsp90 homolog, HtpG, and the yeast Hsp90 reveal large domain rearrangements between the nucleotide-free and the nucleotide-bound forms. We used small-angle X-ray scattering and recently developed molecular modeling methods to characterize the solution structure of HtpG and demonstrate how it differs from known Hsp90 conformations. In addition to this HtpG conformation, we demonstrate that under physiologically relevant conditions, multiple conformations coexist in equilibrium. In solution, nucleotide-free HtpG adopts a more extended conformation than observed in the crystal, and upon the addition of AMPPNP, HtpG is in equilibrium between this open state and a closed state that is in good agreement with the yeast AMPPNP crystal structure. These studies provide a unique view of Hsp90 conformational dynamics and provide a model for the role of nucleotide in effecting conformational change.

  3. Conformation and physical properties of cycloisomaltooligosaccharides in aqueous solution.

    Science.gov (United States)

    Suzuki, Shiho; Yukiyama, Takashi; Ishikawa, Arata; Yuguchi, Yoshiaki; Funane, Kazumi; Kitamura, Shinichi

    2014-01-01

    We studied the conformation and physical properties of cyclic and linear isomaltooligosaccharides in aqueous solution by intrinsic viscosity measurement, small angle X-ray scattering (SAXS) and molecular modeling. We used four cycloisomaltooligosaccharide samples (CIs) with degree of polymerization (DP) 7-10 (CI-7-CI-10) and five linear isomaltooligosaccharide samples (LIs) with DP 7-11 (LI-7-LI-11). The values of α in the Mark-Houwink-Sakurada equation [η]=KM(w)(α) for the CI and LI were determined to be 0.50 and 0.78, respectively. The radii of gyration (R(G)) of CI-7, CI-8, CI-9 and CI-10 determined from SAXS data were 6.7, 6.9, 7.5 and 8.3Å, respectively. The scattering profile of CI-9 compared with those obtained for molecular models indicated that CI molecular chains are less flexible than those for LIs and adopt a rather compact circular conformation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. On the hydration and conformation of cocaine in solution

    Science.gov (United States)

    Gillams, Richard J.; Lorenz, Christian D.; McLain, Sylvia E.

    2017-05-01

    In order to develop theories relating to the mechanism through which cocaine can diffuse across the blood-brain barrier, it is important to understand the interplay between the hydration of the molecule and the adopted conformation. Here key differences in the hydration of cocaine hydrochloride (CHC) and freebase cocaine (CFB) are highlighted on the atomic scale in solution, through the use of molecular dynamics simulations. By adopting different conformations, CHC and CFB experience differing hydration environments. The interplay between these two factors may account for the vast difference in solubility of these two molecules.

  5. Distinct Conformation of ATP Molecule in Solution and on Protein.

    Science.gov (United States)

    Kobayashi, Eri; Yura, Kei; Nagai, Yoshinori

    2013-01-01

    Adenosine triphosphate (ATP) is a versatile molecule used mainly for energy and a phosphate source. The hydrolysis of γ phosphate initiates the reactions and these reactions almost always start when ATP binds to protein. Therefore, there should be a mechanism to prevent spontaneous hydrolysis reaction and a mechanism to lead ATP to a pure energy source or to a phosphate source. To address these questions, we extensively analyzed the effect of protein to ATP conformation based on the sampling of the ATP solution conformations obtained from molecular dynamics simulation and the sampling of ATP structures bound to protein found in a protein structure database. The comparison revealed mainly the following three points; 1) The ribose ring in ATP molecule, which puckers in many ways in solution, tends to assume either C2' exo or C2' endo when it binds to protein. 2) The adenine ring in ATP molecule, which takes open-book motion with the two ring structures, has two distinct structures when ATP binds to protein. 3) The glycosyl-bond and the bond between phosphate and the ribose have unique torsion angles, when ATP binds to protein. The combination of torsion angles found in protein-bound forms is under-represented in ATP molecule in water. These findings suggest that ATP-binding protein exerts forces on ATP molecule to assume a conformation that is rarely found in solution, and that this conformation change should be a trigger for the reactions on ATP molecule.

  6. Conformational Dynamics of DNA G-Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On-line with Mass Spectrometry

    Science.gov (United States)

    Berezovski, Maxim V

    2014-01-01

    Invited for this months cover is the group of Prof. Maxim V. Berezovski. The cover picture shows the two-dimensional separation of unfolded (green) and folded (red) forms of G-quadruplex (GQ) DNA. The first dimension is kinetic capillary electrophoresis (KCE) separation of unfolded and folded DNA with different K+ concentrations in solution; the second dimension is ion mobility mass spectrometry separation of DNA conformers in the gas phase. DNA folding into a compact GQ structure is mediated by K+ ions. For more details, see the Full Paper on p. 58 ff. PMID:24808989

  7. An NMR and ab initio quantum chemical study of acid-base equilibria for conformationally constrained acidic alpha-amino acids in aqueous solution

    DEFF Research Database (Denmark)

    Nielsen, Peter Aadal; Jaroszewski, Jerzy W.; Norrby, Per-Ola

    2001-01-01

    The protonation states of a series of piperidinedicarboxylic acids (PDAs), which are conformationally constrained acidic alpha -amino acids, have been studied by C-13 NMR titration in water. The resulting data have been correlated with theoretical results obtained by HF/6-31+G* calculations using...

  8. Heterotic string solutions and coset conformal field theories

    CERN Document Server

    Giveon, Amit; Tseytlin, Arkady A

    1993-01-01

    We discuss solutions of the heterotic string theory which are analogous to bosonic and superstring backgrounds related to coset conformal field theories. A class of exact `left-right symmetric' solutions is obtained by supplementing the metric, antisymmetric tensor and dilaton of the superstring solutions by the gauge field background equal to the generalised Lorentz connection with torsion. As in the superstring case, these backgrounds are $\\a'$-independent, i.e. have a `semiclassical' form. The corresponding heterotic string sigma model is obtained from the combination of the (1,0) supersymmetric gauged WZNW action with the action of internal fermions coupled to the target space gauge field. The pure (1,0) supersymmetric gauged WZNW theory is anomalous and does not describe a consistent heterotic string solution. We also find (to the order $\\alpha'^3$) a two-dimensional perturbative heterotic string solution with the trivial gauge field background. To the leading order in $\\alpha'$ it coincides with the kno...

  9. Conformational Study of Dibenzyl Ether

    Science.gov (United States)

    Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Hewett, Daniel M.; Zwier, Timothy S.

    2017-06-01

    Understanding the initial stages of polycyclic aromatic hydrocarbon (PAH) aggregation, the onset of soot formation, is an important goal on the pathway to cleaner combustion processes. PAHs with short alkyl chains, present in fuel-rich combustion environments, can undergo reactions that will chemically link aromatic rings together. One such example of a linked diaryl compound is dibenzyl ether, C_{6}H_{5}-CH_{2}-O-CH_{2}-C_{6}H_{5}. The -CH_{2}-O-CH_{2}- linkage has a length and flexibility well-suited to forming a π-stacked conformation between the two phenyl rings. In this talk, we will explore the single-conformation spectroscopy of dibenzyl ether under jet-cooled conditions in the gas phase. Laser-induced fluorescence, chirped pulse Fourier transform microwave (8-18 GHz region), and single-conformation infrared spectroscopy in the alkyl CH stretch region were all carried out on the molecule, thereby interrogating its full array of electronic, vibrational and rotational degrees of freedom. This work is the first step in a broader study to determine the extent of π-stacking in linked aryl compounds as a function of linkage and PAH size.

  10. Exact Solutions to Some Conformable Time Fractional Equations in Benjamin-Bona-Mahony Family

    OpenAIRE

    Korkmaz, Alper

    2016-01-01

    The conformable time fractional forms of some partial differential equations are solved in the study. The existence of chain rule and the derivative of composite function enable the equations to be reduced to some ordinary differential equations by using some particular wave transformations. The modified Kudryashov method implemented to derive the exact solutions for the Benjamin-Bona Mahony (BBM), the symmetric BBM and the equal width (EW) equations in the conformable fractional time derivat...

  11. Conformal invariance and new exact solutions of the elastostatics equations

    Science.gov (United States)

    Chirkunov, Yu. A.

    2017-03-01

    We fulfilled a group foliation of the system of n-dimensional (n ≥ 2) Lame equations of the classical static theory of elasticity with respect to the infinite subgroup contained in normal subgroup of main group of this system. It permitted us to move from the Lame equations to the equivalent unification of two first-order systems: automorphic and resolving. We obtained a general solution of the automorphic system. This solution is an n-dimensional analogue of the Kolosov-Muskhelishvili formula. We found the main Lie group of transformations of the resolving system of this group foliation. It turned out that in the two-dimensional and three-dimensional cases, which have a physical meaning, this system is conformally invariant, while the Lame equations admit only a group of similarities of the Euclidean space. This is a big success, since in the method of group foliation, resolving equations usually inherit Lie symmetries subgroup of the full symmetry group that was not used for the foliation. In the three-dimensional case for the solutions of the resolving system, we found the general form of the transformations similar to the Kelvin transformation. These transformations are the consequence of the conformal invariance of the resolving system. In the three-dimensional case with a help of the complex dependent and independent variables, the resolving system is written as a simple complex system. This allowed us to find non-trivial exact solutions of the Lame equations, which direct for the Lame equations practically impossible to obtain. For this complex system, all the essentially distinct invariant solutions of the maximal rank we have found in explicit form, or we reduced the finding of those solutions to the solving of the classical one-dimensional equations of the mathematical physics: the heat equation, the telegraph equation, the Tricomi equation, the generalized Darboux equation, and other equations. For the resolving system, we obtained double wave of a

  12. Solvation number and conformation of N,N-dimethylacrylamide and N,N-dimethylpropionamide in the coordination sphere of the cobalt(II) ion in solution studied by FT-IR and FT-Raman spectroscopy.

    Science.gov (United States)

    Asada, Mitsunori; Mitsugi, Takushi; Ogura, Takahiro; Fujii, Kenta; Umebayashi, Yasuhiro; Ishiguro, Shin-ichi

    2007-07-01

    The solvation number and conformation of N,N-dimethylacrylamide (DMAA) in the coordination sphere of the cobalt(II) ion in solution were studied, and compared with those of N,N-dimethylpropionamide (DMPA) by means of FT-Raman and FT-IR spectroscopy. Both solvents are present as either the planar cis or nonplanar staggered conformer in equilibrium, and the former is more stable in the bulk. As these solvents solvate the metal ion through the carbonyl O atom of the acryl (DMAA) or propionyl (DMPA) group, the solvation structure around the metal ion is highly congested to reduce the solvation number and/or to lead to a conformational geometry change of solvent. It turns out that the solvation number of the cobalt(II) ion is 4 for both DMAA and DMPA at 298 K, and that DMPA changes its conformation upon solvation, whereas DMAA hardly changes. The enthalpy of conformational change DeltaH degrees for DMPA is 5 kJ mol(-1) in the bulk, and is -9 kJ mol(-1) in the coordination sphere of the cobalt(II) ion. On the other hand, the DeltaH degrees value for DMAA is 9 kJ mol(-1) in the bulk.

  13. The Unusual Conformational Behavior of Polyzwitterionic Brushes in Aqueous Solutions

    Science.gov (United States)

    Mao, Jun; Chen, Wei; Yuan, Guangcui; Yu, Jing; Tirrell, Matthew

    Polyzwitterions constitute a peculiar class of polyelectrolytes, which are electrically neutral polymers containing both a positive and a negative charge on each repeating unit. Surfaces coated with polyzwitterionic brushes are resistant to the nonspecific accumulation of proteins and microorganisms, making them excellent candidates for a wide range of antifouling applications, from biocompatible medical devices to marine coatings. The surrounding environment can dramatically influence the conformational behavior of polyzwitterionic brushes. High-density polyzwitterionic brushes poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) were synthesized using surface initiated atom-transfer radical polymerization, and neutron reflectivity (NR) measurements were performed to investigate the ionic strength dependence of the conformational behaviors of PMPC brushes in monovalent salt solutions. Despite the numerous observations of normal pure polyelectrolyte brushes, NR results showed that both the densely concentrated layer near the substrate surface and the relatively swollen layer into the solution have been observed in different q range in a single neutron reflectivity profile. These results will definitely help us to better understand the relationship between the solution behaviors of zwitterionic polymer brushes and their antifouling properties.

  14. Conformation of d(GGGATCCC)2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling.

    OpenAIRE

    H. Fabian; Hoelzer, W.; Heinemann, U.; Sklenar, H.; Welfle, H

    1993-01-01

    In the crystal, d(GGGATCCC)2 forms an A-DNA double helix as known from a single crystal X-ray diffraction study. Accordingly, in the Raman spectra of crystals the A-family marker bands at 664, 705, 807 and 1101 cm-1 and the spectral characteristics in the region 1200 to 1500 cm-1 clearly demonstrate the A-form as the dominant conformation. Bands at 691, 850, and 1080 cm-1, however, indicate that a minor fraction of the octamer molecules in the crystal is in an unusual, still not unequivocally...

  15. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

    Science.gov (United States)

    Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M. Eugenia; Molteni, Carla

    2017-04-01

    The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

  16. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.

    Science.gov (United States)

    Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M Eugenia; Molteni, Carla

    2017-04-14

    The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

  17. Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides.

    Science.gov (United States)

    Berger, Nadja; Li, Fee; Mallick, Bert; Brüggemann, J Thomas; Sander, Wolfram; Merten, Christian

    2017-01-01

    A set of cyclic tetrapeptides of the general form cyclo (Boc-Cys-Pro-X-Cys-OMe) with X being L-/D-Ala, L-/D-Val, and L-/D-Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs - namely a β-turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β-turn conformational preferences using NMR, VCD, and Raman spectroscopy. Our results provide evidence for a strong influence of a single stereocenter on the structures of the peptides whereas solvent polarity does not significantly affect them. Additionally, the solid state conformational preferences were studied by crystal structure analysis. Overall, a general trend for the conformational preferences of this set of peptides can be concluded from the results of the complementary investigations. © 2016 Wiley Periodicals, Inc.

  18. S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

    DEFF Research Database (Denmark)

    Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

    2002-01-01

    calculations. Nuclear Overhauser effect measurements and computational results for AdoMet indicate a predominantly anti conformation about the glycosidic bond with a variety of conformations about the methionyl C-alpha-C-beta and C-beta-C-gamma bonds. An AdoMet conformation in which the positively charged....... In 20 reported structures of AdoMet-protein complexes, both anti and syn glycosidic torsional angles are found. The methionyl group typically adopts an extended conformation in complexes with enzymes that transfer the methyl group from the sulfonium center, but is more folded in complexes with proteins...

  19. Conformational preferences of natural and C3-modified epothilones in aqueous solution.

    Science.gov (United States)

    Erdélyi, Máté; Pfeiffer, Bernhard; Hauenstein, Kurt; Fohrer, Jörg; Gertsch, Jürg; Altmann, Karl-Heinz; Carlomagno, Teresa

    2008-03-13

    The conformational properties of the microtubule-stabilizing agent epothilone A ( 1a) and its 3-deoxy and 3-deoxy-2,3-didehydro derivatives 2 and 3 have been investigated in aqueous solution by a combination of NMR spectroscopic methods, Monte Carlo conformational searches, and NAMFIS calculations. The tubulin-bound conformation of epothilone A ( 1a), as previously proposed on the basis of solution NMR data, was found to represent a significant fraction of the ensemble of conformations present for the free ligands in aqueous solution.

  20. The effects of denaturants on protein conformation and behavior at air/solution interface.

    Science.gov (United States)

    Chang, Su-Hwa; Chen, Liang-Yu; Chen, Wen-Yih

    2005-03-10

    In this study, we discuss the interfacial behavior of five proteins with different conformational character, and each is investigated in native and denatured states. The protein molecules are layered and spread onto the air/solution interfaces to form protein monolayer. The surface pressure-time (Pi(t)) and surface pressure-area per molecule (Pi-A) isotherms were measured by using the Langmuir-Blodgett (LB) balance consisted of a Nima trough system. The differences between monolayered protein's behaviors at air/solution interface indicate that denaturants, such as urea, guanidinium chloride and dithiothreitol, have different effects on conformational changes of proteins. Additionally, the interfacial behavior of the proteins in our study provides a fundamental profile about the protein structural stability and implies industrial applications in protein refolding process.

  1. Chain Conformation of Phosphorycholine-based Zwitterionic Polymer Brushes in Aqueous Solutions

    Science.gov (United States)

    Mao, Jun; Yu, Jing; Lee, Sungsik; Yuan, Guangcui; Satija, Sushil; Chen, Wei; Tirrell, Matthew

    Polyzwitterionic brushes are resistant to nonspecific accumulation of proteins and microorganisms, making them excellent candidates for antifouling applications. It is well-known that polyzwitterions exhibit the so-called antipolyelectrolyte effect: Polyzwitterionic brushes would adopt a collapsed conformation at a low ionic strength due to the electrostatic inter/intra-chain association; whereas at a high ionic strength, they would exhibit an extended conformation because the electrostatic inter/intra-chain dipole-dipole interaction is weakened. However, poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) is a unique member in polyzwitterionic families. Its ultrahigh affinity to water leads to no detectable shrinks in aqueous solutions even at low ionic strengths. In this study, we synthesized highly dense PMPC brushes via surface initiated radical polymerization and systematically investigate their conformational behaviors at solid-liquid interfaces in the presence of multivalent counterions, combining X-ray and neutron scattering and force measurements. We have demonstrated that despite no obvious changes of the entire lengths of extended PMPC brushes in aqueous solutions, the chain conformations including, but not limited to, polyzwitterion distribution and charge correlation, varied, dependent on salt types, ionic strengths and ion valences.

  2. Density-Dependent Conformable Space-time Fractional Diffusion-Reaction Equation and Its Exact Solutions

    Science.gov (United States)

    Hosseini, Kamyar; Mayeli, Peyman; Bekir, Ahmet; Guner, Ozkan

    2018-01-01

    In this article, a special type of fractional differential equations (FDEs) named the density-dependent conformable fractional diffusion-reaction (DDCFDR) equation is studied. Aforementioned equation has a significant role in the modelling of some phenomena arising in the applied science. The well-organized methods, including the \\exp (-φ (\\varepsilon )) -expansion and modified Kudryashov methods are exerted to generate the exact solutions of this equation such that some of the solutions are new and have been reported for the first time. Results illustrate that both methods have a great performance in handling the DDCFDR equation.

  3. NMR studies of dynamic biomolecular conformational ensembles.

    Science.gov (United States)

    Torchia, Dennis A

    2015-02-01

    Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. Published by Elsevier B.V.

  4. Correlating polymer solution conformation and thin film nanostructure: Implications for BHJ processing

    Science.gov (United States)

    Dattani, Rajeev; Nedoma, Alisyn; Stingelin, Natalie; Nelson, Jenny; Cabral, Joao

    2013-03-01

    We study the solution properties of polymer-fullerene mixtures by a combination of dynamic light scattering, viscometry, small angle neutron scattering and microscopy. Specifically, the kinetics of polymer conformation (Rg and Rh) and interaction changes are mapped as function of polymer-particle concentration, overall concentration in solution and age. A model system of polystyrene and C60 fullerene was selected for this study, in addition to the P3HT/PCBM pair, which is currently explored in photovoltaic applications. The solution properties show a clear correlation to the resulting thin film nanostructured composite morphology. Our future work will further link it to bulk heterojunction solar cell performance. EPSRC and Plastic Electronics DTC

  5. Atomic Force Microscopy Study of Conformational Change of Immobilized Calmodulin

    Science.gov (United States)

    Trajkovic, Sanja; Zhang, Xiaoning; Daunert, Sylvia

    2011-01-01

    Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied conformational change of calmodulin (CaM) immobilized on chemical patterns. 1-cysteine mutated calmodulin was immobilized on a mercapto-terminated surface through the cysteine-Hg-mercapto coupling. Utilizing Atomic Force Microscope (AFM), the average height of the immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incubation in EGTA solution, the average height of protein changed to 2.26 ± 0.21 nm, indicating conformational change of CaM to Apo-CaM. The immobilized CaM also demonstrated conformational change upon the reaction with known calmodulin antagonist chlorpromazine (CPZ). After incubation in CPZ solution, the average height of CPZ-bound CaM increased to 2.32 ± 0.20 nm, demonstrating the immobilized CaM still has the similar response as in bulk solution. These results show that immobilization of calmodulin on a solid support does not interfere with the ability of the protein to bind calcium and calmodulin antagonists. Our results demonstrate the feasibility of employing AFM to probe and understand protein conformational changes. PMID:21766850

  6. The effect of covalently linked RGD peptide on the conformation of polysaccharides in aqueous solutions.

    Science.gov (United States)

    Bernstein-Levi, Ortal; Ochbaum, Guy; Bitton, Ronit

    2016-01-01

    Covalently modified polysaccharides are routinely used in tissue engineering due to their tailored biofunctionality. Understanding the effect of single-chain level modification on the solution conformation of the single chain, and more importantly on the self-assembly and aggregation of the ensemble of chains is expected to improve our ability to control network topology and the properties of the resulting gels. Attaching an RGD peptide to a polysaccharide backbone is a common procedure used to promote cell adhesion in hydrogel scaffolds. Recently it has been shown that the spatial presentation of the RGD sequences affects the cell behavior; thus, understanding the effects of grafted RGD on the conformational properties of the solvated polysaccharide chains is a prerequisite for rational design of polysaccharide-peptide based biomaterials. Here we investigate the effect of covalently linked G4RGDS on the conformational state of the individual chain and chain assemblies of alginate, chitosan, and hyaluronic acid (HA) in aqueous solutions. Two peptide fractions were studied using small-angle X-ray scattering (SAXS) and rheology. In all cases, upon peptide conjugation structural differences were observed. Analysis of the scattering data shows evidence of clustering for a higher fraction of bound peptide. Moreover for all three polysaccharides the typical shear thinning behavior of the natural polysaccharide solutions is replaced by a Newtonian fluid behavior for the lower fraction conjugated peptide while a more pronounced shear thinning behavior is observed for the higher fraction. These results indicate that the fraction of the bounded peptide, determines the behavior of a polysaccharide-peptide conjugates in solution, regardless of the specific nature of the polysaccharide. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. New analytical solutions for conformable fractional PDEs arising in mathematical physics by exp-function method

    Science.gov (United States)

    Tasbozan, Orkun; Çenesiz, Yücel; Kurt, Ali; Baleanu, Dumitru

    2017-11-01

    Modelling of physical systems mathematically, produces nonlinear evolution equations. Most of the physical systems in nature are intrinsically nonlinear, therefore modelling such systems mathematically leads us to nonlinear evolution equations. The analysis of the wave solutions corresponding to the nonlinear partial differential equations (NPDEs), has a vital role for studying the nonlinear physical events. This article is written with the intention of finding the wave solutions of Nizhnik-Novikov-Veselov and Klein-Gordon equations. For this purpose, the exp-function method, which is based on a series of exponential functions, is employed as a tool. This method is an useful and suitable tool to obtain the analytical solutions of a considerable number of nonlinear FDEs within a conformable derivative.

  8. Conformational analysis and vibrational spectroscopic studies on dapsone

    Science.gov (United States)

    Ildiz, Gulce Ogruc; Akyuz, Sevim

    2012-11-01

    In this study, the theoretical conformation analysis of free dapsone has been performed by single point energy calculations at both semi-empirical PM3 and DFT/B3LYP-3-21G theory levels and three stable conformers were determined. Both the IR and Raman spectra of the molecule in solid phase have been recorded. The IR intensities and harmonic vibrational wavenumbers of each conformer were calculated by DFT method at B3LYP/6-31++G(d,p) theory level. For the fundamental characterization, the total energy distribution (TED) calculations of the vibrational modes were done using parallel quantum mechanic solution program (SQM) and the fundamental modes were assigned. The theoretical results are in agreement with the experimental ones.

  9. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    Science.gov (United States)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  10. Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

    Science.gov (United States)

    Ahlstrom, Logan S.; Miyashita, Osamu

    2011-01-01

    The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

  11. Solid state and solution conformation of [Ala7]-phalloidin: a synthetic phallotoxin analogue.

    Science.gov (United States)

    Zanotti, G; Falcigno, L; Saviano, M; D'Auria, G; Bruno, B M; Campanile, T; Paolillo, L

    2001-04-01

    Phallotoxins are toxic compounds produced by poisonous mushroom Amanita phalloides and belong to the class of bicyclic peptides with a transannular thioether bridge. Their intoxication mechanism in the liver involves a specific binding of the toxins to F-actin that, consequently, prevents the depolymerization equilibrium with G-actin. Even though the conformational features of phallotoxins have been worked out in solution, the exact mechanism of interaction with F-actin is still unknown. In this study a toxic phalloidin synthetic derivative, bicyclo(Ala1-D-Thr2-Cys3-cis-4-hydroxy-Pro4-Ala5-2-mercapto-Trp6-Ala7)(S-3-->6) has been synthesized. A substitution at position 7. with an Ala residue replaces the 4,5-dihydroxy-Leu present in the natural phalloidin. This analogue has formed crystals suitable for X-ray analysis, and represents the first case for such a class of compounds. The solid-state structure as well as the solution conformation have been evaluated. NMR techniques have been used to extract interproton distances as restraints in subsequent molecular dynamics calculations. Finally, a direct comparison between structures in solution and in the solid state is presented.

  12. Conformation and Rheological Properties of Calf-Thymus DNA in Solution

    Directory of Open Access Journals (Sweden)

    Lourdes Mónica Bravo-Anaya

    2016-02-01

    Full Text Available Studies of DNA molecule behavior in aqueous solutions performed through different approaches allow assessment of the solute-solvent interactions and examination of the strong influence of conformation on its physicochemical properties, in the presence of different ionic species and ionic concentrations. Firstly, the conformational behavior of calf-thymus DNA molecules in TE buffer solution is presented as a function of temperature. Secondly, their rheological behavior is discussed, as well as the evidence of the critical concentrations, i.e., the overlap and the entanglement concentrations (C* and Ce, respectively from steady state flow and oscillatory dynamic shear experiments. The determination of the viscosity in the Newtonian plateau obtained from flow curves η ( allows estimation of the intrinsic viscosity and the specific viscosities at zero shear when C[η] < 40. At end, a generalized master curve is obtained from the variation of the specific viscosity as a function of the overlap parameter C[η]. The variation of the exponent s obtained from the power law η~ −s for both flow and dynamic results is discussed in terms of Graessley’s analysis. In the semi-dilute regime with entanglements, a dynamic master curve is obtained as a function of DNA concentration (CDNA > 2.0 mg/mL and temperature (10 °C < T < 40 °C.

  13. DNA conformational analysis in solution by uranyl mediated photocleavage

    DEFF Research Database (Denmark)

    Nielsen, Peter E.; Møllegaard, N E; Jeppesen, C

    1990-01-01

    Uranyl mediated photocleavage of double stranded DNA is proposed as a general probing for DNA helix conformation in terms of minor groove width/electronegative potential. Specifically, it is found that A/T-tracts known to constitute strong distamycin binding sites are preferentially photocleaved ......, uranyl photocleavage of the internal control region (ICR) of the 5S-RNA gene yields a cleavage modulation pattern fully compatible with that obtained by DNase I which also--in a more complex way--senses DNA minor groove width....

  14. An NMR and ab initio quantum chemical study of acid-base equilibria for conformationally constrained acidic alpha-amino acids in aqueous solution

    DEFF Research Database (Denmark)

    Nielsen, Peter Aadal; Jaroszewski, Jerzy W.; Norrby, Per-Ola

    2001-01-01

    the polarizable continuum model (PCM) fore the description of water. The PDAs are highly ionizable and contain one or two possible internal hydrogen bonds. In the present study, we show that the PCM model is able to reproduce the relative stabilities of the different protonation states of the PDAs. Furthermore......, our results show that prediction of relative pK(a) values for two different types of ionizable functional groups covering a pK(a) range from 1.6 to 12.1 is possible with a high degree of accuracy....

  15. Red blood cell rouleaux formation in dextran solution: dependence on polymer conformation.

    Science.gov (United States)

    Barshtein, G; Tamir, I; Yedgar, S

    1998-01-01

    The velocity of rouleaux formation (RF), as previously shown, increases with increasing dextran concentration up to a critical concentration (Ca), beyond which the addition of dextran reduces the RF velocity (RFV). de Gennes' model for polymer solutions suggests that dextrans exist in two conformations: a coil structure at low concentrations, which changes to a network beyond a critical concentration (C*). In the present study we examined the relation between Ca and C* for dextrans of different molecular weight, and found that they coincide. This suggests that the change in dextran behavior, from increasing to decreasing RFV, occurs when their conformation changes from coil to network. In addition, it has been reported that in dilute dextran solutions the intercellular distance (D) between RBC in rouleaux increases with the molecular weight of the dextran. We found that D correlates with Rf, the end-to-end distance of the polymer molecule, and for all dextrans D < or = 1.5 Rf. In accord with de Gennes' Model for polymers between surfaces, this corresponds to intercellular interaction with two overlapping surface-associated polymer layers, which may extend "tails" to interact with the opposing cells.

  16. Theoretical in-Solution Conformational/Tautomeric Analyses for Chain Systems with Conjugated Double Bonds Involving Nitrogen(s

    Directory of Open Access Journals (Sweden)

    Peter I. Nagy

    2015-05-01

    Full Text Available Conformational/tautomeric transformations for X=CH–CH=Y structures (X = CH2, O, NH and Y = NH have been studied in the gas phase, in dichloromethane and in aqueous solutions. The paper is a continuation of a former study where s-cis/s-trans conformational equilibria were predicted for analogues. The s-trans conformation is preferred for the present molecules in the gas phase on the basis of its lowest internal free energy as calculated at the B97D/aug-cc-pvqz and CCSD(TCBS (coupled-cluster singles and doubles with non-iterative triples extrapolated to the complete basis set levels. Transition state barriers are of 29–36 kJ/mol for rotations about the central C–C bonds. In solution, an s-trans form is still favored on the basis of its considerably lower internal free energy compared with the s-cis forms as calculated by IEF-PCM (integral-equation formalism of the polarizable continuum dielectric solvent model at the theoretical levels indicated. A tetrahydrate model in the supermolecule/continuum approach helped explore the 2solute-solvent hydrogen bond pattern. The calculated transition state barrier for rotation about the C–C bond decreased to 27 kJ/mol for the tetrahydrate. Considering explicit solvent models, relative solvation free energies were calculated by means of the free energy perturbation method through Monte Carlo simulations. These calculated values differ remarkably from those by the PCM approach in aqueous solution, nonetheless the same prevalent conformation was predicted by the two methods. Aqueous solution structure-characteristics were determined by Monte Carlo. Equilibration of conformers/tautomers through water-assisted double proton-relay is discussed. This mechanism is not viable, however, in non-protic solvents where the calculated potential of mean force curve does not predict remarkable solute dimerization and subsequent favorable orientation.

  17. Theoretical in-Solution Conformational/Tautomeric Analyses for Chain Systems with Conjugated Double Bonds Involving Nitrogen(s)

    Science.gov (United States)

    Nagy, Peter I.

    2015-01-01

    Conformational/tautomeric transformations for X=CH–CH=Y structures (X = CH2, O, NH and Y = NH) have been studied in the gas phase, in dichloromethane and in aqueous solutions. The paper is a continuation of a former study where s-cis/s-trans conformational equilibria were predicted for analogues. The s-trans conformation is preferred for the present molecules in the gas phase on the basis of its lowest internal free energy as calculated at the B97D/aug-cc-pvqz and CCSD(T)CBS (coupled-cluster singles and doubles with non-iterative triples extrapolated to the complete basis set) levels. Transition state barriers are of 29–36 kJ/mol for rotations about the central C–C bonds. In solution, an s-trans form is still favored on the basis of its considerably lower internal free energy compared with the s-cis forms as calculated by IEF-PCM (integral-equation formalism of the polarizable continuum dielectric solvent model) at the theoretical levels indicated. A tetrahydrate model in the supermolecule/continuum approach helped explore the 2solute-solvent hydrogen bond pattern. The calculated transition state barrier for rotation about the C–C bond decreased to 27 kJ/mol for the tetrahydrate. Considering explicit solvent models, relative solvation free energies were calculated by means of the free energy perturbation method through Monte Carlo simulations. These calculated values differ remarkably from those by the PCM approach in aqueous solution, nonetheless the same prevalent conformation was predicted by the two methods. Aqueous solution structure-characteristics were determined by Monte Carlo. Equilibration of conformers/tautomers through water-assisted double proton-relay is discussed. This mechanism is not viable, however, in non-protic solvents where the calculated potential of mean force curve does not predict remarkable solute dimerization and subsequent favorable orientation. PMID:25984602

  18. Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

    Science.gov (United States)

    Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

    2016-09-13

    We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

  19. Solution conformation and properties of the galactoglucan from Rhizobium meliloti strain YE-2(S1).

    Science.gov (United States)

    Cesàro, A; Tomasi, G; Gamini, A; Vidotto, S; Navarini, L

    1992-07-02

    The physicochemical solution properties of the galactoglucan excreted by Rhizobium meliloti strain YE-2(S1) have been investigated by capillary viscometry, potentiometric titration, isothermal mixing microcalorimetry, and circular dichroism. Potentiometric and chiro-optical data, as a function of the degree of ionisation, indicate the absence of a co-operative conformational transition. Solution properties, as a function of ionic strength and temperature, suggest that the galactoglucan adopts a disordered conformation characterised by moderate flexibility. Polyelectrolyte theory is used to fit the enthalpy of dilution data with a suitable linear charge-density parameter. Conformational calculations and chain modelling, using molecular mechanics, give an unperturbed characteristic ratio, (C infinity) of 20, which was smaller than that estimated from intrinsic-viscosity and molecular-weight data for an expanded-coil chain model.

  20. Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Howell, Steven C. [George Washington Univ., Washington, DC (United States)

    2016-01-31

    We set out to determine quantitative information regarding the dynamic conformation of nucleosome arrays in solution using experimental SAXS. Toward this end, we developed a CG simulation algorithm for dsDNA which rapidly generates ensembles of structures through Metropolis MC sampling of a Markov chain.

  1. Analytic solution for the space-time fractional Klein-Gordon and coupled conformable Boussinesq equations

    Science.gov (United States)

    Shallal, Muhannad A.; Jabbar, Hawraz N.; Ali, Khalid K.

    2018-03-01

    In this paper, we constructed a travelling wave solution for space-time fractional nonlinear partial differential equations by using the modified extended Tanh method with Riccati equation. The method is used to obtain analytic solutions for the space-time fractional Klein-Gordon and coupled conformable space-time fractional Boussinesq equations. The fractional complex transforms and the properties of modified Riemann-Liouville derivative have been used to convert these equations into nonlinear ordinary differential equations.

  2. Dominance of eclipsed ferrocene conformer in solutions revealed by the IR fingerprint spectral splitting

    CERN Document Server

    Mohammadi, Narges; Best, Stephen; Appadoo, Dominique; Chantler, Christopher T

    2013-01-01

    A combined high-resolution Fourier transform infrared (FTIR) spectra of ferrocene (Fc) and density functional theory (DFT) based quantum mechanical calculations confirmed the dominance of the eclipsed Fc conformer in the fingerprint region of 400-500 cm-1. The IR spectra of Fc were measured in solutions with a number of non-polar solvents such as acetonitrile, dichloromethane, tetrahydrofuran and dioxane. The measurements agree well with the earlier IR spectra of Lippincott and Nelson (1958) as well as the most recent IR spectral measurement in dichloromethane solution of Duhovic and Diaconescu (2013). All experimental measurements in the solutions unambiguously exhibit an IR spectral splitting of ca. 15 cm-1 in the 480-500 cm-1 region. The DFT based B3LYP/m6-31G(d) quantum mechanical calculations using implicit solvent models in this study indicates that only the ground electronic state of the eclipsed (D5h) Fc splits in the IR fingerprint region of ca. 500 cm-1. The IR spectral splitting characterises the c...

  3. Solution state conformational preferences of dipeptides derived from N-aminoazetidinecarboxylic acid: an assessment of the hydrazino turn.

    Science.gov (United States)

    Altmayer-Henzien, Amandine; Declerck, Valérie; Merlet, Denis; Baltaze, Jean-Pierre; Farjon, Jonathan; Guillot, Régis; Aitken, David J

    2013-06-21

    Four model compounds and four dipeptides containing N-aminoazetidinecarboxylic acid (AAzC) and a particular stereoisomer of 2-aminocyclobutanecarboxylic acid (ACBC) were studied to establish their solution state conformational preferences, particularly regarding the ability of AAzC to induce a three-center hydrogen-bonded folding feature known as a "hydrazino turn". On the basis of IR and NMR experiments, supported by molecular modeling, the AAzC residue adopted a trans configuration amenable to the formation of a cyclic eight-membered hydrogen bond conformation in solution, in all cases studied. The implication of the heterocyclic nitrogen atom of AAzC in the trans-like structure was demonstrated via a refined (1)H-(15)N HMBC experiment giving exploitable data at natural (15)N isotopic abundance, providing unprecedented evidence for the solution state hydrazino turn conformation. The predominance of this secondary structural feature depended on the configuration of the neighboring ACBC residue in the dipeptides: while the trans-ACBC derivatives prefer the hydrazino turn, the cis-ACBC derivatives may also populate low-energy 10-membered hydrogen-bonded ring structures. X-ray diffraction analysis of three compounds confirmed the presence of a solid state hydrazino turn in two cases, with geometries similar to those deduced from the solution state studies, but in the third compound, no intramolecular hydrogen-bonding feature was in evidence.

  4. Solid-state and solution /sup 13/C NMR in the conformational analysis of methadone-hydrochloride and related narcotic analgesics

    Energy Technology Data Exchange (ETDEWEB)

    Sumner, S.C.J.

    1986-01-01

    Solid state and solution /sup 13/C NMR have been used to study the conformations of the racemic mixtures and single enantiomers of methadone hydrochloride, alpha and beta methadol hydrochloride, and alpha and beta acetylmethadol hydrochloride. The NMR spectra acquired for the compounds as solids, and in polar and nonpolar solvents are compared, in order to determine the conformation of the molecules in solution. To determine the reliability of assigning solution conformations by comparing solution and solid state chemical shift data, three bond coupling constants measured in solution are compared with those calculated from X-ray data. The conformations of the racemic mixture and plus enantiomer of methadone hydrochloride have been shown to be very similar in the solid state, where minor differences in conformation can be seen by comparing NMR spectra obtained for the solids. Also shown is that the molecules of methadone hydrochloride have conformations in polar and in nonpolar solvents which are very similar to the conformation of the molecules in the solid state.

  5. Differential Effect of Solution Conditions on the Conformation of the Actinoporins Sticholysin II and Equinatoxin II

    Directory of Open Access Journals (Sweden)

    EDSON V.F. FAUTH

    2014-12-01

    Full Text Available Actinoporins are a family of pore-forming proteins with hemolytic activity. The structural basis for such activity appears to depend on their correct folding. Such folding encompasses a phosphocholine binding site, a tryptophan-rich region and the activity-related N-terminus segment. Additionally, different solution conditions are known to be able to influence the pore formation by actinoporins, as for Sticholysin II (StnII and Equinatoxin II (EqtxII. In this context, the current work intends to characterize the influence of distinct solution conditions in the conformational behavior of these proteins through molecular dynamics (MD simulations. The obtained data offer structural insights into actinoporins dynamics in solution, characterizing its conformational behavior at the atomic level, in accordance with previous experimental data on StnII and EqtxII hemolytic activities.

  6. Conformer-specific geminate recombination following methyl nitrite photolysis in solution

    Science.gov (United States)

    Coulter, Philip M.; Grubb, Michael P.; Orr-Ewing, Andrew J.

    2017-09-01

    The dynamics of the ultraviolet (UV) photoexcitation of methyl nitrite in weakly interacting perfluoromethylcyclohexane solution are investigated using transient absorption spectroscopy. UV excitation in the structured S1 ← S0 absorption band induces dissociation, with geminate recombination and vibrational cooling of syn and anti-conformers of methyl nitrate on a timescale of ∼56 ps. Solvent-induced vibrational cooling favours relaxation to the higher-energy anti-conformer on entropic grounds, and subsequent inter-conversion to the lower-energy syn-conformer is prevented by a 3500 cm-1 barrier. UV excitation to the S2 state produces a transient electronic absorption band resembling the absorption spectrum of NO2.

  7. Nuclear magnetic resonance studies of an N2-guanine adduct derived from the tumorigen dibenzo[a,l]pyrene in DNA: impact of adduct stereochemistry, size, and local DNA sequence on solution conformations.

    Science.gov (United States)

    Rodríguez, Fabián A; Liu, Zhi; Lin, Chin H; Ding, Shuang; Cai, Yuqin; Kolbanovskiy, Alexander; Kolbanovskiy, Marina; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E

    2014-03-25

    The dimensions and arrangements of aromatic rings (topology) in adducts derived from the reactions of polycyclic aromatic hydrocarbon (PAH) diol epoxide metabolites with DNA influence the distortions and stabilities of double-stranded DNA, and hence their recognition and processing by the human nucleotide excision repair (NER) system. Dibenzo[a,l]pyrene (DB[a,l]P) is a highly tumorigenic six-ring PAH, which contains a nonplanar and aromatic fjord region that is absent in the structurally related bay region five-ring PAH benzo[a]pyrene (B[a]P). The PAH diol epoxide-DNA adducts formed include the stereoisomeric 14S and 14R trans-anti-DB[a,l]P-N(2)-dG and the stereochemically analogous 10S- and 10R-B[a]P-N(2)-dG (B[a]P-dG) guanine adducts. However, nuclear magnetic resonance (NMR) solution studies of the 14S-DB[a,l]P-N(2)-dG adduct in DNA have not yet been presented. Here we have investigated the 14S-DB[a,l]P-N(2)-dG adduct in two different sequence contexts using NMR methods with distance-restrained molecular dynamics simulations. In duplexes with dC opposite the adduct deleted, a well-resolved base-displaced intercalative adduct conformation can be observed. In full duplexes, in contrast to the intercalated 14R stereoisomeric adduct, the bulky DB[a,l]P residue in the 14S adduct is positioned in a greatly widened and distorted minor groove, with significant disruptions and distortions of base pairing at the lesion site and two 5'-side adjacent base pairs. These unique structural features are significantly different from those of the stereochemically analogous but smaller B[a]P-dG adduct. The greater size and different topology of the DB[a,l]P aromatic ring system lead to greater structurally destabilizing DNA distortions that are partially compensated by stabilizing DB[a,l]P-DNA van der Waals interactions, whose combined effects impact the NER response to the adduct. These structural results broaden our understanding of the structure-function relationship in NER.

  8. Rigidity, conformation, and solvation of native and oxidized tannin macromolecules in water-ethanol solution

    Science.gov (United States)

    Zanchi, Dražen; Konarev, Petr V.; Tribet, Christophe; Baron, Alain; Svergun, Dmitri I.; Guyot, Sylvain

    2009-06-01

    We studied by light scattering and small angle x-rays scattering (SAXS) conformations and solvation of plant tannins (oligomers and polymers) in mixed water-ethanol solutions. Their structures are not simple linear chains but contain about 6% of branching. Ab initio reconstruction reveals that monomers within a branch are closely bound pairwise. The chains are rather rigid, with the Kuhn length b =13±3 nm, corresponding to about 35 linearly bound monomers. Contribution of solvation layer to SAXS intensity varies in a nonmonotonic way with ethanol content ϕA, which is an indication of amphipathic nature of tannin molecules. Best solvent composition ϕAB is a decreasing function of polymerization degree N, in agreement with increasing water solubility of tannins with N. Polymers longer than b present a power-law behavior I ˜Q-d in the SAXS profile at high momentum transfer Q. The monotonic decrease in d with increasing ϕA (from 2.4 in water to 1.9 in ethanol) points that the tannins are more compact in water than in ethanol, presumably due to attractive intramolecular interactions in water. Tannins were then oxidized in controlled conditions similar to real biological or food systems. Oxidation does not produce any intermolecular condensation, but generates additional intramolecular links. Some oxidation products are insoluble in water rich solvent. For that reason, we identify these species as a fraction of natural tannins called "T1" in the notation of Zanchi et al. [Langmuir 23, 9949 (2007)]. Within the fraction left soluble after oxidation, conformations of polymeric tannins, despite their higher rigidity, remain sensitive to solvent composition.

  9. Evaluation of flexible and rigid (class solution) radiation therapy conformal prostate planning protocols

    Energy Technology Data Exchange (ETDEWEB)

    Coburn, Natalie, E-mail: natalie.coburn@swahs.health.nsw.gov.au [Radiation Oncology Network, Nepean Cancer Care Centre, University of Sydney, Sydney, New South Wales (Australia); Beldham-Collins, Rachael [Radiation Oncology Network, Nepean Cancer Care Centre, University of Sydney, Sydney, New South Wales (Australia); Radiation Oncology Network, Westmead Cancer Care Centre, University of Sydney, Sydney, New South Wales (Australia); Westling, Jelene; Trovato, Jenny [Radiation Oncology Network, Nepean Cancer Care Centre, University of Sydney, Sydney, New South Wales (Australia); Gebski, Val [National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, New South Wales (Australia)

    2012-04-01

    Protocols commonly implemented in radiotherapy work areas may be classified as being either rigid (class solution) or flexible. Because formal evaluation of these protocol types has not occurred within the literature, we evaluated the efficiency of a rigid compared with flexible prostate planning protocol by assessing a series of completed 3D conformal prostate plans. Twenty prostate cancer patients with an average age of 70 years (range, 52-77) and sizes comprising 8 small, 10 medium, and 2 large were planned on the Phillips Pinnacle treatment planning system 6 times by radiation therapists with <2 years, 2-5 years, and >5 years of experience using a rigid and flexible protocol. Plans were critiqued using critical organ doses, confirmation numbers, and conformity index. Plans were then classified as being acceptable or not. Plans produced with the flexible protocol were 53% less likely to require modification (OR 0.47, 95% CI: 0.26, 0.84, p = 0.01). Planners with >5 years of experience were 78% more likely to produce plans requiring modification (OR 1.78, 95% CI: 1.12, 2.83, P = 0.02). Plans according to the flexible protocol took longer (112 min) compared with the time taken using a rigid protocol (68 min) (p < 0.001). The results suggest that further studies are needed; however, we propose that all radiation therapy planners should start with the same limitations, and if an acceptable plan is not reached, then flexibility should be given to improve the plan to meet the desired results.

  10. Synthesis of a new quaternary phosphonium salt: NMR study of the conformational structure and dynamics.

    Science.gov (United States)

    Aganova, Oksana V; Galiullina, Leysan F; Aganov, Albert V; Shtyrlin, Nikita V; Pugachev, Mikhail V; Strel'nik, Alexey D; Koshkin, Sergey A; Shtyrlin, Yurii G; Klochkov, Vladimir V

    2016-04-01

    A novel phosphonium salt based on pyridoxine was synthesized. Conformational analysis of the compound in solution was performed using dynamic NMR experiments and calculations. The obtained results revealed some differences in the conformational transitions and the energy parameters of the conformational exchange of the studied compound in comparison to previously reported data for other phosphorus-containing pyridoxine derivatives. It was shown that increasing the substituent at the C-11 carbon leads to greater differences in the populations of stable states and the corresponding equilibrium energies. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Theoretical studies on the conformations of selenamides

    Indian Academy of Sciences (India)

    Unknown

    Abstract. Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe–NH2 to estimate the Se–N rotational barriers and. N-inversion barriers. Two conformers have been found with syn and anti arrangement of the NH2 hydrogens with respect to Se–H bond. The N inversion barriers ...

  12. Primary structure and solution conditions determine conformational ensemble properties of intrinsically disordered proteins

    Science.gov (United States)

    Mao, Hsuan-Han Alberto

    Intrinsically disordered proteins (IDPs) are a class of proteins that do not exhibit well-defined three-dimensional structures. The absence of structure is intrinsic to their amino acid sequences, which are characterized by low hydrophobicity and high net charge per residue compared to folded proteins. Contradicting the classic structure-function paradigm, IDPs are capable of interacting with high specificity and affinity, often acquiring order in complex with protein and nucleic acid binding partners. This phenomenon is evident during cellular activities involving IDPs, which include transcriptional and translational regulation, cell cycle control, signal transduction, molecular assembly, and molecular recognition. Although approximately 30% of eukaryotic proteomes are intrinsically disordered, the nature of IDP conformational ensembles remains unclear. In this dissertation, we describe relationships connecting characteristics of IDP conformational ensembles to their primary structures and solution conditions. Using molecular simulations and fluorescence experiments on a set of base-rich IDPs, we find that net charge per residue segregates conformational ensembles along a globule-to-coil transition. Speculatively generalizing this result, we propose a phase diagram that predicts an IDP's average size and shape based on sequence composition and use it to generate hypotheses for a broad set of intrinsically disordered regions (IDRs). Simulations reveal that acid-rich IDRs, unlike their oppositely charged base-rich counterparts, exhibit disordered globular ensembles despite intra-chain repulsive electrostatic interactions. This apparent asymmetry is sensitive to simulation parameters for representing alkali and halide salt ions, suggesting that solution conditions modulate IDP conformational ensembles. We refine the ion parameters using a calibration procedure that relies exclusively on crystal lattice properties. Simulations with these parameters recover swollen

  13. A conformational study of proline derivatives

    Directory of Open Access Journals (Sweden)

    M.E. Kamwaya

    2002-12-01

    Full Text Available From the study of the structures and molecular conformations of a number of proline derivatives, some conclusions were drawn. The widening effect of angle Cα-C'-N' is caused by steric repulsion between a hydrogen atom at Cα of the preceding prolyl residue with any other at either Cα or Cδ of the pyrrolidine ring cis to it. This effect is influenced by the distance between the said hydrogen atoms: the nearer this distance is, the greater is the steric repulsion and the wider is the angle of steric repulsion. The ratio of the angle of steric repulsion to the distance between Cα and the following Cα (or Cδ cis to it is approximately 40 and 41 for peptides with trans and cis configurations, respectively. The torsion angle ranges for χ1, χ3, χ 4, θ and φ in these derivatives are widened more than usual. The highest vibration, which more often takes place at either the Cβ or Cγ of the pyrrolidine ring, does so not necessarily at the one that is puckered. A Δ&psi -relationship is established, for the determination of α-helixity or collageneity, also in small peptides and amino acids that contain proline. The Δ&psi-relationship is versatile and gives about +180o and –180o for the two categories, respectively. The distance between the carbonyl and hydroxyl (or otherwise terminal end atoms is minimal (2.2 Å and constant, for all peptides. The ratios of the angles at the carbonyl carbons (O'-C'-N' or (O'-C'-O' to this distance is also constant: 56 and 57 for the cis and trans confirgurations, respectively; i.e. a proline O'-C'-N'- (or O'-C'-O'-test, hereinafter called the CT-test, has been established for the determination of cis and trans configurations. It is also established in these proline derivatives, that whereas puckering takes place at Cβ for the CS form, it does so at Cγ for the C2 form.

  14. Macromolecular conformation of chitosan in dilute solution: A new global hydrodynamic approach

    OpenAIRE

    Morris, Gordon; Castile, J.; Smith, A.; Adams, G. G.; Harding, S. E.

    2009-01-01

    Chitosans of different molar masses were prepared by storing freshly prepared samples for up to 6 months at either 4, 25 or 40 °C. The weight-average molar masses, Mw and intrinsic viscosities, [η] were then measured using size exclusion chromatography coupled to multi-angle laser light scattering (SEC-MALLS) and a "rolling ball" viscometer, respectively. The solution conformation of chitosan was then estimated from:(a)the Mark-Houwink-Kuhn-Sakurada (MHKS) power law relationship [η] = kMwa...

  15. Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers.

    Science.gov (United States)

    Rode, Joanna E; Dobrowolski, Jan Cz; Sadlej, Joanna

    2011-05-01

    The conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point. Figure Phenylisoserine (PhIS) is an active side chain of cytotoxic Paclitaxel medicine. The conformational landscape of phenylisoserine was studied. One zwitterionic and one neutralconformer determine the equilibrium in water whereas in the gas phase the MP2 calculations suggest three PhIS structures to be significantly populated.

  16. Conformal Infinity

    Directory of Open Access Journals (Sweden)

    Frauendiener Jörg

    2004-01-01

    Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  17. Synthesis of selenium-containing Artemisia sphaerocephala polysaccharides: Solution conformation and anti-tumor activities in vitro.

    Science.gov (United States)

    Wang, Junlong; Li, Qingyao; Bao, Aijuan; Liu, Xiurong; Zeng, Junyuan; Yang, Xiaopin; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2016-11-05

    It has been reported in our previous work that selenized Artemisia sphaerocephala polysaccharides (SeASPs) with the Se content range of 168-1703μg/g were synthesized by using Na2SeO3/HNO3/BaCl2 system. In the present work, the solution property of SeASP was studied by using size exclusion chromatography combined with multi angle laser light scattering (SEC-MALLS). A decrease in df values indicated that SeASPs with different conformational features that were highly dependent on MW. SeASPs exhibited a more rigid conformation (df value of 1.29-1.52) in low molecular weight range (MW of 1.026-1.426×10(4)g/mol) and compact spherical conformation in high molecular weight range (MW of 2.268-4.363×10(4)g/mol). It could be due to the degradation of polysaccharide chains in HNO3, which was supported in monosaccharide composition analysis. Congo red (CR) spectrophotometric method and atomic force microscopy (AFM) results also confirmed the conformational transition and the evidence on the shape of the rigid chains. In vitro anti-tumor assays, SeASP2 displayed greater anti-proliferative effects against three tumor cell lines (hepatocellular carcinoma HepG-2 cells, lung adenocarcinom A549 cells and cervical squamous carcinoma Hela cells) in a dose-dependent manner. This suggested that selenylation could significantly enhance the anti-tumor activities of polysaccharide derivatives in vitro. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Evaluation of flexible and rigid (class solution) radiation therapy conformal prostate planning protocols.

    Science.gov (United States)

    Coburn, Natalie; Beldham-Collins, Rachael; Westling, Jelene; Trovato, Jenny; Gebski, Val

    2012-01-01

    Protocols commonly implemented in radiotherapy work areas may be classified as being either rigid (class solution) or flexible. Because formal evaluation of these protocol types has not occurred within the literature, we evaluated the efficiency of a rigid compared with flexible prostate planning protocol by assessing a series of completed 3D conformal prostate plans. Twenty prostate cancer patients with an average age of 70 years (range, 52-77) and sizes comprising 8 small, 10 medium, and 2 large were planned on the Phillips Pinnacle treatment planning system 6 times by radiation therapists with 5 years of experience using a rigid and flexible protocol. Plans were critiqued using critical organ doses, confirmation numbers, and conformity index. Plans were then classified as being acceptable or not. Plans produced with the flexible protocol were 53% less likely to require modification (OR 0.47, 95% CI: 0.26, 0.84, p = 0.01). Planners with >5 years of experience were 78% more likely to produce plans requiring modification (OR 1.78, 95% CI: 1.12, 2.83, P = 0.02). Plans according to the flexible protocol took longer (112 min) compared with the time taken using a rigid protocol (68 min) (p plan is not reached, then flexibility should be given to improve the plan to meet the desired results. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

  19. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

    Directory of Open Access Journals (Sweden)

    Gregory D Friedland

    2009-05-01

    Full Text Available Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR Residual Dipolar Couplings (RDCs. Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

  20. Combining size-exclusion chromatography with differential hydrogen-deuterium exchange to study protein conformational changes.

    Science.gov (United States)

    Makarov, Alexey A; Helmy, Roy

    2016-01-29

    Methods for protein characterization are being actively developed based on the growing importance of protein therapies and applications. The goal of this study was to demonstrate the use of size-exclusion chromatography (SEC) in combination with differential hydrogen-deuterium exchange (HDX) to compare protein global conformational changes at different solution conditions. Using chaotropic mobile phase additive, differential HDX was used to detect a number of solvent accessible labile protons of protein on-column at pH and temperature conditions which provided unrestricted intrinsic H/D exchange (all-or-nothing approach). Varying SEC on-column conditions allowed for protein conformational changes to be observed. Temperature and pressure were independently studied with regards to their effect on the proteins' (insulin, cytochrome C, ubiquitin, and myoglobin) conformational changes in the solution. The obtained ΔHDX profiles revealed protein conformational changes in solution under varied conditions manifested as the difference in the number of protons exchanged to deuterons, or vice-versa. The approach described in this manuscript could prove useful for protein batch-to-batch comparisons, for optimization of chemical reactions with enzyme as catalyst or for protein chemical modification reactions. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Atomic force microscopy study of the conformational change in immobilized calmodulin.

    Science.gov (United States)

    Trajkovic, Sanja; Zhang, Xiaoning; Daunert, Sylvia; Cai, Yuguang

    2011-09-06

    Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied the conformational change in calmodulin (CaM) immobilized on chemical patterns. 1-Cysteine-mutated calmodulin was immobilized on a mercapto-terminated surface through cysteine-Hg-mercapto coupling. Utilizing atomic force microscopy (AFM), the average height of immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incubation in EGTA solution, the average height of the protein changed to 2.26 ± 0.21 nm, indicating the conformational change of CaM to Apo-CaM. Immobilized CaM also demonstrated a conformational change upon the reaction with known calmodulin antagonist chlorpromazine (CPZ). After incubation in CPZ solution, the average height of CPZ-bound CaM increased to 2.32 ± 0.20 nm, demonstrating that immobilized CaM has a similar response to that in bulk solution. These results show that the immobilization of calmodulin on a solid support does not interfere with the ability of the protein to bind calcium and calmodulin antagonists. Our results demonstrate the feasibility of employing AFM to probe and understand protein conformational changes. © 2011 American Chemical Society

  2. Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings.

    Science.gov (United States)

    Azurmendi, Hugo F; Bush, C Allen

    2002-05-13

    The conformations of two synthetic trisaccharides of blood group A and B (alpha-L-Fucp-(1-->2)-[alpha-D-GalpNAc-(1-->3)]-alpha-D-Galp and alpha-L-Fucp-(1-->2)-[alpha-D-Galp-(1-->3)]-alpha-D-Galp, respectively) and of a type A tetrasaccharide alditol, Fucp-(1-->2)-[alpha-D-GalpNAc-(1-->3)]-beta-D-Galp-(1-->3)-GalNAc-ol, were studied by NMR measurements of one-bond C-H residual dipolar couplings in partially oriented liquid crystal solutions. The conformations of the three oligosaccharides were analyzed by generating thousands of structures using a Monte-Carlo method. Two different strategies were applied to calculate theoretical dipolar couplings for these structures. In the first method, the orientation of the molecule was calculated from the optimal fit of the molecular model to the experimental data, while in the second method the orientation tensor was calculated directly from the moment of inertia of the molecular model. Both methods of analysis give similar results but with slightly better agreement with experiment for the former one. The analysis of the results implies a single unique conformation for both blood group epitopes in solution in disagreement with theoretical models suggesting the existence of two conformers in solution.

  3. Single-Chain Conformation for Interacting Poly(N-isopropylacrylamide in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Boualem Hammouda

    2015-04-01

    Full Text Available The demixing phase behavior of Poly(N-isopropylacrylamide (PNIPAM aqueous solution is investigated using small-angle neutron scattering. This polymer phase separates upon heating and demixes around 32 °C. The pre-transition temperature range is characterized by two scattering modes; a low-Q (large-scale signal and a high-Q dissolved chains signal. In order to get insight into this pre-transition region, especially the origin of the low-Q (large-scale structure, the zero average contrast method is used in order to isolate single-chain conformations even in the demixing polymers transition region. This method consists of measuring deuterated and non-deuterated polymers dissolved in mixtures of deuterated and non-deuterated water for which the polymer scattering length density matches the solvent scattering length density. A fixed 4% polymer mass fraction is used in a contrast variation series where the d-water/h-water fraction is varied in order to determine the match point. The zero average contrast (match point sample displays pure single-chain scattering with no interchain contributions. Our measurements prove that the large scale structure in this polymer solution is due to a transient polymer network formed through hydrophobic segment-segment interactions. Scattering intensity increases when the temperature gets close to the phase boundary. While the apparent radius of gyration increases substantially at the Lower Critical Solution Temperature (LCST transition due to strong interchain correlation, the single-chain true radius of gyration has been found to decrease slightly with temperature when approaching the transition.

  4. A conformational study of proline derivatives | Kamwaya | Bulletin of ...

    African Journals Online (AJOL)

    From the study of the structures and molecular conformations of a number of proline derivatives, some conclusions were drawn. The widening effect of angle C-C'-N' is caused by steric repulsion between a hydrogen atom at C of the preceding prolyl residue with any other at either C or C of the pyrrolidine ring cis to it.

  5. Clinical Studies on conformal radiotherapy combined with epidermal ...

    African Journals Online (AJOL)

    Purpose: To study the effect of conformal radiotherapy combined with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) in the second-line treatment of non-small cell lung cancer (NSCLC). Methods: A total of 316 patients attending Shanghai Pulmonary Hospital affiliated to Tongji University, were divided ...

  6. Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants.

    Science.gov (United States)

    Roy, Amrita; Lim, Liangzhong; Srivastava, Shagun; Lu, Yimei; Song, Jianxing

    2017-01-01

    The recent Zika viral (ZIKV) epidemic has been associated with severe neurological pathologies such as neonatal microcephaly and Guillain-Barre syndrome but unfortunately no vaccine or medication is effectively available yet. Zika NS2B-NS3pro is essential for the proteolysis of the viral polyprotein and thereby viral replication. Thus NS2B-NS3pro represents an attractive target for anti-Zika drug discovery/design. Here, we have characterized the solution conformations and catalytic parameters of both linked and unlinked Zika NS2B-NS3pro complexes and found that the unlinked complex manifested well-dispersed NMR spectra. Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100) of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Upon binding to the well-characterized serine protease inhibitor, bovine pancreatic trypsin inhibitor (BPTI), only the extreme C-terminal residues (L86-K100) remain disordered. Additionally, we have identified five flavonoids and one natural phenol rich in edible plants including fruits and vegetables, which inhibit Zika NS2B-NS3pro in a non-competitive mode, with Ki ranging from 770 nM for Myricetin to 34.02 μM for Apigenin. Molecular docking showed that they all bind to a pocket on the back of the active site and their structure-activity relationship was elucidated. Our study provides valuable insights into the solution conformation of Zika NS2B-NS3pro and further deciphers its susceptibility towards allosteric inhibition by natural products. As these natural product inhibitors fundamentally differ from the currently-known active site inhibitors in terms of both inhibitory mode and chemical scaffold, our finding might open a new avenue for development of better allosteric inhibitors to fight ZIKV infection.

  7. TECHNICAL SOLUTIONS FOR MODELING PANTS PATTERNS IN CORRESPONDENCE WITH WOMEN'S CONFORMATIONAL PARTICULARITIES

    Directory of Open Access Journals (Sweden)

    Sabina Olaru

    2013-01-01

    Full Text Available The geometric method used in patterns design of different products categories, gives good results for garments manufacturing in industrial system, meaning type representative bodies. The quality of the results is due to the fact that in geometric method the completion of the basic patterns is achieved by prototype implementation followed by viewing the correspondence between the body and the garment, by dressing the human body or industrial mannequin. In the case that the garment, designed and manufactured for type representative bodies according to the standards is dressed by persons that do not fit the type bodies for whom the product was made, the fenomena called “draping defects” apprears. These unconcordances between wearer body and product obtained in industrial system is due to the conformational features of potential users such as: buttocks prominence and form, hips prominence and form, pelvis width and length, ratio between front and anterior-posterior diameters of the pelvis.Anthropometry researches have shown that for a standardized value of the hip perimeter the secondary dimensions of the area (posterior buttock arch, length from waist the buttock point, lower arch of torso may have different values. In this context, the paper aims to analyze the shape and size of the women’s pelvis and to develop the technical solutions to adapt the basic pattern for “trousers with adjusted silhouette” to concrete particularities of the body shape.

  8. Conformational heterogeneity of methyl 4-hydroxycinnamate: a gas-phase UV-IR spectroscopic study.

    Science.gov (United States)

    Tan, Eric M M; Amirjalayer, Saeed; Smolarek, Szymon; Vdovin, Alexander; Rijs, Anouk M; Buma, Wybren J

    2013-05-02

    UV excitation and IR absorption spectroscopy on jet-cooled molecules is used to study the conformational heterogeneity of methyl 4-hydroxycinnamate, a model chromophore of the Photoactive Yellow Protein (PYP), and to determine the spectroscopic properties of the various conformers. UV-UV depletion spectroscopy identifies four different species with distinct electronic excitation spectra. Quantum chemical calculations argue that these species are associated with different conformers involving the s-cis/s-trans configuration of the ester with respect to the propenyl C-C single bond and the syn/anti orientation of the phenolic OH group. IR-UV hole-burning spectroscopy is used to record their IR absorption spectra in the fingerprint region. Comparison with IR absorption spectra predicted by quantum chemical calculations provides vibrational markers for each of the conformers, on the basis of which each of the species observed with UV-UV depletion spectroscopy is assigned. Although both DFT and wave function methods reproduce experimental frequencies, we find that calculations at the MP2 level are necessary to obtain agreement with experimentally observed intensities. To elucidate the role of the environment, we compare the IR spectra of the isolated conformers with IR spectra of methyl 4-hydroxycinnamate-water clusters, and with IR spectra of methyl 4-hydroxycinnamate in solution.

  9. Computational solution of Katugampola conformable fractional differential equations via RBF collocation method

    Science.gov (United States)

    Usta, Fuat

    2017-04-01

    In conjunction with the development of fractional calculus, conformable derivatives and integrals has been widely used a number of scientific areas. In this talk, we provide a numerical scheme to solve Katugampola conformable fractional differential equations via radial basis function (RBF) collocation technique. In order to confirm our numerical scheme, we present some numerical experiments results.

  10. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes.

    Science.gov (United States)

    Pakkanen, Kirsi I; Madsen, Jan B; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA), enzyme-linked immunosorbent assay (EIA), and enzyme-linked lectin assay (ELLA). The conformation and hydrodynamic diameter of highly purified BSM molecules, as characterized by circular dichroism (CD) spectroscopy and dynamic light scattering (DLS), respectively, showed a slight, yet gradual coiling and compaction in response to the increase in BSM concentration in bulk solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylated C-terminals and the central glycosylated regions, respectively, showed complicated non-linear responses with increasing surface concentration. The results from this study support the conventional amphiphilic, triblock model of BSM in the adsorption onto hydrophobic surface from aqueous solution. The biomolecular probe-based approaches employed in this study, however, provided further details on the conformational changes of BSM on surface, in particular the accessibility of glycosylated and unglycosylated domains with increasing surface concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. On the space of solutions of the Hořava theory at the kinetic-conformal point

    Science.gov (United States)

    Bellorín, Jorge; Restuccia, Alvaro

    2017-10-01

    The nonprojectable Hořava theory at the kinetic-conformal point is defined by setting a specific value of the coupling constant of the kinetic term of the Lagrangian. This formulation has two additional second class-constraints that eliminate the extra mode. We show that the space of solutions of this theory in the Hamiltonian formalism is bigger than the space of solutions in the original Lagrangian formalism. In the Hamiltonian formalism there are certain configurations for the Lagrange multipliers that lead to solutions that cannot be found in the original Lagrangian formulation. We show specific examples in vacuum and with a source. The solution with the source has homogeneous and isotropic spatial hypersurfaces. The enhancement of the space of solutions leaves the possibility that new solutions applicable to cosmology, or to other physical systems, can be found in the Hamiltonian formalism.

  12. Thermodynamic Analysis of the Conformational Transition in Aqueous Solutions of Isotactic and Atactic Poly(Methacrylic Acid and the Hydrophobic Effect

    Directory of Open Access Journals (Sweden)

    Ksenija Kogej

    2016-04-01

    Full Text Available The affinity of amphiphilic compounds for water is important in various processes, e.g., in conformational transitions of biopolymers, protein folding/unfolding, partitioning of drugs in the living systems, and many others. Herein, we study the conformational transition of two isomer forms of poly(methacrylic acid (PMA, isotactic (iPMA and atactic (aPMA, in water. These isomers are chemically equivalent and differ only in the arrangement of functional groups along the chain. A complete thermodynamic analysis of the transition of the PMA chains from the compact to the extended form (comprising the conformational transition in water in the presence of three alkali chlorides is conducted by determining the free energy, enthalpy, and entropy changes of the process as a function of temperature, and therefrom also the heat capacity change. The heat capacity change of the transition is positive (+20 J/K mol for aPMA and negative (−50 J/K mol for iPMA. This result suggests a different affinity of PMA isomers for water. The conformational transition of iPMA is parallel to the transfer of polar solutes into water, whereas that of aPMA agrees with the transfer of nonpolar solutes into water.

  13. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    Omer Acan

    2017-02-01

    Full Text Available In this study, we introduce the conformable variational iteration method based on new defined fractional derivative called conformable fractional derivative. This new method is applied two fractional order ordinary differential equations. To see how the solutions of this method, linear homogeneous and non-linear non-homogeneous fractional ordinary differential equations are selected. Obtained results are compared the exact solutions and their graphics are plotted to demonstrate efficiency and accuracy of the method.

  14. Atomic Force Microscopy Study of Conformational Change of Immobilized Calmodulin

    OpenAIRE

    Trajkovic, Sanja; Zhang, Xiaoning; Daunert, Sylvia; Cai, Yuguang

    2011-01-01

    Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied conformational change of calmodulin (CaM) immobilized on chemical patterns. 1-cysteine mutated calmodulin was immobilized on a mercapto-terminated surface through the cysteine-Hg-mercapto coupling. Utilizing Atomic Force Microscope (AFM), the average height of the immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incub...

  15. Theoretical and conformational studies of a series of cannabinoids

    Science.gov (United States)

    Da Silva, Albérico B. F.; Trsic, Milan

    1995-11-01

    The MNDO semi-empirical method is applied to the study of a series of cannabinoids with the aim of providing an improved understanding of the structure-activity relationship (SAR). The conformation of some groups that seem important in the biological activity (psychoactivity) of these compounds is characterized. Some electronic properties, such as atomic net charges and HOMO and LUMO energies, are correlated with the psychoactive effect.

  16. Molar mass and solution conformation of branched alpha(1 - 4), alpha(1 - 6) Glucans. Part I: Glycogens in water

    OpenAIRE

    Morris, Gordon; Ang, S.; Hill, S. E.; Lewis, S.; Schafer, B.; Nobbmann, U.; Harding, S. E.

    2008-01-01

    Solution molar masses and conformations of glycogens from different sources (rabbit, oyster, mussel and bovine) were analysed using sedimentation velocity in the analytical ultracentrifuge, size-exclusion chromatography coupled to multi-angle laser light scattering (SEC-MALLS), size-exclusion chromatography coupled to a differential pressure viscometer and dynamic light scattering. Rabbit, oyster and mussel glycogens consisted of one population of high molar mass (weight averages ranging from...

  17. Conformational studies of common protein templates in macromolecularly imprinted polymers.

    Science.gov (United States)

    Kryscio, David R; Fleming, Michael Q; Peppas, Nicholas A

    2012-08-01

    Unlike the molecular imprinting of small molecule templates, molecularly imprinted polymers specific to large templates (>1,500 Da), have achieved limited success to date. Conformational stability of these labile macromolecules is one of the main factors that prevent the direct extension of successful procedures from the small molecule regime. We continue our systematic investigation of the effect of common components in macromolecular MIPs on the conformation of protein templates. Circular dichroism was used to show that frequently employed monomers and crosslinkers induce significant changes in the secondary structures of lysozyme and bovine hemoglobin. The extent to which this change occurs, at ligand concentrations far below what are typically used reported work, is cause for concern and provides as rational explanation for the lack of success in this arena. This is because a change in the template structure prior to polymerization would lead to the binding sites formed during polymerization to be specific to this alternate conformation. Subsequent studies with the macromolecule in its native state and the crosslinked network would not be successful. Using this information as a guide, we offer suggestions as to where work in macromolecular imprinted polymers should focus going forward in order for these antibody mimics to reach their vast potential as a new class of biomedical diagnostic devices.

  18. Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants.

    Directory of Open Access Journals (Sweden)

    Amrita Roy

    Full Text Available The recent Zika viral (ZIKV epidemic has been associated with severe neurological pathologies such as neonatal microcephaly and Guillain-Barre syndrome but unfortunately no vaccine or medication is effectively available yet. Zika NS2B-NS3pro is essential for the proteolysis of the viral polyprotein and thereby viral replication. Thus NS2B-NS3pro represents an attractive target for anti-Zika drug discovery/design. Here, we have characterized the solution conformations and catalytic parameters of both linked and unlinked Zika NS2B-NS3pro complexes and found that the unlinked complex manifested well-dispersed NMR spectra. Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100 of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Upon binding to the well-characterized serine protease inhibitor, bovine pancreatic trypsin inhibitor (BPTI, only the extreme C-terminal residues (L86-K100 remain disordered. Additionally, we have identified five flavonoids and one natural phenol rich in edible plants including fruits and vegetables, which inhibit Zika NS2B-NS3pro in a non-competitive mode, with Ki ranging from 770 nM for Myricetin to 34.02 μM for Apigenin. Molecular docking showed that they all bind to a pocket on the back of the active site and their structure-activity relationship was elucidated. Our study provides valuable insights into the solution conformation of Zika NS2B-NS3pro and further deciphers its susceptibility towards allosteric inhibition by natural products. As these natural product inhibitors fundamentally differ from the currently-known active site inhibitors in terms of both inhibitory mode and chemical scaffold, our finding might open a new avenue for development of better allosteric inhibitors to fight ZIKV infection.

  19. Studying conformally flat spacetimes with an elastic stress energy tensor using 1 + 3 formalism

    Science.gov (United States)

    Brito, I.; Ramos, M. P. Machado

    2015-12-01

    Conformally flat spacetimes with an elastic stress-energy tensor having diagonal trace-free anisotropic pressure are investigated using 1 + 3 formalism. The 1 + 3 Bianchi and Jacobi identities and Einstein field equations are written for a particular case with a conformal factor dependent on only one spatial coordinate. Solutions with non zero anisotropic pressure are obtained.

  20. Nuclear magnetic resonance study of alkane conformational statistics.

    Science.gov (United States)

    Burnell, E Elliott; Weber, Adrian C J; de Lange, Cornelis A; Meerts, W Leo; Dong, Ronald Y

    2011-12-21

    NMR spectra of ethane, propane, and n-butane as solutes in the nematic liquid crystals 4-n-pentyl-4(')-cyanobiphenyl (5CB) and Merck ZLI 1132 (1132) are investigated over a wide temperature range. The ratios of dipolar couplings of ethane to propane are constant over the entire temperature range. Assuming that this constancy applies to the butane conformers facilitates the separation of probability from order parameter. This separation allows the investigation of conformational distribution without the need of invoking any model for the anisotropic intermolecular potential. The results give an order matrix that is consistent with that predicted from model potentials that describe the orientational potential in terms of short-range size and shape effects. The isotropic intermolecular potential contribution to the trans-gauche energy difference E(tg) is found to be temperature dependent with the values and variation in agreement with that found when the same results are analyzed using the chord model for anisotropic interactions [A. C. J. Weber and E. E. Burnell, Chem. Phys. Lett. 506, 196 (2011)]. The fit obtained for 9 spectra in 5CB (63 dipolar couplings) has an RMS difference between experimental and calculated dipolar couplings of 2.7 Hz, while that for the 16 spectra in 1132 (112 couplings) is 6.2 Hz; this excellent fit with nine adjustable parameters suggests that the assumption of equal temperature dependencies of the order parameters for ethane, propane, and each conformer of butane is correct. Also the fit parameters (E(tg) and the methyl angle increase) obtained for 1132 and 5CB agree. The results indicate that the chord model, which was designed to treat hydrocarbon chains, is indeed the model of choice for these chains. The temperature variation of E(tg) provides a challenge for theoreticians. Finally, even better fits to the experimental dipolar couplings are obtained when the energy in the Boltzmann factor is used for scaling ethane to butane results

  1. New solutions for conformable fractional Boussinesq and combined KdV-mKdV equations using Jacobi elliptic function expansion method

    Science.gov (United States)

    Tasbozan, Orkun; Çenesiz, Yücel; Kurt, Ali

    2016-07-01

    In this paper, the Jacobi elliptic function expansion method is proposed for the first time to construct the exact solutions of the time conformable fractional two-dimensional Boussinesq equation and the combined KdV-mKdV equation. New exact solutions are found. This method is based on Jacobi elliptic functions. The results obtained confirm that the proposed method is an efficient technique for analytic treatment of a wide variety of nonlinear conformable time-fractional partial differential equations.

  2. Spontaneous breaking of conformal invariance in theories of conformally coupled matter and Weyl gravity

    OpenAIRE

    Edery, A.; Fabbri, Luca; Paranjape, M. B.

    2006-01-01

    We study the theory of Weyl conformal gravity with matter degrees of freedom in a conformally invariant interaction. Specifically, we consider a triplet of scalar fields and SO(3) non-abelian gauge fields, i.e. the Georgi-Glashow model conformally coupled to Weyl gravity. We show that the equations of motion admit solutions spontaneously breaking the conformal symmetry and the gauge symmetry, providing a mechanism for supplying a scale in the theory. The vacuum solution corresponds to anti-de...

  3. Study of polymer molecules and conformations with a nanopore

    Energy Technology Data Exchange (ETDEWEB)

    Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.

    2013-03-12

    The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

  4. Study of polymer molecules and conformations with a nanopore

    Energy Technology Data Exchange (ETDEWEB)

    Golovchenko, Jene A; Li, Jiali; Stein, Derek; Gershow, Marc H

    2015-03-03

    The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

  5. Study of polymer molecules and conformations with a nanopore

    Science.gov (United States)

    Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.

    2010-12-07

    The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

  6. Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals.

    Science.gov (United States)

    Fujimoto, Yukari; Fishkin, Nathan; Pescitelli, Gennaro; Decatur, John; Berova, Nina; Nakanishi, Koji

    2002-06-26

    To gain information on the conformation of the 11-cis-retinylidene chromophore bound to bovine opsin, the enantiomeric pair (2a and 2b) of 11-cis-locked bicyclo[5.1.0]octyl retinal (retCPr) 2 was prepared and its conformation was investigated by NMR, geometry optimization, and CD calculations. This compound is also of interest since it contains a unique moiety in which a chiral cyclopropyl group is flanked by triene and enal chromophores, and hence would clarify the little-known chiroptical contribution of a cyclopropyl ring linked to polyene systems. NMR revealed that the seven-membered ring of retCPr adopts a twist chair conformation. The NMR-derived structure constraints were then used for optimizing the geometry of 2 with molecular mechanics and ab initio methods. This revealed that enantiomer 2a with a 11 beta,12 beta-cyclopropyl group exists as two populations of diastereomers depending on the twist around the 6-s bond; however, the sense of twist around the 12-s is positive in both rotamers. The theoretical Boltzmann-weighted CD obtained with the pi-SCF-CI-DV MO method and experimental spectra were consistent, thus suggesting that the conjugative effect of the cyclopropyl moiety is minimal. It was found that only the beta-cyclopropyl enantiomer 2a, but not the alpha-enantiomer 2b, binds to opsin. This observation, together with earlier retinal analogues incorporation results, led to the conclusion that the chromophore sinks into the N-terminal of the opsin receptor from the side of the 4-methylene and 15-aldehyde, and that the binding cleft accommodates 11-cis-retinal with a slightly positive twist around C12/C13. A reinterpretation of the previously published negative CD couplet of 11,12-dihydrorhodopsin also leads to a chromophoric C12/C13 twist conformation with the 13-Me in front as in 1b. Such a conformation for the chromophore accounts for both the observed biostereoselectivity of retCPr 2a and the observed negative couplet of 11,12-dihydro-Rh7.

  7. Conformation transitions of a polyelectrolyte chain: a replica-exchange Monte-Carlo study.

    Science.gov (United States)

    Chi, Peng; Li, Baohui; Shi, An-Chang

    2011-08-01

    The thermodynamic behavior of a strongly charged polyelectrolyte chain immersed in a salt-free solution is studied using replica-exchange Monte-Carlo simulations. The results reveal that the chain can assume a variety of conformations, and it undergoes two phase transitions upon cooling. The first transition is identified as a continuous counterion condensation transition while the second one as a first-order coil-globule transition. In the globular state, the counterions and the charged chain segments are densely packed forming a three-dimensional Wigner crystal.

  8. Conformational analysis of a Chlamydia-specific disaccharide {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl in aqueous solution and bound to a monoclonal antibody: Observation of intermolecular transfer NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Sokolowski, Tobias; Haselhorst, Thomas; Scheffler, Karoline [Medizinische Universitaet, Institut fuer Chemie (Germany); Weisemann, Ruediger [Bruker Analytik GmbH, Silberstreifen (Germany); Kosma, Paul [Institut fuer Chemie der Universitaet fuer Bodenkultur Wien (Austria); Brade, Helmut; Brade, Lore [Forschungszentrum Borstel, Zentrum fuer Medizin und Biowissenschaften Parkallee 22 (Germany); Peters, Thomas [Medizinische Universitaet, Institut fuer Chemie (Germany)

    1998-07-15

    The disaccharide {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo (Kdo: 3-deoxy-d-manno-oct-2-ulosonic acid) represents a genus-specific epitope of the lipopolysaccharide of the obligate intracellular human pathogen Chlamydia. The conformation of the synthetically derived disaccharide {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl was studied in aqueous solution, and complexed to a monoclonal antibody S25-2. Various NMR experiments based on the detection of NOEs (or transfer NOEs) and ROEs (or transfer ROEs) were performed. A major problem was the extensive overlap of almost all {sup 1}H NMR signals of {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl. To overcome this difficulty, HMQC-NOESY and HMQC-trNOESY experiments were employed. Spin diffusion effects were identified using trROESY experiments, QUIET-trNOESY experiments and MINSY experiments. It was found that protein protons contribute to the observed spin diffusion effects. At 800 MHz, intermolecular trNOEs were observed between ligand protons and aromatic protons in the antibody binding site. From NMR experiments and Metropolis Monte Carlo simulations, it was concluded that {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl in aqueous solution exists as a complex conformational mixture. Upon binding to the monoclonal antibody S25-2, only a limited range of conformations is available to {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl. These possible bound conformations were derived from a distance geometry analysis using transfer NOEs as experimental constraints. It is clear that a conformation is selected which lies within a part of the conformational space that is highly populated in solution. This conformational space also includes the conformation found in the crystal structure. Our results provide a basis for modeling studies of the antibody-disaccharide complex.

  9. Molecular conformation of the full-length tumor suppressor NF2/Merlin—a small angle neutron scattering study

    Science.gov (United States)

    Khajeh, Jahan Ali; Ju, Jeong Ho; Atchiba, Moussoubaou; Allaire, Marc; Stanley, Christopher; Heller, William T.; Callaway, David J.E.; Bu, Zimei

    2014-01-01

    Summary The tumor suppressor protein Merlin inhibits cell proliferation upon establishing cell-cell contacts. Because Merlin has high sequence similarity to the Ezrin-Radixin-Moesin (ERM) family of proteins, the structural model of ERM protein autoinhibition and cycling between closed/resting and open/active conformational states is often employed to explain Merlin function. However, recent biochemical studies suggest alternative molecular models of Merlin function. Here, we have determined the low resolution molecular structure and binding activity of Merlin and a Merlin(S518D) mutant that mimics the inactivating phosphorylation at S518 using small angle neutron scattering (SANS) and binding experiments. SANS shows that in solution both Merlin and Merlin(S518D) adopt a closed conformation, but binding experiments indicate that a significant fraction of either Merlin or Merlin(S518D) is capable of binding to the target protein NHERF1. Upon binding to the phosphatidylinositol 4,5-bisphosphate lipid, the wild-type Merlin adopts a more open conformation than in solution, but Merlin(S518D) remains in a closed conformation. This study supports a rheostat model of Merlin in NHERF1 binding, and contributes to resolve a controversy about the molecular conformation and binding activity of Merlin. PMID:24882693

  10. Molecular conformation of the full-length tumor suppressor NF2/Merlin--a small-angle neutron scattering study.

    Science.gov (United States)

    Ali Khajeh, Jahan; Ju, Jeong Ho; Atchiba, Moussoubaou; Allaire, Marc; Stanley, Christopher; Heller, William T; Callaway, David J E; Bu, Zimei

    2014-07-29

    The tumor suppressor protein Merlin inhibits cell proliferation upon establishing cell-cell contacts. Because Merlin has high level of sequence similarity to the Ezrin-Radixin-Moesin family of proteins, the structural model of Ezrin-Radixin-Moesin protein autoinhibition and cycling between closed/resting and open/active conformational states is often employed to explain Merlin function. However, recent biochemical studies suggest alternative molecular models of Merlin function. Here, we have determined the low-resolution molecular structure and binding activity of Merlin and a Merlin(S518D) mutant that mimics the inactivating phosphorylation at S518 using small-angle neutron scattering and binding experiments. Small-angle neutron scattering shows that, in solution, both Merlin and Merlin(S518D) adopt a closed conformation, but binding experiments indicate that a significant fraction of either Merlin or Merlin(S518D) is capable of binding to the target protein NHERF1. Upon binding to the phosphatidylinositol 4,5-bisphosphate lipid, the wild-type Merlin adopts a more open conformation than in solution, but Merlin(S518D) remains in a closed conformation. This study supports a rheostat model of Merlin in NHERF1 binding and contributes to resolving a controversy about the molecular conformation and binding activity of Merlin. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Some invariant solutions for non-conformal perfect fluid plates in 5 ...

    Indian Academy of Sciences (India)

    –(2.7) demands. (W + 8πT)W = 0 [6],. (2.10) where T = ρ − 3p, while. W = 2. P2t. [− ˙u2u u + 2t( ˙u 2 − ¨uu ) − u 3 ¨u − 2u ˙u (2 − ˙uu )] + u 2. Pt2 . (2.11). W can easily be proved to be an eigenvalue of the Weyl's conformal curvature tensor.

  12. Conformational Analysis of Proteins in Highly Concentrated Solutions by Dialysis-Coupled Hydrogen/Deuterium Exchange Mass Spectrometry

    DEFF Research Database (Denmark)

    Houde, Damian; Esmail Nazari, Zeinab; Bou-Assaf, George M

    2016-01-01

    When highly concentrated, an antibody solution can exhibit unusual behaviors, which can lead to unwanted properties, such as increased levels of protein aggregation and unusually high viscosity. Molecular modeling, along with many indirect biophysical measurements, has suggested that the cause...... for these phenomena can be due to short range electrostatic and/or hydrophobic protein-protein interactions. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for investigating protein conformation, dynamics, and interactions. However, "traditional" continuous dilution labeling HDX......-MS experiments have limited utility for the direct analysis of solutions with high concentrations of protein. Here, we present a dialysis-based HDX-MS (di-HDX-MS) method as an alternative HDX-MS labeling format, which takes advantage of passive dialysis rather than the classic dilution workflow. We applied...

  13. Conformation of eight-membered benzoannulated lactams by combined NMR and DFT studies.

    Science.gov (United States)

    Witosińska, Agnieszka; Musielak, Bogdan; Serda, Paweł; Owińska, Maria; Rys, Barbara

    2012-11-02

    The title compounds were synthesized, and their structure and conformational behavior in solution (NMR and DFT), in the gas phase (DFT), and, for some of them, in the solid state (X-ray) were investigated. The variable-temperature NMR spectra were employed to determine the conformational equilibria and the activation energy of the conformational changes of the eight-membered ring. The coalescence effects are assigned to racemization of the chiral ground-state conformation with a ring inversion barrier in the range of 38-100 kJ mol(-1) depending on the relative setting of the two strong conformational constraints: benzoannulation and the amide function. The second conformational process, interconversion between two different conformers, in the molecules of benzo[c]azocin-3-one, benzo[d]azocin-2-one, and benzo[d]azocin-4-one was observed. The natures of the conformers observed in solution were elucidated by analysis of experimental and calculated NMR data. The present results are discussed in conjunction with previous experimental and theoretical data on (Z,Z)-cyclooctadienes and their benzo analogues.

  14. Vibrational analysis and conformational study of 3-methylamino-2-acetyl propenenitrile and 3-methylamino-2-methylsulfonyl propenenitrile

    Science.gov (United States)

    Polovková, J.; Gatial, A.; Milata, V.; Černuchová, P.; Prónayová, N.; Liptaj, T.; Matějka, P.

    2007-03-01

    This study presents the comparison of conformational behaviour of two similar push-pull ethylenes in which the possibility to form an intramolecular hydrogen bond exists. The IR, Raman and NMR spectroscopic studies as well as ab initio MP2 and DFT B3LYP theoretical calculations using 6-31G** basis set confirmed that the presence of intramolecular hydrogen bond has an important influence on conformational behaviour of such type compounds. 3-methylamino-2-acetyl propenenitrile (MAAPN) H 3C sbnd NH sbnd CH dbnd C(CN)(COCH 3) was prepared as pure Z-isomer with intramolecular hydrogen bond while 3-methylamino-2-methylsulfonyl propenenitrile (MASPN) H 3C sbnd NH sbnd CH dbnd C(CN)(SO 2CH 3) as pure E-isomer. MAAPN in polar solutions partially underlies to the isomerization. Such process has not been observed for MASPN which exists in solution in two conformers with the anti and syn orientation of the methylamino group towards the C dbnd C double bond, anti conformer being about 2.0 ± 0.4 kJ mol -1 more stable. The vibrational spectra of studied molecules were assigned on the base of normal coordinate calculations and potential energy distribution (PED). The use of different polarizable continuum models (IPCM, PCM) included in SCRF theory leads to controversial results in ground-state energy calculations in solutions of various polarity.

  15. Theoretical study on fulvic acid structure, conformation and aggregation

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez-Puebla, R.A. [Department of Applied Chemistry, Public University of Navarra, Campus Arrosadia, E-31006 Pamplona (Spain); Valenzuela-Calahorro, C. [Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, E-18071 Granada (Spain); Garrido, J.J. [Department of Applied Chemistry, Public University of Navarra, Campus Arrosadia, E-31006 Pamplona (Spain)]. E-mail: j.garrido@unavarra.es

    2006-04-01

    The ubiquitous presence of humic substances (HS), combined with their ability to provide multiple sites for chemical reaction, makes them relevant to numerous biogeochemical processes such as mineral weathering, nutrient bioavailability, and contaminant transport. The reactivity of HS depends on their functional group chemistry and microstructure, which are in turn influenced by the composition of the surrounding media. In order to help towards an understanding of structure conformations and aggregation process of HS in soils and waters and to get a better knowledge of these kinds of materials, a fulvic acid (FA) has been modelled as a function of its ionic state under different conditions. Our proposed theoretical model based on the Temple-Northeastern-Birmingham (TNB) monomer fits well with experimental observations on the solubility (dipolar moment) and electronic and vibrational spectra of FAs. The presence of water molecules has a great stabilization effect on the electrostatic energy; this effect is greater as ionized rate increases. In vacuum, the non-ionized aggregated species are more stable than monomers because of the increase in their interaction due to H-bonding and non-bonding forces. When the molecules are ionized, no aggregation process takes place. In solution, the FA concentration is a critical factor for the aggregation. The system containing two FA molecules probably did not form aggregates because its equivalent concentration was too low. When the concentration was increased, the system gave rise to the formation of aggregates. The ionic state is another critical factor in the aggregation process. The ionized FA has a higher electric negative charge, which increases the energetic barriers and inhibits the approximation of FA caused by the Brownian movement.

  16. Viscosity analysis of the temperature dependence of the solution conformation of ovalbumin.

    Science.gov (United States)

    Monkos, K

    2000-05-31

    The viscosity of ovalbumin aqueous solutions was studied as a function of temperature and of protein concentration. Viscosity-temperature dependence was discussed on the basis of the modified Arrhenius formula at temperatures ranging from 5 to 55 degrees C. The activation energy of viscous flow for hydrated and unhydrated ovalbumin was calculated. Viscosity-concentration dependence, in turn, was discussed on the basis of Mooney equation. It has been shown that the shape parameter S decreases with increasing temperature, and self-crowding factor K does not depend on temperature. At low concentration limit the numerical values of the intrinsic viscosity and of Huggins coefficient were calculated. A master curve relating the specific viscosity etasp to the reduced concentration c[eta], over the whole range of temperature, was obtained and the three ranges of concentrations: diluted, semi-diluted and concentrated, are discussed. It has been proved that the Mark-Houvink-Kuhn-Sakurada (MHKS) exponent for ovalbumin does not depend on temperature.

  17. Exact Solutions to (3+1) Conformable Time Fractional Jimbo–Miwa, Zakharov–Kuznetsov and Modified Zakharov–Kuznetsov Equations

    Science.gov (United States)

    Korkmaz, Alper

    2017-05-01

    Exact solutions to conformable time fractional (3+1)-dimensional equations are derived by using the modified form of the Kudryashov method. The compatible wave transformation reduces the equations to an ODE with integer orders. The predicted solution of the finite series of a rational exponential function is substituted into this ODE. The resultant polynomial equation is solved by using algebraic operations. The method works for the Jimbo–Miwa, the Zakharov–Kuznetsov, and the modified Zakharov–Kuznetsov equations in conformable time fractional forms. All the solutions are expressed in explicit forms.

  18. Infrared study on annealing effect on conformation of zinc stearate.

    Science.gov (United States)

    Ishioka, Tsutomu; Kiritani, Atsushi; Kojima, Takuya

    2007-04-01

    The molecular conformation and thermal transition behavior of two zinc stearate specimens, unannealed one and annealed one, were compared. The unannealed specimen has one thermal transition at 134 degrees C. Annealing was made by increasing temperature to 150 degrees C and cooling to room temperature slowly. This annealed specimen has an exothermic peak at 103 degrees C, and endothermic shoulders and a peak at 118, 124 and 131 degrees C, respectively. The observed frequencies of all bands of the unannealed specimen at room temperature are assigned to the all-trans conformation. We found new bands at 858, 823, 793, 766, 688, and 604 cm-1 for the annealed specimen. Based on the normal mode analyses, these bands are assigned to the TGT conformation at the COO end, where T means trans and G means gauche. The annealed specimen consists of almost all-trans molecule but partial molecules have the TGT conformation.

  19. Polarimetry as a tool for the study of solutions of chiral solutes.

    Science.gov (United States)

    Orlova, Anna V; Andrade, Renato R; da Silva, Clarissa O; Zinin, Alexander I; Kononov, Leonid O

    2014-01-13

    Optical rotation of aqueous solutions of D-levoglucosan was studied experimentally in the 0.03-4.0 mol L(-1) concentration range and a nonlinear concentration dependence of specific optical rotation (SR) was revealed. Discontinuities observed in the concentration plot of SR (at 0.1, 0.3, 0.5, 1.0, and 2.0 mol L(-1)) are well correlated with those found by static and dynamic light scattering and identify concentration ranges in which different solution domains (supramers) may exist. The average SR experimental value for a D-levoglucosan aqueous solution ([α]D(28) -58.5±8.7 deg dm(-1) cm(-3) g(-1)) was found to be in good agreement with values obtained by theoretical calculation (TD-DFT/GIAO) of SR for 15 different conformers revealed by conformational sampling at the PCM/B3LYP/6-311++G(2d,2p)//B3LYP/6-31+G(d,p) level, which were shown to be strongly affected by the solvation microenvironment (0, 1, 2, and 3 explicit solvent molecules considered) due to local geometrical changes induced in the solute molecule. This exceptionally high sensitivity of SR makes polarimetry a unique method capable of sensing changes in the structure of supramers detected in this study. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Semi-automated screen for global protein conformational changes in solution by ion mobility spectrometry-massspectrometry combined with size-exclusion chromatography and differential hydrogen-deuterium exchange.

    Science.gov (United States)

    Pierson, Nicholas A; Makarov, Alexey A; Strulson, Christopher A; Mao, Yun; Mao, Bing

    2017-05-05

    Development of methodologies for studying protein higher-order structure in solution helps to establish a better understanding of the intrinsic link between protein conformational structure and biological function and activity. The goal of this study was to demonstrate a simultaneous screening approach for global protein conformational changes in solution through the combination of ion mobility spectrometry-mass spectrometry (IMS-MS) with differential hydrogen-deuterium exchange (ΔHDX) on the size-exclusion chromatography (SEC) platform in a single on-line workflow. A semi-automated experimental setup based on the use of SEC on-column conditions allowed for tracking of protein conformational changes in solution as a function of acetonitrile concentration. In this setup, the SEC protein elution data was complemented by the ΔHDX profile which showed global protein conformational changes as a difference in the number of deuterons exchanged to protons. The ΔHDX data, in turn, was complemented by the changes in the drift time by IMS-MS. All three orthogonal techniques were applied for studying global higher-order structure of the proteins ubiquitin, cytochrome c and myoglobin, in solution simultaneously. The described approach allows for the use of a crude sample (or mixture of proteins) and could be suitable for rapid comparison of protein batch-to-batch higher-order structure or for optimizing conditions for enzymatic reactions. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Importance of poly(ethylene glycol) conformation for the synthesis of silver nanoparticles in aqueous solution

    Science.gov (United States)

    In the formation of silver nanoparticles (NPs) using silver nitrate in a poly(ethylene glycol) (PEG) aqueous solution, which acts as both a reducing and stabilizing agent, the PEG chain structure was found to play a significant role. Even though PEG 100 (100 kg/mol) has limited reducing sites of hyd...

  2. Phase behavior in quaternary ammonium ionic liquid-propanol solutions: Hydrophobicity, molecular conformations, and isomer effects

    Science.gov (United States)

    Abe, Hiroshi; Kohki, Erica; Nakada, Ayumu; Kishimura, Hiroaki

    2017-07-01

    In ionic liquids (ILs), the effects of a quaternary ammonium cation containing a hydroxyl group were investigated and compared with the effect of a standard quaternary ammonium cation. The cation possessing a hydroxyl group is choline, Chol+, and the anion is bis(trifluoromethylsulfonyl)imide, TFSI-. Crystal polymorphism of pure [Chol][TFSI] was observed upon both cooling and heating by simultaneous X-ray diffraction and differential scanning calorimetry measurements. In contrast, [N3111][TFSI] (N3111+: N-trimethyl-N-propylammonium), a standard IL, demonstrated simple crystallization upon cooling. By adding 1-propanol or 2-propanol, the phase behaviors of the [Chol][TFSI]-based and [N3111][TFSI]-based mixtures were clearly distinguished. By Raman spectroscopy, the TFSI- anion conformers in the liquid state were shown to vary according to the propanol concentration, propanol isomer, and type of cation. The anomalous behaviors of pure [Chol][TFSI] and its mixtures are derived from hydrogen bonding of the hydroxyl group of Chol+ cation coupled with the hydrophobicity and packing efficiency of propanol.

  3. Solution structure of Atg8 reveals conformational polymorphism of the N-terminal domain

    Energy Technology Data Exchange (ETDEWEB)

    Schwarten, Melanie, E-mail: m.schwarten@fz-juelich.de [Institut fuer Strukturbiologie und Biophysik, ISB-3, Forschungszentrum Juelich, 52425 Juelich (Germany); Institut fuer Physikalische Biologie und BMFZ, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf (Germany); Stoldt, Matthias, E-mail: m.stoldt@fz-juelich.de [Institut fuer Strukturbiologie und Biophysik, ISB-3, Forschungszentrum Juelich, 52425 Juelich (Germany); Institut fuer Physikalische Biologie und BMFZ, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf (Germany); Mohrlueder, Jeannine, E-mail: j.mohrlueder@fz-juelich.de [Institut fuer Strukturbiologie und Biophysik, ISB-3, Forschungszentrum Juelich, 52425 Juelich (Germany); Willbold, Dieter, E-mail: dieter.willbold@uni-duesseldorf.de [Institut fuer Strukturbiologie und Biophysik, ISB-3, Forschungszentrum Juelich, 52425 Juelich (Germany); Institut fuer Physikalische Biologie und BMFZ, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf (Germany)

    2010-05-07

    During autophagy a crescent shaped like membrane is formed, which engulfs the material that is to be degraded. This membrane grows further until its edges fuse to form the double membrane covered autophagosome. Atg8 is a protein, which is required for this initial step of autophagy. Therefore, a multistage conjugation process of newly synthesized Atg8 to phosphatidylethanolamine is of critical importance. Here we present the high resolution structure of unprocessed Atg8 determined by nuclear magnetic resonance spectroscopy. Its C-terminal subdomain shows a well-defined ubiquitin-like fold with slightly elevated mobility in the pico- to nanosecond timescale as determined by heteronuclear NOE data. In comparison to unprocessed Atg8, cleaved Atg8{sup G116} shows a decreased mobility behaviour. The N-terminal domain adopts different conformations within the micro- to millisecond timescale. The possible biological relevance of the differences in dynamic behaviours between both subdomains as well as between the cleaved and uncleaved forms is discussed.

  4. Gauge Natural Formulation of Conformal Theory of Gravity

    CERN Document Server

    Campigotto, M

    2014-01-01

    We consider conformal gravity as a gauge natural theory. We study its conservation laws and superpotentials. We also consider the Mannheim and Kazanas spherically symmetric vacuum solution and discuss conserved quantities associated to conformal and diffeomorphism symmetries.

  5. On conformally related -waves

    Indian Academy of Sciences (India)

    Conformal transformations; conformal Killing vectors; -waves. Abstract. Brinkmann [1] has shown that conformally related distinct Ricci flat solutions are -waves. Brinkmann's result has been generalized to include the conformally invariant source terms. It has been shown that [4] if g i k and g ¯ i k ( = − 2 g i k , : a ...

  6. How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations.

    Science.gov (United States)

    Yang, Yang; Cui, Qiang; Sahai, Nita

    2010-06-15

    Bone sialoprotein (BSP) is a highly phosphorylated, acidic, noncollagenous protein in bone matrix. Although BSP has been proposed to be a nucleator of hydroxyapatite (Ca(5)(PO(4))(3)OH), the major mineral component of bone, no detailed mechanism for the nucleation process has been elucidated at the atomic level to date. In the present work, using a peptide model, we apply molecular dynamics (MD) simulations to study the conformational effect of a proposed nucleating motif of BSP (a phosphorylated, acidic, 10 amino-acid residue sequence) on controlling the distributions of Ca(2+) and inorganic phosphate (Pi) ions in solution, and specifically, we explore whether a nucleating template for orientated hydroxyapatite could be formed in different peptide conformations. Both the alpha-helical conformation and the random coil structure have been studied, and inorganic solutions without the peptide are simulated as reference. Ca(2+) distributions around the peptide surface and interactions between Ca(2+) and Pi in the presence of the peptide are examined in detail. From the MD simulations, although in some cases for the alpha-helical conformation, we observe that a Ca(2+) equilateral triangle forms around the surface of peptide, which matches the distribution of Ca(2+) ions on the (001) face of the hydroxyapatite crystal, we do not consistently find a stable nucleating template formation in general for either the helical conformation or the random coil structure. Therefore, independent of conformations, the BSP nucleating motif is more likely to help nucleate an amorphous calcium phosphate cluster, which ultimately converts to crystalline hydroxyapatite.

  7. Photoreactive "nanorulers" detect a novel conformation of full length HDAC3-SMRT complex in solution.

    Science.gov (United States)

    Abdelkarim, Hazem; Brunsteiner, Michael; Neelarapu, Raghupathi; Bai, He; Madriaga, Antonett; van Breemen, Richard B; Blond, Sylvie Y; Gaponenko, Vadim; Petukhov, Pavel A

    2013-11-15

    Histone deacetylase 3 (HDAC3) is a promising epigenetic drug target for multiple therapeutic applications. Direct interaction between the Deacetylase Activating Domain of the silencing mediator for retinoid or thyroid-hormone receptors (SMRT-DAD) is required for activation of enzymatic activity of HDAC3. The structure of this complex and the nature of interactions with HDAC inhibitors in solution are unknown. Using novel photoreactive HDAC probes, "nanorulers", we determined the distance between the catalytic site of the full-length HDAC3 and SMRT-DAD in solution at physiologically relevant conditions and found it to be substantially different from that predicted by the X-ray model with a Δ379-428 aa truncated HDAC3. Further experiments indicated that in solution this distance might change in response to chemical stimuli, while the enzymatic activity remained unaffected. These observations were further validated by Saturation Transfer Difference (STD) NMR experiments. We propose that the observed changes in the distance are an important part of the histone code that remains to be explored. Mapping direct interactions and distances between macromolecules with such "nanorulers" as a function of cellular events facilitates better understanding of basic biology and ways for its manipulation in a cell- and tissue-specific manner.

  8. a Theoretical and Experimental Study of the Conformation of Peroxynitrite Anion (onoo(minus)) and its Stability.

    Science.gov (United States)

    Tsai, Jyh-Hsin Michael

    Peroxynitrite anion (ONOO^-), the reaction product of superoxide (O_2 {cdot}^-) and nitric oxide (cdotNO), is a strong and relatively long-lived oxidant produced by activated macrophages and neutrophils. At physiological pH, peroxynitrous acid forms a hydroxyl radical-like species and has been implicated in pulmonary edema, myocardial ischemia and stroke. Peroxynitrite is remarkably stable in both an alkaline solution and a crystalline state, which appears to be related to the molecule being locked in the cis conformation. To study the conformation of peroxynitrite, Raman spectra with different isotopic substitutions (O^{14}NOO ^-, O^{15} NOO^-, and ^ {18}O^{15}NOO ^-) in alkaline aqueous solutions were recorded in the 200-1800 cm^{ -1} region. The Raman spectra revealed only a single isomer with peaks observed at 375, 642, 791, 931 and 1564 cm^{-1} for O ^{14}NOO^ -. A sixth band was most likely hidden beneath a strong nitrate band centered at 1047 cm^ {-1} or too weak to be observed. The solid state Raman spectra of alkali peroxynitrites are similar to the aqueous solution spectra and consistent with only one isomer being present. A new peak which corresponded to the missing band in aqueous spectra was observed at around 1000 cm^{-1} in the Raman spectra of alkali peroxynitrites. Furthermore, the ^{15}N-NMR spectrum of peroxynitrite revealed only one peak at 178.0 ppm down -field from nitrate, also suggesting the presence of only one stable conformation. Ab initio quantum chemical calculations predicted that the cis conformation is more stable than the trans conformation by 3-4 kcal/mol. The vibrational frequency predictions from the cis conformation are in better agreement with the observed spectra than those from the trans conformation. The Raman torsional band of aqueous peroxynitrite was exceptionally broad, which suggests that peroxynitrite has strong solvent interactions with water molecules. The Raman spectra of peroxynitrite diluted in methanol were also

  9. Conformational Studies on γ - Benzyl- L- Glutamate and L- Valine Containing Block Copolypeptides

    OpenAIRE

    Ajay Kumar

    2010-01-01

    Conformational studies on γ - benzyl-L- glutamate and L- valine containing block copolypeptides are reported using IR and CD spectra. The block copolypeptides contain valine block in the center and on both sides of the valine are γ - benzyl- L- glutamate blocks. The changes in conformation with increase in chain length of γ - benzyl- L- glutamate blocks are observed. When the chain length of γ - benzyl-L- glutamate block is 13, the block copolypeptide crystallized into beta conformation. With...

  10. Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

    DEFF Research Database (Denmark)

    Wu, Xiaoping; Fang, Ming; Liu, Lin

    2013-01-01

    Background: Genome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. However, studies using GWAS for conformation traits of cattle is comparatively less. This study aims to use GWAS to find the candidates genes for body conformation traits.Re...

  11. DFT study of bridged oligo(bithiophene)s. Conformational analysis and opto-electronic properties

    OpenAIRE

    Si Mohamed Bouzzine; Mohamed Hamidi; Mohammed Bouachrine

    2009-01-01

    In this paper, we have studied the conformational and opto-electronic properties of several oligomers of bridged oligo(bithiophene)s (BTX)n , n=1 to 4 with (X: CH2, SiH2, C=O, C=S and C=C(CN)2). The conformational analysis shows that the most stable conformation is anti-planar conformation. The opto-electronic properties of the octamer (OTX) lead us to suggest that this oligomer is a good model to reflect opto-electronic properties for the parent polymer.

  12. DFT study of bridged oligo(bithiophenes. Conformational analysis and opto-electronic properties

    Directory of Open Access Journals (Sweden)

    Si Mohamed Bouzzine

    2009-08-01

    Full Text Available In this paper, we have studied the conformational and opto-electronic properties of several oligomers of bridged oligo(bithiophenes (BTXn , n=1 to 4 with (X: CH2, SiH2, C=O, C=S and C=C(CN2. The conformational analysis shows that the most stable conformation is anti-planar conformation. The opto-electronic properties of the octamer (OTX lead us to suggest that this oligomer is a good model to reflect opto-electronic properties for the parent polymer.

  13. Conformational Heterogeneity of Methyl 4-Hydroxycinnamate: A Gas-Phase UV-IR Spectroscopic Study

    NARCIS (Netherlands)

    Tan, E.M.M.; Amirjalayer, S.; Smolarek, S.; Vdovin, A.; Rijs, A.M.; Buma, W.J.

    2013-01-01

    UV excitation and IR absorption spectroscopy on Jet cooled molecules is used to study the conformational heterogeneity of methyl 4-hydroxycinnamate, a model chromophore of the Photoactive Yellow Protein (PYP), and to determine the spectroscopic properties of the various conformers UV-UV depletion

  14. Social Conformity and Autism Spectrum Disorder: A Child-Friendly Take on a Classic Study

    Science.gov (United States)

    Yafai, Abdul-Fattah; Verrier, Diarmuid; Reidy, Lisa

    2014-01-01

    Perhaps surprisingly, given the importance of conformity as a theoretical construct in social psychology and the profound implications autism has for social function, little research has been done on whether autism is associated with the propensity to conform to a social majority. This study is a modern, child-friendly implementation of the…

  15. Absolute configuration and conformational analysis of sesquiterpene lactone glycoside studied by vibrational circular dichroism spectroscopy

    Science.gov (United States)

    Michalski, Oskar; Kisiel, Wanda; Michalska, Klaudia; Setnicka, Vladimir; Urbanova, Marie

    2007-12-01

    The absolute configuration of the guaiane-type sesquiterpene lactone 8-epiisolippidiol-3- O-β- D-glucopyranoside, isolated from plants of the genus Crepis, and the predominant solution-state conformation in CD 3OD were determined by comparison of experimental and calculated VCD spectra. It has been found that the reported stereostructure of the compound corresponds to its absolute configuration.

  16. Conformal basis for flat space amplitudes

    Science.gov (United States)

    Pasterski, Sabrina; Shao, Shu-Heng

    2017-09-01

    We study solutions of the Klein-Gordon, Maxwell, and linearized Einstein equations in R1 ,d +1 that transform as d -dimensional conformal primaries under the Lorentz group S O (1 ,d +1 ). Such solutions, called conformal primary wavefunctions, are labeled by a conformal dimension Δ and a point in Rd, rather than an on-shell (d +2 )-dimensional momentum. We show that the continuum of scalar conformal primary wavefunctions on the principal continuous series Δ ∈d/2 +i R of S O (1 ,d +1 ) spans a complete set of normalizable solutions to the wave equation. In the massless case, with or without spin, the transition from momentum space to conformal primary wavefunctions is implemented by a Mellin transform. As a consequence of this construction, scattering amplitudes in this basis transform covariantly under S O (1 ,d +1 ) as d -dimensional conformal correlators.

  17. Workers’ Conformism

    Directory of Open Access Journals (Sweden)

    Nikolay Ivantchev

    2013-10-01

    Full Text Available Conformism was studied among 46 workers with different kinds of occupations by means of two modified scales measuring conformity by Santor, Messervey, and Kusumakar (2000 – scale for perceived peer pressure and scale for conformism in antisocial situations. The hypothesis of the study that workers’ conformism is expressed in a medium degree was confirmed partly. More than a half of the workers conform in a medium degree for taking risk, and for the use of alcohol and drugs, and for sexual relationships. More than a half of the respondents conform in a small degree for anti-social activities (like a theft. The workers were more inclined to conform for risk taking (10.9%, then – for the use of alcohol, drugs and for sexual relationships (8.7%, and in the lowest degree – for anti-social activities (6.5%. The workers who were inclined for the use of alcohol and drugs tended also to conform for anti-social activities.

  18. Theoretical study of the conformation and energy of supercoiled DNA

    Energy Technology Data Exchange (ETDEWEB)

    Hunt, Nathaniel George [Lawrence Berkeley Lab., CA (United States). Structural Biology Div.; California Univ., Berkeley, CA (United States). Dept. of Physics

    1992-01-01

    The two sugar-phosphate backbones of the DNA molecule wind about each other in helical paths. For circular DNA molecules, or for linear pieces of DNA with the ends anchored, the two strands have a well-defined linking number, Lk. If Lk differs from the equilibrium linking number Lk0, the molecule is supercoiled. The linking difference ΔLk = Lk-Lk0 is partitioned between torsional deformation of the DNA, or twist (ΔTw), and a winding of the DNA axis about itself known as writhe (Wr). In this dissertation, the conformation and energy of supercoiled DNA are examined by treating DNA as an elastic cylinder. Finite-length and entropic effects are ignored, and all extensive quantities are treated as linear densities. Two classes of conformation are considered: the plectonemic or interwound form, in which the axis of the DNA double helix winds about itself in a double superhelix, and the toroidal shape in which the axis is wrapped around a torus. Minimum energy conformation are found. For biologically relevant values of specific linking differences, the plectonemic DNA, the superhelical pitch angle α is in the range 45° < α ≤ 90°. For low values of specific linking difference |σ| (σ = ΔLk/Lk0), most linking difference is in writhe. As |σ| increases, a greater proportion of linking difference is in twist. Interaction between DNA strands is treated first as a hard-body excluded volume and then as a screened electrostatic repulsion. Ionic strength is found to have a large effect, resulting in significantly greater torsional stress in supercoiled DNA at low ionic strength.

  19. Zwitterionic conformers of pyrrolysine and their interactions with metal ions--a theoretical study.

    Science.gov (United States)

    Das, Gunajyoti

    2013-08-01

    A total of 16 pyrrolysine conformers in their zwitterionic forms are studied in gas and simulated aqueous phase using a polarizable continuum model (PCM). These conformers are selected on the basis of our study on the intrinsic conformational properties of non-ionic pyrrolysine molecule in gas phase [Das and Mandal (2013) J Mol Model 19:1695-1704]. In aqueous phase, the stable zwitterionic pyrrolysine conformers are characterized by full geometry optimization and vibrational frequency calculations using B3LYP/6-311++G(d,p) level of theory. Single point calculations are also carried out at MP2/6-311++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. The calculated relative energy range of the conformers at B3LYP/6-311++G(d,p) level is 5.19 kcal mol(-1) whereas the same obtained by single point calculations at MP2/6-311++G(d,p) level is 4.58 kcal mol(-1). A thorough analysis reveals that four types of intramolecular H-bonds are present in the conformers; all of which play key roles in determining the energetics and in imparting the observed conformations to the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of the H-bonds. This study also points out that conformers with diverse structural motifs may differ in their thermodynamical stability by a narrow range of relative energy. The effects of metal coordination on the relative stability order and structural features of the conformers are examined by complexing five zwitterionic conformers of pyrrolysine with Cu(+2) through their carboxylate groups. The interaction enthalpies and Gibbs energies, rotational constants, vibrational frequencies and dipole moments of the metal complexes calculated at B3LYP level are also reported. The zwitterionic

  20. Conformational changes and orientation of Humicola lanuginosa lipase on a solid hydrophobic surface: an in situ interface Fourier transform infrared-attenuated total reflection study.

    Science.gov (United States)

    Noinville, Sylvie; Revault, Madeleine; Baron, Marie-Hélène; Tiss, Ali; Yapoudjian, Stéphane; Ivanova, Margarita; Verger, Robert

    2002-01-01

    This study was done to better understand how lipases are activated at an interface. We investigated the conformational and solvation changes occurring during the adsorption of Humicola lanuginosa lipase (HLL) onto a hydrophobic surface using Fourier transform infrared-attenuated total reflection spectroscopy. The hydrophobic surfaces were obtained by coating silicon attenuated total reflection crystal with octadecyltrichlorosilane. Analysis of vibrational spectra was used to compare the conformation of HLL adsorbed at the aqueous-solid interface with its conformation in solution. X-ray crystallography has shown that HLL exists in two conformations, the closed and open forms. The conformational changes in HLL caused by adsorption onto the surface were compared with those occurring in three reference proteins, bovine serum albumin, lysozyme, and alpha-chymotrypsin. Adsorbed protein layers were prepared using proteins solutions of 0.005 to 0.5 mg/mL. The adsorptions of bovine serum albumin, lysozyme, and alpha-chymotrypsin to the hydrophobic support were accompanied by large unfoldings of ordered structures. In contrast, HLL underwent no secondary structure changes at first stage of adsorption, but there was a slight folding of beta-structures as the lipase monolayer became complete. Solvation studies using deuterated buffer showed an unusual hydrogen/deuterium exchange of the peptide CONH groups of the adsorbed HLL molecules. This exchange is consistent with the lipase being in the native open conformation at the water/hydrophobic interface. PMID:11964257

  1. Exploring the conformational landscape of menthol, menthone, and isomenthone: A microwave study

    Science.gov (United States)

    Schmitz, David; Shubert, V.; Betz, Thomas; Schnell, Melanie

    2015-03-01

    The rotational spectra of the monoterpenoids menthol, menthone, and isomenthone are reported in the frequency range of 2-8.5GHz, obtained with broadband Fourier-transform microwave spectroscopy. For menthol only one conformation was identified under the cold conditions of the molecular jet, whereas three conformations were observed for menthone and one for isomenthone. The conformational space of the different molecules was extensively studied using quantum chemical calculations, and the results were compared with molecular parameters obtained by the measurements. Finally, a computer program is presented, which was developed to automatically identify different species in a dense broadband microwave spectrum using calculated ab initio rotational constants as input.

  2. Temperature Drift of Conformational Equilibria of Butyl Alcohols Studied by Near-Infrared Spectroscopy and Fully Anharmonic DFT.

    Science.gov (United States)

    Grabska, Justyna; Beć, Krzysztof B; Ozaki, Yukihiro; Huck, Christian W

    2017-03-09

    Conformational isomerism of aliphatic alcohols with respect to the internal rotation of C-O(H) group and its impact on near-infrared (NIR) spectra has been known in the literature. However, no attempt has ever been made to investigate systematically whether and how the conformational flexibility of the aliphatic chain determines the observed NIR data of aliphatic alcohols. In the present study NIR spectra of four kinds of butyl alcohols, 1-butanol, 2-butanol, isobutanol, and tert-butyl alcohol, were investigated in diluted (0.1 M) CCl4 solutions. The experimental NIR spectra of butyl alcohols were accurately reproduced and explained in a fully anharmonic DFT study by means of generalized second-order vibrational perturbation theory (GVPT2). Entire conformational populations were taken into account in each case. On the basis of the theoretical study, influences of conformational flexibility with respect to internal rotations not only about the C-O bond, but also about the C-C bonds have been well evidenced in the experimental spectra. The conformational isomerism affects significantly the shape of NIR spectra. The temperature-dependent NIR spectra of butyl alcohols show changes in the band shape and a blue-shift of the overtone band due to the stretching mode of free OH group, and its intensity decreases with increasing temperature. These effects can be closely monitored by two-dimensional correlation spectroscopy (2D-COS). In this work, the experimental 2D-COS patterns have been successfully reproduced, based on DFT calculated NIR spectra of conformational isomers of the studied molecules and their Boltzmann coefficients over the corresponding temperature range. Thus, the experimentally observed effects are fully reflected in the DFT study, which leads to the conclusion that the main factor in the temperature-dependent spectral changes of 2νOH band of aliphatic alcohols in the diluted phase, where no self-association occurs, is played by the changes in the

  3. Conformational aspects of dibenzo-tetroxecin: A structural, Raman spectroscopic and computational study

    Science.gov (United States)

    Gordon, Keith C.; McAdam, C. John; Moratti, Stephen C.; Shillito, Georgina E.; Simpson, Jim

    2017-10-01

    Crystalline dibenzo-tetroxecin (I) has been prepared from a reaction between catechol and dichloromethane and its molecular and crystal structure, together with the Raman spectrum of the material in the solid state and in solution, is reported. The molecular structure shows the molecule adopts an anti or stepped conformation. Density functional theory (DFT) optimisation and frequency calculations using the B3LYP functional with the 6-31G(d) basis set showed the presence of syn- and anti-conformers of (I), with the anti-conformer predicted to be the lower in energy by 13.6 kJ mol-1. The vibrational frequencies and relative Raman intensities of the anti-conformer are well modelled by the DFT calculations. The bond lengths and angles obtained for the anti-conformer are also in good agreement with the crystal structure. The crystal structure of (I) is stabilised by intermolecular Csbnd H⋯O hydrogen bonds that generate a three dimensional network.

  4. Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

    CERN Document Server

    Yusuff, Olaniyi K; Bussi, Giovanni; Raugei, Simone

    2012-01-01

    Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\\alpha}1{\\beta}2 and {\\alpha}2{\\b...

  5. Influence of conformity on the wear of total knee replacement: An experimental study.

    Science.gov (United States)

    Brockett, Claire L; Carbone, Silvia; Fisher, John; Jennings, Louise M

    2018-02-01

    Wear of total knee replacement continues to be a significant factor influencing the clinical longevity of implants. Historically, failure due to delamination and fatigue directed design towards more conforming inserts to reduce contact stress. As new generations of more oxidatively stable polyethylene have been developed, more flexibility in bearing design has been introduced. The aim of this study was to investigate the effect of insert conformity on the wear performance of a fixed bearing total knee replacement through experimental simulation. Two geometries of insert were studied under standard gait conditions. There was a significant reduction in wear with reducing implant conformity. This study has demonstrated that bearing conformity has a significant impact on the wear performance of a fixed bearing total knee replacement, providing opportunities to improve clinical performance through enhanced material and design selection.

  6. Polyelectrolyte Conformation, Interactions and Hydrodynamics as Studied by Light Scattering.

    Science.gov (United States)

    Ghosh, Snehasish

    Polyelectrolyte conformation, interactions and hydrodynamics show a marked dependence on the ionic strength (C_{rm s}) of the medium, the concentration (C_{rm p}) of the polymer itself and their charge density (xi). The apparent electrostatic persistence length obtained from static light scattering varied approximately as the inverse square root of C _{rm s} for highly pure, high molecular weight hyaluronate (HA) as well as for variably ionized acrylamide/sodium acrylate copolymers (NaPAA), and linearly with xi. The experimental values of persistence length and second virial coefficient (A_2) are compared to predictions from theories based on the Debye-Huckel approximation for the Poisson-Boltzmann equation and on excluded-volume. Although the mean square radius of gyration () depended strongly on C _{rm s}. decreasing with increasing C_{rm s} for both HA and NaPAA indicating clear evidence of polyion expansion, dynamic light scattering values of the translational diffusion coefficient (D) remains constant when extrapolated to infinite polymer concentration for both the polymers. The behavior of D is compared to predictions from coupled mode theory in the linear limit. The effects of NaOH on the conformations, interactions, diffusion and hydrolysis rates of HA are characterized in detail using static, dynamic and time-dependent light scattering supplemented by size exclusion chromatography (SEC). For the HA , A_2 and the hydrolysis rates all resemble superposing titration curves, while the D remains independent of both the concentration of NaOH, and the contraction of . The indication is that the interactions, conformations and the hydrolysis rates are all controlled by the titration of the HA hydroxyl groups by the NaOH to yield -O ^-, which (i) destroys single strand hydrogen bonds, leading to de-stiffening and contraction of the HA coil and a large decrease in intermolecular interaction, and (ii) slowly depolymerizes HA. The experimental results of HA

  7. A Simulation Study of Conformal Cooling Channels in Plastic Injection Molding

    OpenAIRE

    Omar A. Mohamed, S.H. Masood, Abul Saifullah

    2013-01-01

    In injection molding process, the cooling channel performance is one of the most crucial factors because it has significant effect on both production rate and the quality of the plastic part. In order to reduce the cycle time, and control the uniform distribution of temperature, it is necessary to create conformal cooling channels, which conform to the shape of the mold cavity and core. This paper presents a simulation study of different types of cooling channe...

  8. Playing nice: a multi-methodological study on the effects of social conformity on memory

    Science.gov (United States)

    Deuker, Lorena; Müller, Anna R.; Montag, Christian; Markett, Sebastian; Reuter, Martin; Fell, Juergen; Trautner, Peter; Axmacher, Nikolai

    2013-01-01

    Conformity is an important aspect of social behavior. Two main motives have been identified: people may adapt their behavior to “play nice” despite knowing better (normative conformity) or they may accept the others' opinion as a valid source of information (informative conformity). Neuroimaging studies can help to distinguish between these two possibilities. Here, we present a functional magnetic resonance imaging (fMRI) study on memory conformity in a real group situation. We investigated the effects of group pressure on activity in hippocampus and anterior cingulate cortex (ACC) which likely support informative and normative memory conformity, respectively. Furthermore, we related the single nucleotide polymorphism (SNP) rs4680 [called Catechol-O-methyltransferase (COMT) Val158Met] on the gene coding for COMT to both behavior and fMRI activation. Homozygous Met-allele carriers (Val−) behaved more conformist than carriers of at least one Val-allele (Val+). In the neuroimaging data, we compared trials in which subjects were confronted with a majority of incorrect group responses to trials in which they were confronted with a majority of correct group responses. We found increased hippocampal activity when the majority of the group was correct, possibly indicating retrieval processes. Moreover, we observed enhanced activity in the ACC when the majority of the group was incorrect, suggesting that conformity was mostly normative. Most interestingly, this latter effect was more pronounced for Val− as compared to Val+ participants. This offers a speculative explanation for the higher behavioral levels of social conformity in Val− allele carriers, because their subjectively perceived conflict in the presence of an incorrect group majority may have been higher. Overall, this study demonstrates how the mechanisms leading to complex social behavior such as conformity can be studied by combining genetic analyses and fMRI in social neuroscience paradigms. PMID

  9. Playing nice: a multi-methodological study on the effects of social conformity on memory.

    Science.gov (United States)

    Deuker, Lorena; Müller, Anna R; Montag, Christian; Markett, Sebastian; Reuter, Martin; Fell, Juergen; Trautner, Peter; Axmacher, Nikolai

    2013-01-01

    Conformity is an important aspect of social behavior. Two main motives have been identified: people may adapt their behavior to "play nice" despite knowing better (normative conformity) or they may accept the others' opinion as a valid source of information (informative conformity). Neuroimaging studies can help to distinguish between these two possibilities. Here, we present a functional magnetic resonance imaging (fMRI) study on memory conformity in a real group situation. We investigated the effects of group pressure on activity in hippocampus and anterior cingulate cortex (ACC) which likely support informative and normative memory conformity, respectively. Furthermore, we related the single nucleotide polymorphism (SNP) rs4680 [called Catechol-O-methyltransferase (COMT) Val158Met] on the gene coding for COMT to both behavior and fMRI activation. Homozygous Met-allele carriers (Val-) behaved more conformist than carriers of at least one Val-allele (Val+). In the neuroimaging data, we compared trials in which subjects were confronted with a majority of incorrect group responses to trials in which they were confronted with a majority of correct group responses. We found increased hippocampal activity when the majority of the group was correct, possibly indicating retrieval processes. Moreover, we observed enhanced activity in the ACC when the majority of the group was incorrect, suggesting that conformity was mostly normative. Most interestingly, this latter effect was more pronounced for Val- as compared to Val+ participants. This offers a speculative explanation for the higher behavioral levels of social conformity in Val- allele carriers, because their subjectively perceived conflict in the presence of an incorrect group majority may have been higher. Overall, this study demonstrates how the mechanisms leading to complex social behavior such as conformity can be studied by combining genetic analyses and fMRI in social neuroscience paradigms.

  10. Conformal Infinity

    Directory of Open Access Journals (Sweden)

    Frauendiener Jörg

    2000-08-01

    Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, ``conformal infinity'' is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  11. Capturing high temperature protein conformations for low-temperature study using ultra-fast cooling

    Science.gov (United States)

    Moreau, David; Atakisi, Hakan; Thorne, Robert

    protocols for cooling biomolecular crystals for x-ray cryocrystallography are poorly controlled, leading to crystal-to-crystal and within-crystal non-isomorphism. Furthermore, cooling times below the protein-solvent glass transition of .1 s provide ample time for biological temperature conformations to depopulate and shift. To address these issues, methods and apparatus for cooling biomolecular crystals at rates approaching 100,000 K/s have been developed. These cooling rates are sufficient to eliminate ice formation on cooling without use of cryoprotectants, and to quench additional high-temperature conformations for low-temperature study. Time scales for conformational relaxation can be characterized using variable cooling rates. Possible extension of these methods to maximize conformational quenching will be discussed.

  12. A study of the conformational isomerism of 1-iodobutane by high resolution rotational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Arsenault, Eric A.; Obenchain, Daniel A.; Blake, Thomas A.; Cooke, S. A.; Novick, Stewart E.

    2017-05-01

    The first microwave study of 1-iodobutane, performed by Steinmetz et al.in 1977) led to the determination of the B + C parameter for the anti-anti­and gauche-anti-conformers. Nearly 40 years later, this reinvestigation of 1- iodobutane, by high-resolution microwave spectroscopy, led to the determina­tion of rotational constants, centrifugal distortion constants, nuclear quadrupole coupling constants (NQCCs), and nuclear-sp rotation constants belonging to both of the two previously mentioned conformers, in addition to the gauche­ gauche-conformer, which was observed in this frequency regime for the first time. Comparisons between the three conformers of 1-iodobutanc and other iodo- and bromoalkanes are made, specifically through an analysis of the nuclear quadrupole coupling constants belonging to the iodine and bromine atoms in the respective chemical environments.

  13. Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics.

    OpenAIRE

    Cognet, J A; Gabarro-Arpa, J; Le Bret, M; van der Marel, G A; van Boom, J H; Fazakerley, G V

    1991-01-01

    We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three dimensional solution structure of the non-selfcomplementary oligonucleotide, d(GAGGAGGCACG). d(CGTGCGTCCTC) in which the central base pair is G.G. This is the first structural determination of a G.G mismatch in a oligonucleotide. Two dimensional nuclear magnetic resonance spectra show that the bases of the mismatched pair are stacked into the helix and that the helix adopts ...

  14. On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

    Energy Technology Data Exchange (ETDEWEB)

    Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S., E-mail: myerson@mit.edu [Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 66-568, Cambridge, Massachusetts 02139 (United States); Simpson, Jeffrey [Department of Chemistry Instrumentation Facility, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 18-0090, Cambridge, Massachusetts 02139 (United States); Fry, John C.; Biermann, Kari L. [Connect Consulting, 6 Hollands Field, Horsham RH123HQ (United Kingdom); Yurttas, Nese [Cargill, Inc., Global Food Technology, 2301 Crosby Road, Wayzata, Minnesota 55391 (United States)

    2015-12-28

    The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

  15. On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

    Science.gov (United States)

    Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Simpson, Jeffrey; Fry, John C.; Yurttas, Nese; Biermann, Kari L.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S.

    2015-12-01

    The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

  16. Development of a sensor to study the DNA conformation using molecular logic gates.

    Science.gov (United States)

    Roy, Arpan Datta; Dey, Dibyendu; Saha, Jaba; Chakraborty, Santanu; Bhattacharjee, D; Hussain, Syed Arshad

    2015-02-05

    This communication reports our investigations on the Fluorescence Resonance Energy Transfer (FRET) between two laser dyes Acriflavine and Rhodamine B in absence and presence of DNA at different pH. It has been observed that energy transfer efficiency is largely affected by the presence of DNA as well as the pH of the system. It is well known that with increase in pH, DNA conformation changes from double stranded to single stranded (denaturation) and finally form random coil. Based on our experimental results two different types of molecular logic gates namely, XOR and OR logic have been demonstrated which can be used to have an idea about DNA conformation in solution. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Role of solution conformation and flexibility of short peptide ligands that bind to the p56(lck) SH2 domain

    NARCIS (Netherlands)

    Dekker, Frank J; de Mol, Nico J; Bultinck, Patrick; Kemmink, Johan; Hilbers, Hans W; Liskamp, Rob M J; Dekker, Frank

    2003-01-01

    A general approach in drug design is making ligands more rigid in order to avoid loss in conformational entropy (deltaS(conf)) upon receptor binding. We hypothesized that in the high affinity binding of pYEEI peptide ligands to the p56(lck) SH2 domain this loss in deltaS(conf) might be diminished

  18. Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

    Science.gov (United States)

    Andersen, Ole Juul; Grouleff, Julie; Needham, Perri; Walker, Ross C; Jensen, Frank

    2015-11-19

    Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.

  19. Density functional theory studies of MTSL nitroxide side chain conformations attached to an activation loop

    CERN Document Server

    Concilio, Maria Grazia; Bayliss, Richard; Burgess, Selena G

    2016-01-01

    A quantum-mechanical (QM) method rooted on density functional theory (DFT) has been employed to determine conformations of the methane-thiosulfonate spin label (MTSL) attached to a fragment extracted from the activation loop of Aurora-A kinase. The features of the calculated energy surface revealed low energy barriers between isoenergetic minima and the system could be described in a population of 76 rotamers that can be also considered for other systems since it was found that the X3, X4 and X5 do not depend on the previous two dihedral angles. Conformational states obtained were seen to comparable to those obtained in the {\\alpha}-helix systems studied previously, indicating that the protein backbone does not affect the torsional profiles significantly and suggesting the possibility to use determined conformations for other protein systems for further modelling studies.

  20. Quartz crystal microbalance study of ionic strength and pH-dependent polymer conformation and protein adsorption/desorption on PAA, PEO, and mixed PEO/PAA brushes.

    Science.gov (United States)

    Delcroix, M F; Demoustier-Champagne, S; Dupont-Gillain, C C

    2014-01-14

    The conformation of polymer chains grafted on a substrate influences protein adsorption. In a previous study, adsorption/desorption of albumin was demonstrated on mixed poly(ethylene oxide) (PEO)/poly(acrylic acid) (PAA) brushes, triggered by solutions of adequate pH and ionic strength (I). In the present work, homolayers of PEO or PAA are submitted to saline solutions with pH from 3 to 9 and I from 10(-5) to 10(-1) M, and their conformation is evaluated in real time using quartz crystal microbalance with dissipation monitoring (QCM-D). Shrinkage/swelling of PAA chains and hydration and salt condensation in the brush are evidenced. The adsorption of human serum albumin (HSA) onto such brushes is also monitored in these different saline solutions, leading to a deep understanding of the influence of polymer chain conformation, modulated by pH and I, on protein adsorption. A detailed model of the conformation of PEO/PAA mixed brushes depending on pH and I is then proposed, providing a rationale for the identification of conditions for the successive adsorption and desorption of proteins on such mixed brushes. The adsorption/desorption of albumin on PEO/PAA is demonstrated using QCM-D.

  1. Spontaneous breaking of conformal invariance in theories of conformally coupled matter and Weyl gravity

    Energy Technology Data Exchange (ETDEWEB)

    Edery, A [Department of Physics, Bishop' s University, Lennoxville, QC J1M 1Z7 (Canada); Fabbri, Luca [Theory Group, INFN Section of Bologna, Department of physics, University of Bologna, Via Irnerio 46, C.A.P. 40126, Bologna (Italy); Paranjape, M B [Groupe de physique des particules, Universite de Montreal, C.P. 6128, succ. centre-ville, Montreal, QC H3C 3J7 (Canada)

    2006-11-21

    We study the theory of Weyl conformal gravity with matter degrees of freedom in a conformally invariant interaction. Specifically, we consider a triplet of scalar fields and SO(3) non-Abelian gauge fields, i.e. the Georgi-Glashow model conformally coupled to Weyl gravity. We show that the equations of motion admit solutions spontaneously breaking the conformal symmetry and the gauge symmetry, providing a mechanism for supplying a scale in the theory. The vacuum solution corresponds to anti-de Sitter spacetime, while localized soliton solutions correspond to magnetic monopoles in asymptotically anti-de Sitter spacetime. This mechanism strengthens the reasons for considering conformally invariant matter-gravity theory, which has shown promising indications concerning the problem of missing matter in galactic rotation curves.

  2. Conformational Studies of ε- CBz- L- Lysine and L- Valine Block Copolypeptides

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    2010-01-01

    Full Text Available Conformational studies of ε-CBz-L-lysine and L-valine block copoylpeptides using x- ray diffraction and CD spectra are described. The block copolypeptides contain valine block in the center and on both side of the valine are ε-CBz-L-lysine blocks. The conformation of the copolypeptides changes with increases in the chain length of ε- CBz-L- lysine blocks. When length of ε- CBZ- L- lysine blocks is 9, the block copolypeptide has exclusive beta sheet structure. With the increase in chain length of ε-CBz-L-lysine blocks from 9 to 14, the block copolypeptide shows presence of both alpha helix and beta sheet components. With further increase in chain length of ε- CBz- L- lysine blocks, the beta sheet component disappears and block copolypeptides exhibits exclusive α -helix conformation.

  3. Exploring the conformational landscape of menthol, menthone, and isomenthone: A microwave study

    Directory of Open Access Journals (Sweden)

    David eSchmitz

    2015-03-01

    Full Text Available The rotational spectra of the monoterpenoids menthol, menthone, and isomenthone are reportedin the frequency range of 2−8.5GHz, obtained with broadband Fourier-transform microwave spectroscopy.For menthol only one conformation was identified under the cold conditions of the molecularjet, whereas three conformations were observed for menthone and one for isomenthone. Theconformational space of the different molecules was extensively studied using quantum chemicalcalculations, and the results were compared with molecular parameters obtained by the measurements.Finally, a computer program is presented, which was developed to automatically identifydifferent species in a dense broadband microwave spectrum using calculated ab initio rotationalconstants as input.

  4. Clinical Studies on conformal radiotherapy combined with epidermal ...

    African Journals Online (AJOL)

    study commenced, and pathological specimens. (including surgical pathological tissues and sections, lung puncture or biopsy specimens, sputum basal cell detection, lymph node or other metastasis puncture or biopsy specimens, fiber optic bronchoscope biopsy or brush biopsy, or lavage fluid basal cell detection, etc). 2.

  5. Conformity and Order: A Grammar Handbook Case Study.

    Science.gov (United States)

    Merola, Nicole

    1998-01-01

    Presents a case study, which attends closely to the 1941, 1946 version of the "Harbrace College Handbook" (HCH) and reads its exercises through a Foucauldian lens. Suggests that the exercises contained within the HCH discipline not only the student as writer, but also the student as thinker. (SC)

  6. The Conformational Landscape of L-Threonine Matrix Isolation Infrared and {AB-INITIO Studies

    Science.gov (United States)

    Dubey, Pankaj; Mukhopadhyay, Anamika; Viswanathan, K. S.

    2017-06-01

    Amino acids, containing hydroxy side chains such as L-threonine and tyrosine play an important role in molecular recognition, such as in the docking of propofol, which is a commonly used anaesthetic. A rich conformational landscape of these amino acids makes them interesting candidates in the study of intra and intermolecular interactions. In this work, the conformational landscape of L-threonine was studied, as it can be expected to serve as a basis for understanding structure and functions of polypeptides and other biomolecules. The matrix isolation technique (MI) coupled with a high temperature effusive molecular beam (EMB) nozzle was used to trap conformers of amino acid, which were then characterized using FTIR spectroscopy. The usefulness of MI-EMB-FTIR spectroscopy is that it can trap structures corresponding to the local minima along with the global minimum and hence allows for a better exploration of the potential energy surface. A major challenge in conformational analysis of amino acids using matrix isolation FTIR arises from its non-volatile nature. A home built heating system which was mounted close to the cryotip, was used to evaporate the non-volatile amino acids. Our infrared spectra show that three conformations were trapped in the matrix. Experimental results were supported by {ab-initio calculations performed using the CCSD(T), MP2 and M06-2X methods together with 6-311++G(d,p) and aug/cc-pVDZ basis sets. The side chains of the amino acids appeared to have an influence on the preferential stabilisation of a particular backbone structure of amino acids. Factors such as entropy, anomeric effect and intramolecular H-bonding were also found to play an important role in determining conformal preferences, which will be discussed.

  7. A new study of Brazilian concrete strength conformance

    Directory of Open Access Journals (Sweden)

    W.C. Santiago

    Full Text Available ABSTRACT This paper presents a new evaluation of the strength compliance of concretes produced in Brazil. It is based on experimental results of over twenty-seven thousand concrete samples from different parts of the country. Results show that a significant part of Brazilian concrete do not reach the characteristic strength (fck specified in design, and the percentage of nonconforming samples tend to be higher than 5%. This study also reveals the concrete produced in the South and Midwest regions have less variability than the ones produced in the other regions of the country. These results emphasize the importance of a rigorous control in manufacturing and reception of concretes in order to reduce the nonconforming cases.

  8. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

    Directory of Open Access Journals (Sweden)

    Keskin Ozlem

    2007-05-01

    Full Text Available Abstract Background How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.

  9. The powerful high pressure tool for protein conformational studies

    Directory of Open Access Journals (Sweden)

    Marchal S.

    2005-01-01

    Full Text Available The pressure behavior of proteins may be summarized as a the pressure-induced disordering of their structures. This thermodynamic parameter has effects on proteins that are similar but not identical to those induced by temperature, the other thermodynamic parameter. Of particular importance are the intermolecular interactions that follow partial protein unfolding and that give rise to the formation of fibrils. Because some proteins do not form fibrils under pressure, these observations can be related to the shape of the stability diagram. Weak interactions which are differently affected by hydrostatic pressure or temperature play a determinant role in protein stability. Pressure acts on the 2º, 3º and 4º structures of proteins which are maintained by electrostatic and hydrophobic interactions and by hydrogen bonds. We present some typical examples of how pressure affects the tertiary structure of proteins (the case of prion proteins, induces unfolding (ataxin, is a convenient tool to study enzyme dissociation (enolase, and provides arguments to understand the role of the partial volume of an enzyme (butyrylcholinesterase. This approach may have important implications for the understanding of the basic mechanism of protein diseases and for the development of preventive and therapeutic measures.

  10. Dynamical spacetimes in conformal gravity

    National Research Council Canada - National Science Library

    Hongsheng Zhang; Yi Zhang; Xin-Zhou Li

    2017-01-01

    The conformal gravity remarkably boosts our prehension of gravity theories. We find a series of dynamical solutions in the W2-conformal gravity, including generalized Schwarzschild–Friedmann–Robertson–Walker (GSFRW...

  11. Binding of Cimetidine to Balb/C Mouse Liver Catalase; Kinetics and Conformational Studies.

    Science.gov (United States)

    Jahangirvand, Mahboubeh; Minai-Tehrani, Dariush; Yazdi, Fatemeh; Minai-Tehrani, Arash; Razmi, Nematollah

    2016-01-01

    Catalase is responsible for converting hydrogen peroxide (H2O2) into water and oxygen in cells. This enzyme has high affinity for hydrogen peroxide and can protect the cells from oxidative stress damage. Catalase is a tetramer protein and each monomer contains a heme group. Cimetidine is a histamine H2 receptor blocker which inhibits acid release from stomach and is used for gasterointestinal diseases. In this research, effect of cimetidine on the activity of liver catalase was studied and the kinetic parameters of this enzyme and its conformational changes were investigated. Cell free extract of mouse liver was used for the catalase assay. The activity of the catalase was detected in the absence and presence of cimetidine by monitoring hydrogen peroxide reduction absorbance at 240 nm. The purified enzyme was used for conformational studies by Fluorescence spectrophotometry. The data showed that cimetidine could inhibit the enzyme in a non-competitive manner. Ki and IC50 values of the drug were determined to be about 0.75 and 0.85 uM, respectively. The Arrhenius plot showed that activation energy was 6.68 and 4.77 kJ/mol in the presence and absence of the drug, respectively. Fluorescence spectrophotometry revealed that the binding of cimetidine to the purified enzyme induced hyperchromicity and red shift which determined the conformational change on the enzyme. Cimetidine could non-competitively inhibit the liver catalase with high affinity. Binding of cimetidine to the enzyme induced conformational alteration in the enzyme.

  12. Genome-wide association study of conformation and milk yield in mixed-breed dairy goats.

    Science.gov (United States)

    Mucha, Sebastian; Mrode, Raphael; Coffey, Mike; Kizilaslan, Mehmet; Desire, Suzanne; Conington, Joanne

    2017-12-28

    Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic

  13. NMR studies of differences in the conformations and dynamics of ligand complexes formed with mutant dihydrofolate reductases

    Energy Technology Data Exchange (ETDEWEB)

    Birdsall, B.; Andrews, J.; Ostler, G.; Tendler, S.J.B.; Feeney, J.; Roberts, G.C.K.; Davies, R.W.; Cheung, H.T.A. (National Institute for Medical Research, London (England))

    1989-02-07

    Two mutants of Lactobacillus casei dihydrofolate reductase, Trp 21 {yields} Leu and Asp 26 {yields} Glu, have been prepared by using site-directed mutagenesis methods, and their ligand binding and structural properties have been compared with those of the wild-type enzyme. {sup 1}H, {sup 13}C, and {sup 31}P NMR studies have been carried out to characterize the structural changes in the complexes of the mutant and wild-type enzymes. Replacement of the conserved Trp 21 by a Leu residue causes a decrease in activity of the enzyme and reduces the NADPH binding constant by a factor of 400. The binding of substrates and substrate analogues is only slightly affected. {sup 1}H NMR studies of the Trp 21 {yields} Leu enzyme complexes have confirmed the original resonance assignments for Trp 21. In complexes formed with methotrexate and the mutant enzyme, the results indicate some small changes in conformation occurring as much as 14 {angstrom} away from the site of substitution. For the enzyme-NADPH complexes, the chemical shifts of nuclei in the bound coenzyme indicate that the nicotinamide ring binds differently in complexes with the mutant and the wild-type enzyme. There are complexes where the wild-type enzyme has been shown to exist in solution as a mixture of conformations, and studies on the corresponding complexes with the Trp 21 {yields} Leu mutant indicate that the delicately poised equilibria can be perturbed. Some conformational adjustments are required to allow the carboxylate of Glu 26 to bind effectively to the N1 proton of inhibitors such as methotrexate and trimethoprim.

  14. Conformational study of protein interactions with hydrogen-passivated amorphous silicon surfaces: Effect of pH

    Science.gov (United States)

    Brahmi, Yamina; Filali, Larbi; Sib, Jamal Dine; Bouhekka, Ahmed; Benlakehal, Djamel; Bouizem, Yahya; Kebab, Aissa; Chahed, Larbi

    2017-11-01

    The adsorption of Bovine Serum Albumin (BSA) proteins on amorphous silicon (a-Si) surfaces was studied with respect to solution pH. Thin films of a-Si were deposited using radio-frequency magnetron sputtering at room temperature and then treated in a hydrogen ambient to form a hydrogenated a-Si surface layer (a-Si:H). The interactions of the as-deposited and hydrogenated surfaces with the proteins at neutral, acidic, and basic environments was probed by means of Fourier transform infrared attenuated total reflection (FTIR-ATR) spectroscopy, Spectroscopic Ellipsometry (SE), and Atomic Force Microscopy (AFM), to study the influence of the charge of proteins on their adsorption and conformation on the a-Si:H surface, compared with the a-Si surface. The results show that the charge of the proteins has a significant effect on their interactions with these two substrates but in dissimilar ways. For the as-deposited substrate, these interactions are predictably coulombic since the surface is charged. For the hydrogenated substrate, the adsorption of the proteins depends on their conformation which is heavily affected by pH, and the size of their footprint (adsorption mode) on the surface.

  15. Elucidation of IP6 and Heparin Interaction Sites and Conformational Changes in Arrestin-1 by Solution NMR†

    Science.gov (United States)

    Zhuang, Tiandi; Vishnivetskiy, Sergey A.; Gurevich, Vsevolod V.; Sanders, Charles R.

    2010-01-01

    Arrestins specifically bind activated and phosphorylated G protein-coupled receptors, and orchestrate both receptor trafficking, and channel signaling to G protein-independent pathways via direct interactions with numerous non-receptor partners. Here we report the first successful use of solution NMR to map the binding sites in arrestin-1 (visual arrestin) for two polyanionic compounds that mimic phosphorylated light-activated rhodopsin: inositol hexaphosphate (IP6) and heparin. This yielded a more complete identification of residues involved in the binding with these ligands than has previously been feasible. IP6 and heparin appear to bind to the same site on arrestin-1, centered on a positively charged region in the N-domain. We present the first direct evidence that both IP6 and heparin induced a complete release of the arrestin C-tail. These observations provide novel insight into the nature of arrestin transition from basal to active state and demonstrate the potential of NMR-based methods in the study of protein-protein interactions involving members of the arrestin family. PMID:21050017

  16. From static to rotating to conformal static solutions: rotating imperfect fluid wormholes with(out) electric or magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Azreg-Ainou, Mustapha [Baskent University, Department of Mathematics, Ankara (Turkey)

    2014-05-15

    We derive a shortcut stationary metric formula for generating imperfect fluid rotating solutions, in Boyer-Lindquist coordinates, from spherically symmetric static ones. We explore the properties of the curvature scalar and stress-energy tensor for all types of rotating regular solutions we can generate without restricting ourselves to specific examples of regular solutions (regular black holes or wormholes). We show through examples how it is generally possible to generate an imperfect fluid regular rotating solution via radial coordinate transformations. We derive rotating wormholes that are modeled as imperfect fluids and discuss their physical properties. These are independent on the way the stress-energy tensor is interpreted. A solution modeling an imperfect fluid rotating loop black hole is briefly discussed. We then specialize to the recently discussed stable exotic dust Ellis wormhole as emerged in a source-free radial electric or magnetic field, and we generate its, conjecturally stable, rotating counterpart. This turns out to be an exotic imperfect fluid wormhole, and we determine the stress-energy tensor of both the imperfect fluid and the electric or magnetic field. (orig.)

  17. DFT studies of the conformation and relative energies of alpha-maltotetraose (DP-4): An amylose fragment at atomic resolution

    Science.gov (United States)

    DFT optimization studies of more than one hundred conformations of a-maltotetraose have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments of predominately 4C1 chair residues include tightly bent forms, helix, band-flips, kinks, boat, and some 1C4 conformers. The three do...

  18. Study of spontaneously broken conformal symmetry in curved space-times

    Energy Technology Data Exchange (ETDEWEB)

    Janson, M.M.

    1977-05-01

    Spontaneous breakdown of Weyl invariance (local scale invariance) in a conformally-invariant extension of a gauge model for weak and electromagnetic interactions is considered. The existence of an asymmetric vacuum for the Higgs field, phi, is seen to depend on the space-time structure via the Gursey-Penrose term, approximately phi/sup +/phi R, in the action. (R denotes the scalar curvature.) The effects of a prescribed space-time structure on spontaneously broken Weyl invariance is investigated. In a cosmological space-time, it is found that initially, in the primordial fireball, the symmetry must hold exactly. Spontaneous symmetry breaking (SSB) develops as the universe expands and cools. Consequences of this model include a dependence of G/sub F/, the effective weak interaction coupling strength, on ''cosmic time.'' It is seen to decrease monotonically; in the present epoch (G/sub F//G/sub F/)/sub TODAY/ approximately less than 10/sup -10/ (year)/sup -1/. The effects of the Schwarzschild geometry on SSB are explored. In the interior of a neutron star the Higgs vacuum expectation value, and consequently G/sub F/, is found to have a radial dependence. The magnitude of this variation does not warrant revision of present models of neutron star structures. Another perspective on the problem considered a theory of gravitation (conformal relativity) to be incorporated in the conformally invariant gauge model of weak and electromagnetic interactions. If SSB develops, the vacuum gravitational field equations are the Einstein field equations with a cosmological constant. The stability of the asymmetric vacuum solution is investigated to ascertain whether SSB can occur.

  19. Electronically Rich N-Substituted Tetrahydroisoquinoline 3-Carboxylic Acid Esters: Concise Synthesis and Conformational Studies.

    Science.gov (United States)

    Al-Horani, Rami A; Desai, Umesh R

    2012-02-25

    Recent work in our laboratory has shown that the highly substituted, electronically rich 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (THIQ3CA) scaffold is a key building block for a novel class of promising anticoagulants (Al-Horani et al. J. Med. Chem.2011, 54, 6125-6138). The synthesis of THIQ3CA analogs, especially containing specific, electronically rich substituents, has been a challenge and essentially no efficient methods have been reported in the literature. We describe three complementary, glycine donor-based strategies for high yielding synthesis of highly substituted, electronically rich THIQ3CA esters. Three glycine donors studied herein include hydantoin 1, (±)-Boc-α-phosphonoglycine trimethyl ester 2 and (±)-Z-α-phosphonoglycine trimethyl ester 3. Although the synthesis of THIQ3CA analogs could be achieved using either of the three, an optimal, high yielding approach for the desired THIQ3CA esters was best achieved using 3 in three mild, efficient steps. Using this approach, a focused library of advanced N-arylacyl, N-arylalkyl, and bis-THIQ3CA analogs was synthesized. Variable temperature and solvent-dependent NMR chemical shift studies indicated the presence of two major conformational rotamers in 3:1 proportion for N-arylacyl-THIQ3CA analogs, which were separated by a high kinetic barrier of ~17 kcal/mol. In contrast, N-arylalkyl and bis-THIQ3CA variants displayed no rotamerism, which implicates restricted rotation around the amide bond as the origin for high-barrier conformational interconversion. This phenomenon is of major significance because structure-based drug design typically utilizes only one conformation. Overall, the work presents fundamental studies on the synthesis and conformational properties of highly substituted, electronically rich THIQ3CA analogs.

  20. Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

    DEFF Research Database (Denmark)

    Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter

    2013-01-01

    In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously rep...

  1. Single-molecule fluorescence polarization study of conformational change in archaeal group II chaperonin.

    Directory of Open Access Journals (Sweden)

    Ryo Iizuka

    Full Text Available Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which forms a built-in lid on the central cavity. Although many studies on the change in lid conformation coupled to the binding and hydrolysis of nucleotides have been conducted, the molecular mechanism of lid closure remains poorly understood. Here, we performed a single-molecule polarization modulation to probe the rotation of the helical protrusion of a chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1. We detected approximately 35° rotation of the helical protrusion immediately after photorelease of ATP. The result suggests that the conformational change from the open lid to the closed lid state is responsible for the approximately 35° rotation of the helical protrusion.

  2. Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study.

    Directory of Open Access Journals (Sweden)

    Tatyana G Karabencheva-Christova

    Full Text Available Circular Dichroism (CD spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII, with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.

  3. Conformal Nets II: Conformal Blocks

    Science.gov (United States)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-08-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  4. Study of TATP: stability of TATP solutions.

    Science.gov (United States)

    Pachman, Jiri; Matyáš, Robert

    2011-04-15

    Stability of raw TATP (3,3,6,6,9,9-hexamethyl-1,2,4,5,7,8-hexoxonane) samples in solutions of common solvents was studied to highlight problems faced by forensic labs in identification and analysis of organic peroxide samples. The TATP samples were prepared by reaction of acetone and hydrogen peroxide (30%) with the aid of following catalysts: hydrochloric, sulfuric, nitric, perchloric and methanesulfonic acid. Acetone, acetonitrile, methanol and acetonitrile/water solutions of TATP samples were prepared and stored at 50°C. Various degrees of stability were observed for particular combination of catalyst and solvent ranging from totally unstable (catalyst-H(2)SO(4)/any solvent) to very stable (catalyst-HCl/solvent acetonitrile). Purification of crude TATP by re-crystallization results in product stable in all investigated solvents. Stability of solution prepared from re-crystallized DADP (3,3,6,6-tetramethyl-1,2,4,5-tetroxane) was found to be on the same level as the stability of solution of re-crystallized TATP. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  5. The importance of being Aib. Aggregation and self-assembly studies on conformationally constrained oligopeptides.

    Science.gov (United States)

    Venanzi, Mariano; Gatto, Emanuela; Formaggio, Fernando; Toniolo, Claudio

    2017-02-01

    The role of the conformationally constrained α-aminoisobutyric acid (Aib) residue in the aggregation and self-assembly properties of oligopeptides is discussed, critically reviewing our recent work in the field. In this connection, three significant case studies are presented: (i) aggregation propensity of Aib homo-oligopeptides of different length; (ii) perturbation of the conformational and aggregation properties of Ala-based pentapeptides by a single Aib versus Ala substitution; and (iii) build up of self-assembled monolayers formed by Aib homo-hexapeptide building blocks. The peptides investigated were all functionalized by a fluorescent probe, that is, a naphthyl group in the first case-study and a pyrenyl group in the other two, with the aim at applying optical spectroscopy techniques and evaluating the relevance of aromatic interactions in the aggregation process. Microscopy techniques at nanometric resolution and results of molecular dynamics simulations are also presented to analyze how the conformational properties of the peptide building blocks would affect the morphology of the peptide aggregates from the nanoscale to the mesoscale. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

  6. Computational studies on sirtuins from Trypanosoma cruzi: structures, conformations and interactions with phytochemicals.

    Science.gov (United States)

    Sacconnay, Lionel; Angleviel, Melissa; Randazzo, Giuseppe Marco; Queiroz, Marcos Marçal Ferreira; Queiroz, Emerson Ferreira; Wolfender, Jean-Luc; Carrupt, Pierre-Alain; Nurisso, Alessandra

    2014-02-01

    The silent-information regulator 2 proteins, otherwise called sirtuins, are currently considered as emerging anti-parasitic targets. Nicotinamide, a pan-sirtuin inhibitor, is known to cause kinetoplast alterations and the arrested growth of T. cruzi, the protozoan responsible for Chagas disease. These observations suggested that sirtuins from this parasite (TcSir2rp1 and TcSir2rp3) could play an important role in the regulation of the parasitic cell cycle. Thus, their inhibition could be exploited for the development of novel anti-trypanosomal compounds. Homology modeling was used to determine the three-dimensional features of the sirtuin TcSir2rp1 from T. cruzi. The apo-form of human SIRT2 and the same structure solved in complex with its co-substrate NAD(+) allowed the modeling of TcSir2rp1 in the open and closed conformational states. Molecular docking studies were then carried out. A library composed of fifty natural and diverse compounds that are known to be active against this parasite, was established based on the literature and virtually screened against TcSir2rp1 and TcSir2rp3, which was previously modeled by our group. In this study, two conformational states of TcSir2rp1 were described for the first time. The molecular docking results of compounds capable of binding sirtuins proved to be meaningful when the closed conformation of the protein was taken into account for calculations. This specific conformation was then used for the virtual screening of antritrypanosomal phytochemicals against TcSir2rp1 and TcSir2rp3. The calculations identified a limited number of scaffolds extracted from Vismia orientalis, Cussonia zimmermannii, Amomum aculeatum and Anacardium occidentale that potentially interact with both proteins. The study provided reliable models for future structure-based drug design projects concerning sirtuins from T. cruzi. Molecular docking studies highlighted not only the advantages of performing in silico interaction studies on their closed

  7. Computational studies on sirtuins from Trypanosoma cruzi: structures, conformations and interactions with phytochemicals.

    Directory of Open Access Journals (Sweden)

    Lionel Sacconnay

    2014-02-01

    Full Text Available BACKGROUND: The silent-information regulator 2 proteins, otherwise called sirtuins, are currently considered as emerging anti-parasitic targets. Nicotinamide, a pan-sirtuin inhibitor, is known to cause kinetoplast alterations and the arrested growth of T. cruzi, the protozoan responsible for Chagas disease. These observations suggested that sirtuins from this parasite (TcSir2rp1 and TcSir2rp3 could play an important role in the regulation of the parasitic cell cycle. Thus, their inhibition could be exploited for the development of novel anti-trypanosomal compounds. METHODS: Homology modeling was used to determine the three-dimensional features of the sirtuin TcSir2rp1 from T. cruzi. The apo-form of human SIRT2 and the same structure solved in complex with its co-substrate NAD(+ allowed the modeling of TcSir2rp1 in the open and closed conformational states. Molecular docking studies were then carried out. A library composed of fifty natural and diverse compounds that are known to be active against this parasite, was established based on the literature and virtually screened against TcSir2rp1 and TcSir2rp3, which was previously modeled by our group. RESULTS: In this study, two conformational states of TcSir2rp1 were described for the first time. The molecular docking results of compounds capable of binding sirtuins proved to be meaningful when the closed conformation of the protein was taken into account for calculations. This specific conformation was then used for the virtual screening of antritrypanosomal phytochemicals against TcSir2rp1 and TcSir2rp3. The calculations identified a limited number of scaffolds extracted from Vismia orientalis, Cussonia zimmermannii, Amomum aculeatum and Anacardium occidentale that potentially interact with both proteins. CONCLUSIONS: The study provided reliable models for future structure-based drug design projects concerning sirtuins from T. cruzi. Molecular docking studies highlighted not only the advantages

  8. Photoreactive “Nanorulers” Detect a Novel Conformation of Full length HDAC3-SMRT Complex in Solution

    Science.gov (United States)

    Abdelkarim, Hazem; Brunsteiner, Michael; Neelarapu, Raghupathi; Bai, He; Madriaga, Antonett; van Breemen, Richard B.; Blond, Sylvie Y.; Gaponenko, Vadim; Petukhov, Pavel A.

    2013-01-01

    Histone deacetylase 3 (HDAC3) is a promising epigenetic drug target for multiple therapeutic applications. Direct interaction between the Deacetylase Activating Domain of the silencing mediator for retinoid or thyroid hormone receptors (SMRT-DAD) is required for activation of enzymatic activity of HDAC3. The structure of this complex and the nature of interactions with HDAC inhibitors in solution are unknown. Using novel photoreactive HDAC probes – “nanorulers”, we determined the distance between the catalytic site of the full-length HDAC3 and SMRT-DAD in solution at physiologically relevant conditions and found it to be substantially different from that predicted by the X-ray model with a Δ379-428aa truncated HDAC3. Further experiments indicated that in solution this distance might change in response to chemical stimuli, while the enzymatic activity remained unaffected. These observations were further validated by Saturation Transfer Difference (STD) NMR experiments. We propose that the observed changes in the distance are an important part of the histone code that remains to be explored. Mapping direct interactions and distances between macromolecules with such “nanorulers” as a function of cellular events facilitates better understanding of basic biology and ways for its manipulation in cell and tissue specific manner. PMID:24010878

  9. Finite-element solution to multidimensional multisource electromagnetic problems in the frequency domain using non-conforming meshes

    Science.gov (United States)

    Soloveichik, Yury G.; Persova, Marina G.; Domnikov, Petr A.; Koshkina, Yulia I.; Vagin, Denis V.

    2018-03-01

    We propose an approach to solving multisource induction logging problems in multidimensional media. According to the type of induction logging tools, the measurements are performed in the frequency range of 10 kHz to 14 MHz, transmitter-receiver offsets vary in the range of 0.5-8 m or more, and the trajectory length is up to 1 km. For calculating the total field, the primary-secondary field approach is used. The secondary field is calculated with the use of the finite-element method (FEM), irregular non-conforming meshes with local refinements and a direct solver. The approach to constructing basis functions with the continuous tangential components (from Hcurl(Ω)) on the non-conforming meshes from the standard shape vector functions is developed. On the basis of this method, the algorithm of generating global matrices and a vector of the finite-element equation system is proposed. We also propose the method of grouping the logging tool positions, which makes it possible to significantly increase the computational effectiveness. This is achieved due to the compromise between the possibility of using the 1-D background medium, which is very similar to the investigated multidimensional medium for a small group, and the decrease in the number of the finite-element matrix factorizations with the increasing number of tool positions in one group. For calculating the primary field, we propose the method based on the use of FEM. This method is highly effective when the 1-D field is required to be calculated at a great number of points. The use of this method significantly increases the effectiveness of the primary-secondary field approach. The proposed approach makes it possible to perform modelling both in the 2.5-D case (i.e. without taking into account a borehole and/or invasion zone effect) and the 3-D case (i.e. for models with a borehole and invasion zone). The accuracy of numerical results obtained with the use of the proposed approach is compared with the one

  10. Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5.

    Science.gov (United States)

    Garza-Garcia, Acely; Esposito, Diego; Rieping, Wolfgang; Harris, Richard; Briggs, Cherry; Brown, Marion H; Driscoll, Paul C

    2008-04-18

    The lymphocyte receptor CD5 influences cell activation by modifying the strength of the intracellular response initiated by antigen engagement. Regulation through CD5 involves the interaction of one or more of its three scavenger receptor cysteine-rich domains present in the extracellular region. Here, we present the 3D solution structure of a non-glycosylated double mutant of the N-terminal domain of human CD5 expressed in Escherichia coli (eCD5d1m), which has enhanced solubility compared to the non-glycosylated wild-type (eCD5d1). In common with a glycosylated form expressed in Pichia pastoris, the [(15)N,(1)H]-correlation spectra of both eCD5d1 and eCD5d1m exhibit non-uniform temperature-dependent signal intensities, indicating extensive conformational fluctuations on the micro-millisecond timescale. Although approximately one half of the signals expected for the domain are absent at 298 K, essentially complete resonance assignments and a solution structure could be obtained at 318 K. Because of the sparse nature of the experimental restraint data and the potentially important contribution of conformational exchange to the nuclear Overhauser effect peak intensity, we applied inferential structure determination to calculate the eCD5d1m structure. The inferential structure determination ensemble has similar features to that obtained by traditional simulated annealing methods, but displays superior definition and structural quality. The eCD5d1m structure is similar to other members of the scavenger receptor cysteine-rich superfamily, but the position of the lone alpha helix differs due to interactions with the unique N-terminal region of the domain. The availability of an experimentally tractable form of CD5d1, together with its 3D structure, provides new tools for further investigation of its function within intact CD5.

  11. PEGylation of proteins in organic solution: a case study for interferon beta-1b.

    Science.gov (United States)

    Peng, Fei; Wang, Yinjue; Sun, Lijing; Liu, Yongdong; Hu, Tao; Zhang, Guifeng; Ma, Guanghui; Su, Zhiguo

    2012-09-19

    Conventional protein PEGylation is carried out in aqueous solution. However, some hydrophobic proteins seem to be stable in organic solution. In this study, a novel approach of PEGylating IFN-β-1b in an organic solution of 2-butanol (2-BuOH) was investigated. Compared with protein PEGylation in aqueous solution, the overall modification yields increased more than 37%, while the yield of mono-PEGylated products could be increased by 36%. Furthermore, the PEGylated IFN-β-1b, which was obtained in organic solution, demonstrated 18% more antiviral potency than those derived from aqueous solution. The PEGylation step could be directly connected to the previous protein separation step for process integration. Dynamic light scattering (DLS) and atomic force microscope (AFM) analysis revealed that IFN-β-1b formed aggregates both in water and in 2-BuOH solutions. However, the aggregates were much smaller and more homogeneous in 2-BuOH than those in aqueous solution, thereby providing larger solvent accessible protein surfaces, which resulted in a more productive PEGylation process. In addition, the results of circular dichroism (CD), fluorescence spectra, and peptide mapping suggested that the increased bioactivity came from the difference in PEGylation site distribution due to solution environment that induced conformational discrepancy. The results of this study show that PEGylation of IFN-β-1b in organic solution is a facile and efficient process, which might find applications for other hydrophobic proteins.

  12. Conformal house

    DEFF Research Database (Denmark)

    Ryttov, Thomas Aaby; Sannino, Francesco

    2010-01-01

    fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions...... at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms...

  13. Statistical Study to Check the Conformity of Aggregate in Kirkuk City to Requirement of Iraqi Specification

    Directory of Open Access Journals (Sweden)

    Ammar Saleem Khazaal

    2018-01-01

    Full Text Available This research reviews a statistical study to check the conformity of aggregates (Coarse and Fine was used in Kirkuk city to the requirements of the Iraqi specifications. The data of sieve analysis (215 samples of aggregates being obtained from of National Central Construction Laboratory and Technical College Construction Laboratory in Kirkuk city have analyzed using the statistical program SAS. The results showed that 5%, 17%, and 18% of fine aggregate samples are passing sieve sizes 10 mm, 4.75 mm, and 2.36 mm, respectively, which were less than the minimum limit allowed by the Iraqi specifications for each sieve. The percentages passing sieve sizes 1.18mm, 600micrometers, and 300micrometers were more than the upper limit of specification by 5%, 20%, and 30% respectively. The samples were passing sieve sizes 1.18mm, and 600micrometers less than the minimum limit of specification by 17%, and 4%, respectively. The results showed that the deviation in a sieve size of 150 micrometers for the upper limit of the specification performs 2% of the total number of samples. For Coarse aggregate, the samples passing sieves size 37.5mm and 20mm were comforting the Iraqi specifications by 100% and 83% respectively, it has found that the samples were passing sieve sizes 10 mm was 5% was more than the higher limit of Iraqi specifications, and 27% of these samples were less than the minimum limit, whereas sample passing sieve size 5mm was 1% which is more than the upper limit of the Iraqi specification. As a result of statistical analysis of data for fine aggregate, it has found that the samples were passing sieve sizes 10 mm, 2.36 mm, 1.18 mm and 150micrometers conforming from statistical point of view the Iraqi specifications, whereas the samples were passing sieve sizes 4.75 mm, 600micrometers and 300 micrometers didn’t conform. Statistical analysis of the results of the coarse aggregates also showed that conforming to sieve sizes of 37.5 mm and 20 mm and

  14. Comparative structural and vibrational study of the four lowest energy conformers of serotonin

    Science.gov (United States)

    Jha, Omkant; Yadav, T. K.; Yadav, R. A.

    2017-02-01

    A computational investigation of all possible lowest energy conformers of serotonin was carried out at the B3LYP/6-311 ++G** level. Out of the 14 possible lowest energy conformers, the first 4 conformers were investigated thoroughly for the optimized geometries, fundamental frequencies, the potential energy distributions, APT and natural charges, natural bond orbital (NBO) analysis, MEP, Contour map, total density array, HOMO, LUMO energies. The second third and fourth conformers are energetically at higher temperatures of 78, 94 and 312 K respectively with respect to the first one. Bond angles and bond lengths do not show significant variations while the dihedral angles vary significantly in going from one conformer to the other. Some of the vibrational modes of the indole moiety are conformation dependent to some extent whereas most of the normal modes of vibration of amino-ethyl side chain vary significantly in going from one conformer to conformer. The MEP for the four conformers suggested that the sites of the maximum positive and negative ESP change on changing the conformation. The charges at some atomic sites also change significantly from conformer to conformer.

  15. Conformational relaxation dynamics of a poly(N-isopropylacrylamide) aqueous solution measured using the laser temperature jump transient grating method.

    Science.gov (United States)

    Inoue, Hayato; Katayama, Kenji; Iwai, Kaoru; Miura, Atsushi; Masuhara, Hiroshi

    2012-04-28

    We observed phase transition and phase relaxation processes of a poly(N-isopropylacrylamide) (PNIPAM) aqueous solution using the heterodyne transient grating (HD-TG) method combined with the laser temperature jump technique. The sample temperature was instantaneously raised by about 1.0 K after irradiation of a pump pulse to crystal violet (CV) molecules for heating, and the phase transition was induced for the sample with an initial temperature just below the lower critical solution temperature (LCST); the following phase relaxation dynamics was observed. Turbidity relaxation was observed in both the turbidity and HD-TG responses, while another relaxation process was observed only in the HD-TG response, namely via the refractive index change. It is suggested that this response is due to formation of globule molecules or their assemblies since they would have nothing to do with turbidity change but would affect the refractive index, which is dependent on the molar volume of a chemical species. Furthermore, the grating spacing dependence of the HD-TG responses suggests that the response was caused by the counter propagating diffusion of the coil molecules as a reactant species and the globule molecules as a product species and the lifetime of the globule molecules ranged from 1.5 to 5 seconds. Thus, we conclude that the turbidity reflects the dynamics of aggregate conditions, not molecular conditions. The coil and globule sizes were estimated from the obtained diffusion coefficient. The sizes of the coil molecules did not change at the initial temperatures below the LCST but increased sharply as it approaches LCST. We propose that the coil-state molecules associate due to hydrophobic interaction when the initial temperature was higher than LCST minus 0.5 K and that the globule-state molecules generated from the coil-state molecules showed a similar trend in temperature. The phase transition was also induced by heating under a microscope, and the relaxation process

  16. Performances study of UWB monopole antennas using half-elliptic radiator conformed on elliptical surface

    Energy Technology Data Exchange (ETDEWEB)

    Djidel, S.; Bouamar, M.; Khedrouche, D., E-mail: dkhedrouche@yahoo.com [LASS (Laboratoired’Analyse des Signaux et Systèmes), Department of Electronics, University of M’sila BP.166, Route Ichebilia, M’sila, 28000 Algeria (Algeria)

    2016-04-21

    This paper presents a performances study of UWB monopole antenna using half-elliptic radiator conformed on elliptical surface. The proposed antenna, simulated using microwave studio computer CST and High frequency simulator structure HFSS, is designed to operate in frequency interval over 3.1 to 40 GHz. Good return loss and radiation pattern characteristics are obtained in the frequency band of interest. The proposed antenna structure is suitable for ultra-wideband applications, which is, required for many wearable electronics applications.

  17. Contesting the "Nature" Of Conformity: what Milgram and Zimbardo's studies really show.

    Science.gov (United States)

    Haslam, S Alexander; Reicher, Stephen D

    2012-01-01

    Understanding of the psychology of tyranny is dominated by classic studies from the 1960s and 1970s: Milgram's research on obedience to authority and Zimbardo's Stanford Prison Experiment. Supporting popular notions of the banality of evil, this research has been taken to show that people conform passively and unthinkingly to both the instructions and the roles that authorities provide, however malevolent these may be. Recently, though, this consensus has been challenged by empirical work informed by social identity theorizing. This suggests that individuals' willingness to follow authorities is conditional on identification with the authority in question and an associated belief that the authority is right.

  18. Contesting the "Nature" Of Conformity: what Milgram and Zimbardo's studies really show.

    Directory of Open Access Journals (Sweden)

    S Alexander Haslam

    Full Text Available Understanding of the psychology of tyranny is dominated by classic studies from the 1960s and 1970s: Milgram's research on obedience to authority and Zimbardo's Stanford Prison Experiment. Supporting popular notions of the banality of evil, this research has been taken to show that people conform passively and unthinkingly to both the instructions and the roles that authorities provide, however malevolent these may be. Recently, though, this consensus has been challenged by empirical work informed by social identity theorizing. This suggests that individuals' willingness to follow authorities is conditional on identification with the authority in question and an associated belief that the authority is right.

  19. Contesting the “Nature” Of Conformity: What Milgram and Zimbardo's Studies Really Show

    Science.gov (United States)

    Haslam, S. Alexander; Reicher, Stephen. D.

    2012-01-01

    Understanding of the psychology of tyranny is dominated by classic studies from the 1960s and 1970s: Milgram's research on obedience to authority and Zimbardo's Stanford Prison Experiment. Supporting popular notions of the banality of evil, this research has been taken to show that people conform passively and unthinkingly to both the instructions and the roles that authorities provide, however malevolent these may be. Recently, though, this consensus has been challenged by empirical work informed by social identity theorizing. This suggests that individuals' willingness to follow authorities is conditional on identification with the authority in question and an associated belief that the authority is right. PMID:23185132

  20. Conformal methods in general relativity

    CERN Document Server

    Valiente Kroon, Juan A

    2016-01-01

    This book offers a systematic exposition of conformal methods and how they can be used to study the global properties of solutions to the equations of Einstein's theory of gravity. It shows that combining these ideas with differential geometry can elucidate the existence and stability of the basic solutions of the theory. Introducing the differential geometric, spinorial and PDE background required to gain a deep understanding of conformal methods, this text provides an accessible account of key results in mathematical relativity over the last thirty years, including the stability of de Sitter and Minkowski spacetimes. For graduate students and researchers, this self-contained account includes useful visual models to help the reader grasp abstract concepts and a list of further reading, making this the perfect reference companion on the topic.

  1. Conformation transitions of a single polyelectrolyte chain in a poor solvent: a replica-exchange lattice Monte-Carlo study.

    Science.gov (United States)

    Wang, Lang; Wang, Zheng; Jiang, Run; Yin, Yuhua; Li, Baohui

    2017-03-15

    The thermodynamic behaviors of a strongly charged polyelectrolyte chain in a poor solvent are studied using replica-exchange Monte-Carlo simulations on a lattice model, focusing on the effects of finite chain length and the solvent quality on the chain conformation and conformation transitions. The neutralizing counterions and solvent molecules are considered explicitly. The thermodynamic quantities that vary continuously with temperature over a wide range are computed using the multiple histogram reweighting method. Our results suggest that the strength of the short-range hydrophobic interaction, the chain length, and the temperature of the system, characterized by ε, N, and T, respectively, are important parameters that control the conformations of a charged chain. When ε is moderate, the competition between the electrostatic energy and the short-range hydrophobic interaction leads to rich conformations and conformation transitions for a longer chain with a fixed length. Our results have unambiguously demonstrated the stability of the n-pearl-necklace structures, where n has a maximum value and decreases with decreasing temperature. The maximum n value increases with increasing chain length. Our results have also demonstrated the first-order nature of the conformation transitions between the m-pearl and the (m-1)-pearl necklaces. With the increase of ε, the transition temperature increases and the first-order feature becomes more pronounced. It is deduced that at the thermodynamic limit of infinitely long chain length, the conformational transitions between the m-pearl and the (m-1)-pearl necklaces may remain first order when ε > 0 and m = 2 or 3. Pearl-necklace conformations cannot be observed when either ε is too large or N is too small. To observe a pearl-necklace conformation, the T value needs to be carefully chosen for simulations performed at only a single temperature.

  2. QSAR study and conformational analysis of 4-arylthiazolylhydrazones derived from 1-indanones with anti-Trypanosoma cruzi activity.

    Science.gov (United States)

    Noguera, Guido J; Fabian, Lucas E; Lombardo, Elisa; Finkielsztein, Liliana

    2015-10-12

    A set of 4-arylthiazolylhydrazones derived from 1-indanones (TZHs) previously synthesized and assayed against Trypanosoma cruzi, the causative agent of Chagas disease, were explored in terms of conformational analysis. We found that TZHs can adopt four minimum energy conformations: cis (A, B and C) and trans. The possible bioactive conformation was selected by a 3D-QSAR model. Different molecular parameters were calculated to produce QSAR second-generation models. These QSAR results are discussed in conjunction with conformational analysis from molecular modeling studies. The main factor to determine the activity of the compounds was the partial charge at the N(3) atom (qN3). The predictive ability of the QSAR equations proposed was experimentally validated. The QSAR models developed in this study will be helpful to design novel potent TZHs. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study.

    Directory of Open Access Journals (Sweden)

    Vijayan ManickamAchari

    Full Text Available The rational design of a glycolipid application (e.g. drug delivery with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20% in the hydrophobic region of the lamellar crystal (LC phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.

  4. Thermal Performance Study of Composite Phase Change Material with Polyacrylicand Conformal Coating.

    Science.gov (United States)

    Kee, Shin Yiing; Munusamy, Yamuna; Ong, Kok Seng; Cornelis Metselaar, Hendrik Simon; Chee, Swee Yong; Lai, Koon Chun

    2017-07-28

    The composite PCM was prepared by blending polymethyl methacrylate (PMMA) and myristic acid (MA) in different weight percentages. The MA and PMMA were selected as PCM and supporting material, respectively. As liquid MA may leak out during the phase transition, this study proposes the use of two coatings, namely a polyacrylic coating and a conformal coating to overcome the leakage problem. Both coatings were studied in terms of the leakage test, chemical compatibility, thermal stability, morphology, and reliability. No leakage was found in the PCMs with coatings compared to those without under the same proportions of MA/PMMA, thus justifying the use of coatings in the present study. The chemically compatibility was confirmed by FTIR spectra: the functional groups of PCMs were in accordance with those of coatings. DSC showed that the coatings did not significantly change the melting and freezing temperatures, however, they improved the thermal stability of composite PCMs as seen in TGA analysis. Furthermore, the composite PCMs demonstrated good thermal reliability after 1000 times thermal cycling. The latent heat of melting reduced by only 0.16% and 1.02% for the PCMs coated with conformal coating and polyacrylic coating, respectively. Therefore, the proposed coatings can be considered in preparing fatty acid/PMMA blends attributed to the good stability, compatibility and leakage prevention.

  5. [Study on temperature & EMF co-effects on insulin conformation and biological functions by fluorescence and Raman spectroscopy].

    Science.gov (United States)

    Yan, Zhe; Chen, Shu-de; Qiao, Deng-jiang

    2008-06-01

    Our previous studies had suggested that the intercellular signal molecule might be an important target of electromagnetic fields. Insulin, an intercellule signal molecule, plays a critical role in transferring life information. The studies on effects of pulsed electric fields (PEF) on insulin molecule are meaningful for explaining the mechanism of biological effects of electromagnetic fields. The PEF, which we used, with its highest electric field (2 x 10(6) V x m(-1)) coupled into the insulin buffer, was about 1 V x cm(-1) cm, with a repeating frequency of 50 Hz. In the present study, the changes of insulin conformation induced by PEF were studied by fluorescence spectroscopy. Insulin solution was exposed to 50 Hz PEF with different electric field intensities for 5-35 min, which caused a time-and dose-dependent decrease in fluorescence intensities of insulin. Further, insulin solution was exposed to PEF at different temperatures to investigate the effects of PEF co-operated with temperature on insulin. The results indicated that the difference in temperature (about 5 degrees C) could induce conflict results, which is due to the effects of PEF co-operated with temperature rather than only to the effect of temperature. The authors calculated that the increase in temperature induced by PEF was 0.07 degrees C (less than 0.1 degrees C). So the effects of PEF were scarcely explained by thermal effects, it belongs to "non-thermal effects" of electric fields. So it was concluded that temperature is a considerably important factor in "non-thermal effects" of electric fields, and the ignorance of variety of temperature probably result in the contrary conclusion. Further, Raman spectroscopy was used to investigate the details of structure of insulin treated by PEF co-operated with temperature. The results of Raman spectroscopy verified the effects of PEF co-operated with temperature on insulin. And the reductions of the S-S band intensity at 510 cm(-1), the skeletal C

  6. Real-Time Ada Problem Solution Study

    Science.gov (United States)

    1989-03-24

    Method - Tools Solution Timeframe - Short-term Solution Approach - Remedial Solution 2 - Use a compiler which provides "fast" interrupt procesoing . A...applications will experience timing overhead impacts due to tasking features like task allocation, task activation/ termination , task switching...overhead compared to the processing done within the task itself: 26 Task Normal Description Overhead Proc. (usec) (usec) 1. Task activation and termination

  7. Partnering for A Solution: A Case Study

    Science.gov (United States)

    Jimenez-Smith, Deyrah

    2003-01-01

    A material-related issue has been identified, which has the potential of impacting the Space Program. Although "in-house" efforts have been underway to solve the problem, a solution has not yet been reached. This presentation shows how a GIDEP member organization is using a Problem Advisory as a solution approach in an effort to receive information from other industry and/or government organizations that may contribute in finding a solution.

  8. A Projective-to-Conformal Fefferman-Type Construction

    Science.gov (United States)

    Hammerl, Matthias; Sagerschnig, Katja; Šilhan, Josef; Taghavi-Chabert, Arman; Zádník, Vojtĕch

    2017-10-01

    We study a Fefferman-type construction based on the inclusion of Lie groups SL(n+1) into Spin(n+1,n+1). The construction associates a split-signature (n,n)-conformal spin structure to a projective structure of dimension n. We prove the existence of a canonical pure twistor spinor and a light-like conformal Killing field on the constructed conformal space. We obtain a complete characterisation of the constructed conformal spaces in terms of these solutions to overdetermined equations and an integrability condition on the Weyl curvature. The Fefferman-type construction presented here can be understood as an alternative approach to study a conformal version of classical Patterson-Walker metrics as discussed in recent works by Dunajski-Tod and by the authors. The present work therefore gives a complete exposition of conformal Patterson-Walker metrics from the viewpoint of parabolic geometry.

  9. CONFORMATIONAL EQUILIBRIUM AND SPECTROSCOPIC PROPERTIES OF CALIX[4]ARENE: THEORETICAL STUDY USING AB INITIO METHOD

    Directory of Open Access Journals (Sweden)

    Hanggara Sudrajat

    2010-06-01

    Full Text Available Molecular structures were optimized for the calix[4]arene by ab initio method at the Hartree-Fock level of theory using LANL2DZ and 6-311G basis sets. Conformational equilibrium of four calix[4]arene conformers are reported. The results are compared with experiment, force field, and semiempirical molecular orbital calculations. General trends in relative stabilities of calix[4]arene decrease in following order: cone > partial-cone > 1,2-alternate > 1,3-alternate. The most stable conformer is the cone conformer that is stabilized by an array of four hydrogen bonds and these results agree with the reported experimental observations. All structures were analyzed using theoretical IR, UV-Vis, and 1H NMR spectra attributed to the conformational equilibrium at the Hartree-Fock level of theory using LANL2DZ basis set.     Keywords: ab initio calculation, calix[4]arene, conformations, cone

  10. Conformational Search on the Lewis X Structure by Molecular Dynamic: Study of Tri- and Pentasaccharide

    Directory of Open Access Journals (Sweden)

    N. Khebichat

    2012-01-01

    Full Text Available Carbohydrates play vital roles in many biological processes, such as recognition, adhesion, and signalling between cells. The Lewis X determinant is a trisaccharide fragment implicated as a specific differentiation antigen, tumor antigen, and key component of the ligand for the endothelial leukocyte adhesion molecule, so it is necessary or essential to determine and to know their conformational and structural properties. In this work, conformational analysis was performed using molecular dynamics (MD simulation with the AMBER10 program package in order to study the dynamic behavior of of the Lewis X trisaccharide (β-D-Gal-(1,4-[α-L-Fuc-(1,3]-β-D-GlcNAc-OMe and the Lewis X pentasaccharide (β-D-Gal-(1,4-[α-L-Fuc-(1,3]-β-D-GlcNAc-(1,3-β-D-Gal-(1,4-β-D-Glu-OMe in explicit water model at 300 K for 10 ns using the GLYCAM 06 force field.

  11. Anisotropic stellar models admitting conformal motion

    Science.gov (United States)

    Banerjee, Ayan; Banerjee, Sumita; Hansraj, Sudan; Ovgun, Ali

    2017-04-01

    We address the problem of finding static and spherically symmetric anisotropic compact stars in general relativity that admit conformal motions. The study is framed in the language of f( R) gravity theory in order to expose opportunity for further study in the more general theory. Exact solutions of compact stars are found under the assumption that spherically symmetric spacetimes admit conformal motion with anisotropic matter distribution in nature. In this work, two cases have been studied for the existence of such solutions: first, we consider the model given by f(R)=R and then f(R)=aR+b . Finally, specific characteristics and physical properties have been explored analytically along with graphical representations for conformally symmetric compact stars in f( R) gravity.

  12. Transportation Conformity

    Science.gov (United States)

    This section provides information on: current laws, regulations and guidance, policy and technical guidance, project-level conformity, general information, contacts and training, adequacy review of SIP submissions

  13. Conformal Carroll groups

    OpenAIRE

    Duval, C.; Gibbons, G W; Horvathy, P. A.

    2014-01-01

    Conformal extensions of Levy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labelled by an integer $k$. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to Conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by "Carrollian photons". Motion both in the Newton-Cartan and Carroll spaces may be related t...

  14. Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space.

    Science.gov (United States)

    Bermejo, Guillermo A; Strub, Marie-Paule; Ho, Chien; Tjandra, Nico

    2009-07-15

    We demonstrate the feasibility of elucidating the bound ("closed") conformation of a periplasmic binding protein, the glutamine-binding protein (GlnBP), in solution, using paramagnetic relaxation enhancements (PREs) arising from a single paramagnetic group. GlnBP consists of two globular domains connected by a hinge. Using the ligand-free ("open") conformation as a starting point, conjoined rigid-body/torsion-angle simulated annealing calculations were performed using backbone (1)H(N)-PREs as a major source of distance information. Paramagnetic probe flexibility was accounted for via a multiple-conformer representation. A conventional approach where the entire PRE data set is enforced at once during simulated annealing yielded poor results due to inappropriate conformational sampling of the probe. On the other hand, significant improvements in coordinate accuracy were obtained by estimating the probe sampling space prior to structure calculation. Such sampling is achieved by refining the ensemble of probe conformers with intradomain PREs only, keeping the protein backbone fixed in the open form. Subsequently, while constraining the probe to the previously found conformations, the domains are allowed to move relative to each other under the influence of the non-intradomain PREs, giving the hinge region torsional degrees of freedom. Thus, by partitioning the protocol into "probe sampling" and "backbone sampling" stages, structures significantly closer to the X-ray structure of ligand-bound GlnBP were obtained.

  15. Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method.

    Science.gov (United States)

    Han, Mengzhi; Xu, Ji; Ren, Ying

    2017-03-01

    Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two methods, parallel tempering well-tempered ensemble (PT-WTE) and replica exchange with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Dual conformal transformations of smooth holographic Wilson loops

    Energy Technology Data Exchange (ETDEWEB)

    Dekel, Amit [Nordita, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, SE-106 91 Stockholm (Sweden)

    2017-01-19

    We study dual conformal transformations of minimal area surfaces in AdS{sub 5}×S{sup 5} corresponding to holographic smooth Wilson loops and some other related observables. To act with dual conformal transformations we map the string solutions to the dual space by means of T-duality, then we apply a conformal transformation and finally T-dualize back to the original space. The transformation maps between string solutions with different boundary contours. The boundary contours of the minimal surfaces are not mapped back to the AdS boundary, and the regularized area of the surface changes.

  17. Integrating the Study of Conformity and Culture in Humans and Nonhuman Animals

    Science.gov (United States)

    Claidiere, Nicolas; Whiten, Andrew

    2012-01-01

    Conformity--defined here by the fact that an individual displays a particular behavior because it is the most frequent the individual witnessed in others--has long been recognized by social psychologists as one of the main categories of social influence. Surprisingly, it is only recently that conformity has become an active topic in animal and…

  18. Rotational Spectroscopy and Conformational Studies of 4-PENTYNENITRILE, 4-PENTENENITRILE, and Glutaronitrile

    Science.gov (United States)

    Hays, Brian M.; Mehta-Hurt, Deepali; Jawad, Khadija M.; Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Zhang, Di; Zwier, Timothy S.

    2017-06-01

    The pure rotational spectra of 4-pentynenitrile, 4-pentenenitrile, and glutaronitrile were acquired using chirped pulse Fouirer transform microwave spectroscopy. 4-pentynenitrile and 4-pentenenitrile are the recombination products of two resonance stabilized radicals, propargyl + cyanomethyl or allyl + cyanomethyl, respectively, and are thus anticipated to be significant among the more complex nitriles in Titan's atmosphere. Indeed, these partially unsaturated alkyl cyanides have been found in laboratory analogs of tholins and are also expected to have interesting photochemistry. The optimized structures of all conformers below predicted energies of 500 \\wn were calculated for each molecule. Both of the conformers, trans and gauche, for 4-pentynenitrile have been identified and assigned. Five conformers were assigned in 4-pentenenitrile. The eclipsed conformers, with respect to the vinyl group, dominate the spectrum but some population was found in the syn conformers including the syn-gauche conformer, calculated to be 324 \\wn above the global minimum. The glutaronitrile spectrum contained only the two conformers below 500 \\wn, with reduced amount of the gauche trans conformer. The assigned spectra and structural assignments will be presented.

  19. Dosimetric study using different leaf-width MLCs for treatment planning of dynamic conformal arcs and intensity-modulated radiosurgery.

    Science.gov (United States)

    Jin, Jian-Yue; Yin, Fang-Fang; Ryu, Samuel; Ajlouni, Munther; Kim, Jae Ho

    2005-02-01

    This paper systematically studied the dosimetric difference between a 3 mm micro multileaf collimator (MLC), a 5 mm MLC, and a 10 mm MLC for stereotactic radiosurgery using the Brainscan treatment planning system. Thirty-four cases treated with the dynamic conformal arcs technique and 20 cases treated with the intensity modulated radiosurgery/fractionated radiotherapy (IMRS/ IMRT) technique were retrospectively studied. The conformity index, the percentage target coverage, and the dose-volume histogram (DVH) for organs-at-risk (OARs) were used for dosimetric analysis and comparison for different treatment techniques, target volumes, and treatment sites. For the dynamic conformal arcs technique, there were statistically significant differences in the conformity indices between different leaf-width MLCs. The ratio of the conformity indices between different MLCs depended on the target volume. The average conformity index ratios between the 5 mm MLC and the 3 mm MLC were 1.37+/-0.09, 1.12+/-0.04, 1.08+/-0.02 and 1.04+/-0.01, respectively, for patients with the target volume (V) in groups: (1) V 27 CC. The average conformity index ratios between the 10 and 3 mm MLCs were 2.00+/-0.33, 1.45+/-0.09, 1.28+/-0.09, and 1.18+/-0.05 for patients in these four volume groups, respectively. No statistically significant difference was found for the target coverage among different MLCs. For the IMRS/IMRT technique, the average conformity index and target coverage ratios were 1.01+/-0.05 and 1.00+/-0.02, respectively, between the 5 and 3 mm MLCs, and were 1.04+/-0.07 and 0.97+/-0.02, respectively, between the 10 and 3 mm MLCs. The 3 mm MLC showed slightly better overall OAR DVHs than the 5 and 10 mm MLCs, especially for the cranial site with small-volume OARs defined. The results suggest that for the dynamic conformal arcs technique, the narrower leaf-width MLC provides better dose conformity than the wider leaf-width MLCs. This advantage decreases when the target volume increases

  20. Calorimetric studies of macromolecular aqueous solutions

    NARCIS (Netherlands)

    Blandamer, M.J; Cullis, P.M.; Engberts, J.B.F.N.

    Both titration and differential scanning microcalorimetric techniques are shown to yield important information concerning the properties of macromolecules in aqueous solution. Application of titration calorimetry is examined in me context of deaggregation of canonic micelles (e.g.

  1. NMR studies of the conformation and motion of tetrahydrofuran in graphite intercalation compounds

    Energy Technology Data Exchange (ETDEWEB)

    Caplan, Daniel Franz [Univ. of California, Berkeley, CA (United States)

    1991-11-01

    The behavior of tetrahydrofuran (THF) molecules intercalated in graphite layers in compounds Cs(THF){sub 1.3}C{sub 24} and K(THF){sub 2.5}C{sub 24} was studied by proton NMR. The graphite layers in these compounds impose a uniform ordering on the THF molecules, giving rise to sharp NMR spectra. Experimental and simulated proton NMR spectra were used to investigate geometry, orientation and conformation of intercalated THF, and to determine whether pseudorotation, a large amplitude low-frequency vibration observed in gaseous THF, can also occur in the constrained environment provided by the graphite intercalation compounds. Deuterium and multiple quantum proton NMR spectra were also simulated in order to determine if these techniques could further refine the proton NMR results.

  2. NATO Advanced Study Institute on Photophysical and Photochemical Tools in Polymer Science : Conformation, Dynamics, Morphology

    CERN Document Server

    1986-01-01

    In 1980 the New York Academy of Sciences sponsored a three-day conference on luminescence in biological and synthetic macromolecules. After that meeting, Professor Frans DeSchryver and I began to discuss the possibility of organizing a different kind of meeting, with time for both informal and in-depth discussions, to examine certain aspects of the application of fluorescence and phosphorescence spectroscopy to polymers. Our ideas developed through discussions with many others, particularly Professor Lucien Monnerie. By 1983, when we submitted our proposal to NATO for an Advanced Study Institute, the area had grown enormous ly. It is interesting in retrospect to look back on the points which emerged from these discussions as the basis around which the scientific program would be organized and the speakers chosen. We decided early on to focus on applications of these methods to provide information about polymer molecules and polymer systems: The topics would all relate to the conformation and dynamics of macro...

  3. An Examination of Teachers' Views Regarding the Conformity of Social Studies Textbooks to the Critical Thinking Standards

    Science.gov (United States)

    Aybek, Birsel; Aslan, Serkan

    2016-01-01

    This present study aims to describe the classroom teachers' views towards the conformity of elementary school 4th grade social studies textbooks to the critical thinking standards. A descriptive study, this research is a screening model. The sample of the study constitutes 122 classroom teachers. As a data collection tool; a scale was developed…

  4. Conformal Methods in General Relativity

    Science.gov (United States)

    Valiente Kroon, Juan A.

    2016-07-01

    List of symbols; Preface; 1. Introduction; Part I. Geometric Tools: 2. Differential Geometry; 3. Spacetime spinors; 4. Space spinors; 5. Conformal Geometry; Part II. General Relativity and Conformal Geometry: 6. Conformal extensions of exact solutions; 7. Asymptotic simplicity; 8. The conformal Einstein field equations; 9. Matter models; 10. Asymptotics; Part III. Methods of PDE Theory: 11. The conformal constraint equations; 12. Methods of the theory of hyperbolic differential equations; 13. Hyperbolic reductions; 14. Causality and the Cauchy problem in General Relativity; Part IV. Applications: 15. De Sitter-like spacetimes; 16. Minkowski-like spacetimes; 17. Anti-de Sitter-like spacetimes; 18. Characteristic problems for the conformal field equations; 19. Static solutions; 20. Spatial infinity; 21. Perspectives; References; Index.

  5. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    non-linear responses with increasing surface concentration. The results from this study support the conventional amphiphilic, triblock model of BSM in the adsorption onto hydrophobic surface from aqueous solution.The biomolecular probe-based approaches employed in this study, however, provided further...

  6. The Idea of Conformation in the Study of Systemic Socio-Economic Transformations

    Directory of Open Access Journals (Sweden)

    Olga Valentinovna Brizhak

    2016-12-01

    Full Text Available The author shows the idea of conformation at studying the issues of intracorporate structure, corporate capital and economic (productive relations in the context of specific systemic socio-economic transformations. The dynamism and depth of current changes makes reflect on their nature, their objective conditionality, their dependence on existing factors. The problems of systemic market reforms are projected to private transformations. They relate both to individual economic entities (firms, companies, corporations, and to individual regions and territories of the national economy. In such conditions the aims of economic system development are changing and being corrected, and the possibilities are being reestimated. In the process of reforming the Russian economy some of the borrowed elements were rejected as inadequate and socially unacceptable. The other part was modified and embedded in public life in the course of implementation, so that they often served the opposite purposes in comparison with those for which they were borrowed. The article reveals the mission of conformation as a seamless integration of this process into the context of systemic socio-economic reforms, ensuring the necessary proportionality of transformations, the prevention of arousing gaps that threaten the sustainable movement in the corporate sector and systemic organization of economic relations at the intra-corporate level. Core development of contradictions, sprouts of post-market relations, components of the traditional capitalist market organization in terms of socio-economic transformation of Russia have impact on the economic behavior of corporations and on the specifics of intracorporate relations and interests. The corporation’s behavior is always focused on the specifics of domestic relations, the stability of legal and political system, property rights protection, preservation of national culture, etc. The author carries out the present research on the

  7. Theoretical study on fulvic acid structure, conformation and aggregation. A molecular modelling approach.

    Science.gov (United States)

    Alvarez-Puebla, R A; Valenzuela-Calahorro, C; Garrido, J J

    2006-04-01

    The ubiquitous presence of humic substances (HS), combined with their ability to provide multiple sites for chemical reaction, makes them relevant to numerous biogeochemical processes such as mineral weathering, nutrient bioavailability, and contaminant transport. The reactivity of HS depends on their functional group chemistry and microstructure, which are in turn influenced by the composition of the surrounding media. In order to help towards an understanding of structure conformations and aggregation process of HS in soils and waters and to get a better knowledge of these kinds of materials, a fulvic acid (FA) has been modelled as a function of its ionic state under different conditions. Our proposed theoretical model based on the Temple-Northeastern-Birmingham (TNB) monomer fits well with experimental observations on the solubility (dipolar moment) and electronic and vibrational spectra of FAs. The presence of water molecules has a great stabilization effect on the electrostatic energy; this effect is greater as ionized rate increases. In vacuum, the non-ionized aggregated species are more stable than monomers because of the increase in their interaction due to H-bonding and non-bonding forces. When the molecules are ionized, no aggregation process takes place. In solution, the FA concentration is a critical factor for the aggregation. The system containing two FA molecules probably did not form aggregates because its equivalent concentration was too low. When the concentration was increased, the system gave rise to the formation of aggregates. The ionic state is another critical factor in the aggregation process. The ionized FA has a higher electric negative charge, which increases the energetic barriers and inhibits the approximation of FA caused by the Brownian movement.

  8. Neural signatures of social conformity: A coordinate-based activation likelihood estimation meta-analysis of functional brain imaging studies.

    Science.gov (United States)

    Wu, Haiyan; Luo, Yi; Feng, Chunliang

    2016-12-01

    People often align their behaviors with group opinions, known as social conformity. Many neuroscience studies have explored the neuropsychological mechanisms underlying social conformity. Here we employed a coordinate-based meta-analysis on neuroimaging studies of social conformity with the purpose to reveal the convergence of the underlying neural architecture. We identified a convergence of reported activation foci in regions associated with normative decision-making, including ventral striatum (VS), dorsal posterior medial frontal cortex (dorsal pMFC), and anterior insula (AI). Specifically, consistent deactivation of VS and activation of dorsal pMFC and AI are identified when people's responses deviate from group opinions. In addition, the deviation-related responses in dorsal pMFC predict people's conforming behavioral adjustments. These are consistent with current models that disagreement with others might evoke "error" signals, cognitive imbalance, and/or aversive feelings, which are plausibly detected in these brain regions as control signals to facilitate subsequent conforming behaviors. Finally, group opinions result in altered neural correlates of valuation, manifested as stronger responses of VS to stimuli endorsed than disliked by others. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Conformations of dimethyl carbonate and its complexes with water: A matrix isolation infrared and ab initio study

    Science.gov (United States)

    Kar, Bishnu Prasad; Ramanathan, N.; Sundararajan, K.; Viswanathan, K. S.

    2012-09-01

    Conformations of dimethyl carbonate (DMC) were studied using matrix isolation infrared spectroscopy. Infrared spectra of DMC trapped in inert gas matrixes, using an effusive source at 298 and 423 K, showed evidence of both the ground state (cis-cis), and higher energy (cis-trans) conformers. Experiments were also performed using a supersonic jet source to deposit the matrix, to look for conformational cooling in the expansion process. The structures and vibrational frequencies of these conformers were computed at the B3LYP/6-31++G** level of theory. Natural bond orbital analyses were performed to understand the role of the delocalization interactions in conformational preferences. Complexes of DMC with H2O were also studied. A 1:1 DMC-H2O complex was identified in the matrix isolation experiments, where the carbonyl oxygen of DMC served as the proton acceptor for the hydrogen bonded complex. This observation was corroborated by computations performed on the complex at the B3LYP/6-31++G** level. Our computations also indicated another minimum, corresponding to an alkoxy bonded DMC-H2O complex, which was less exothermic; however, this complex was not identified in our experiments. Atoms-in-molecules theory was also performed to understand the nature of the intermolecular interaction in the DMC-H2O complex.

  10. A model-free temperature-dependent conformational study of n-pentane in nematic liquid crystals

    Science.gov (United States)

    Burnell, E. Elliott; Weber, Adrian C. J.; Dong, Ronald Y.; Meerts, W. Leo; de Lange, Cornelis A.

    2015-01-01

    The proton NMR spectra of n-pentane orientationally ordered in two nematic liquid-crystal solvents are studied over a wide temperature range and analysed using covariance matrix adaptation evolutionary strategy. Since alkanes possess small electrostatic moments, their anisotropic intermolecular interactions are dominated by short-range size-and-shape effects. As we assumed for n-butane, the anisotropic energy parameters of each n-pentane conformer are taken to be proportional to those of ethane and propane, independent of temperature. The observed temperature dependence of the n-pentane dipolar couplings allows a model-free separation between conformer degrees of order and conformer probabilities, which cannot be achieved at a single temperature. In this way for n-pentane 13 anisotropic energy parameters (two for trans trans, tt, five for trans gauche, tg, and three for each of gauche+ gauche+, pp, and gauche+ gauche-, pm), the isotropic trans-gauche energy difference Etg and its temperature coefficient Etg ' are obtained. The value obtained for the extra energy associated with the proximity of the two methyl groups in the gauche+ gauche- conformers (the pentane effect) is sensitive to minute details of other assumptions and is thus fixed in the calculations. Conformer populations are affected by the environment. In particular, anisotropic interactions increase the trans probability in the ordered phase.

  11. Study of the conformational change of adsorbed proteins on biomaterial surfaces using hydrogen-deuterium exchange with mass spectroscopy.

    Science.gov (United States)

    Kim, Jinku

    2016-05-01

    There is no doubt that protein adsorption plays a crucial role in determining biocompatibility of biomaterials. Despite the information of the identity and composition of blood plasma/serum proteins adsorbed on surfaces of biomaterials to understand which proteins are involved in blood/biomaterial interactions, it still does not provide information about the conformations and orientations of adsorbed protein, which are very important in determining biological responses to biomaterials. Therefore, our laboratory has developed an experimental technology to probe protein conformations on materials that is applicable to mixtures of proteins. Herein, the new application of hydrogen/deuterium (H/D) exchange combined with mass spectrometry was applied to determine conformational changes of adsorbed proteins at biomaterial surfaces. The results suggest that there may be a significant conformational change in adsorbed proteins at 'low' bulk concentrations that leads to a large change in the kinetics of H/D exchange as compared to 'high' bulk concentrations. This technique may eventually be useful for the study of the kinetics of protein conformational changes. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. General Conformity

    Science.gov (United States)

    The General Conformity requirements ensure that the actions taken by federal agencies in nonattainment and maintenance areas do not interfere with a state’s plans to meet national standards for air quality.

  13. CONFORMATIONAL EQUILIBRIA OF BULGED SITES IN DUPLEX DNA STUDIED BY EPR SPECTROSCOPY

    OpenAIRE

    Smith, Alyssa L.; Cekan, Pavol; Brewood, Greg P.; Okonogi, Tamara M.; Alemayehu, Saba; Hustedt, Eric J.; Benight, Albert S.; Sigurdsson, Snorri Th.; Robinson, Bruce H.

    2009-01-01

    Conformational flexibility in nucleic acids provides a basis for complex structures, binding, and signaling. One-base bulges directly neighboring single-base mismatches in nucleic acids can be present in a minimum of two distinct conformations, complicating the examination of the thermodynamics by calorimetry or UV-monitored melting techniques. To provide additional information about such structures, we demonstrate how electron paramagnetic resonance (EPR) active spin-labeled base analogues, ...

  14. DICOM Standard Conformance in Veterinary Medicine in Germany: a Survey of Imaging Studies in Referral Cases.

    Science.gov (United States)

    Brühschwein, Andreas; Klever, Julius; Wilkinson, Tom; Meyer-Lindenberg, Andrea

    2018-02-01

    In 2016, the recommendations of the DICOM Standards Committee for the use of veterinary identification DICOM tags had its 10th anniversary. The goal of our study was to survey veterinary DICOM standard conformance in Germany regarding the specific identification tags veterinarians should use in veterinary diagnostic imaging. We hypothesized that most veterinarians in Germany do not follow the guidelines of the DICOM Standards Committee. We analyzed the metadata of 488 imaging studies of referral cases from 115 different veterinary institutions in Germany by computer-aided DICOM header readout. We found that 25 (5.1%) of the imaging studies fully complied with the "veterinary DICOM standard" in this survey. The results confirmed our hypothesis that the recommendations of the DICOM Standards Committee for the consistent and advantageous use of veterinary identification tags have found minimal acceptance amongst German veterinarians. DICOM does not only enable connectivity between machines, DICOM also improves communication between veterinarians by sharing correct and valuable metadata for better patient care. Therefore, we recommend that lecturers, universities, societies, authorities, vendors, and other stakeholders should increase their effort to improve the spread of the veterinary DICOM standard in the veterinary world.

  15. Effect of grafted PEG chain conformation on albumin and lysozyme adsorption: A combined study using QCM-D and DPI.

    Science.gov (United States)

    Jin, Jing; Han, Yuanyuan; Zhang, Chang; Liu, Jingchuan; Jiang, Wei; Yin, Jinghua; Liang, Haojun

    2015-12-01

    In this study, elucidation of protein adsorption mechanism is performed using dual polarization interferometry (DPI) and quartz crystal microbalance with dissipation (QCM-D) to study adsorption behaviors of bovine serum albumin (BSA) and lysozyme (LYZ) on poly (ethylene glycol) (PEG) layers. From the analysis of DPI, PEG2000 and PEG5000 show tight and loose mushroom conformations, respectively. Small amount of LYZ could displace the interfacial water surrounding the tight mushroomed PEG2000 chains by hydrogen bond attraction, leading to protein adsorption. The loose mushroomed PEG5000 chains exhibit a more flexible conformation and high elastic repulsion energy that could prevent protein adsorption of all BSA and most of LYZ. From the analysis of QCM, PEG2000 and PEG5000 show tight and extended brush conformations. The LYZ adsorbed mass has critical regions of PEG2000 (0.19 chain/nm(2)) and PEG5000 (0.16 chain/nm(2)) graft density. When graft density of PEG is higher than the critical region (brush conformations), the attraction of hydrogen bonds between PEG and LYZ is the dominant factor. When graft density of PEG is lower than the critical region (mushroom conformations), elastic repulsion between PEG and proteins is driven by the high conformation entropy of PEG chains, which is the dominant force of steric repulsion in PEG-protein systems. Therefore, the adsorption of BSA is suppressed by the high elastic repulsion energy of PEG chains, whereas the adsorption of LYZ is balanced by the interactions between the repulsion of entropy elasticity and the attraction of hydrogen bonds. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Multiple receptor conformers based molecular docking study of fluorine enhanced ethionamide with mycobacterium enoyl ACP reductase (InhA).

    Science.gov (United States)

    Khan, Akib Mahmud; Shawon, Jakaria; Halim, Mohammad A

    2017-10-01

    A major limitation in current molecular docking method is that of failure to account for receptor flexibility. Herein we report multiple receptor conformers based molecular docking as a practical alternative to account for the receptor flexibility. Multiple (forty) conformers of Mycobacterium Enoyl ACP Reductase (InhA) are generated from Molecular Dynamics simulation and twenty crystallographic structures of InhA bound to different inhibitors are obtained from the Protein Data Bank. Fluorine directed modifications are performed to currently available anti-tuberculosis drug ethionamide. The modified drugs are optimized using B3LYP 6-31G (d,p) level of theory. Dipole moment, frontier orbital gap and thermodynamical properties such as electronic energy, enthalpy and Gibbs free energy of these optimized drugs are investigated. These drugs are subsequently docked against the conformers of InhA. Molecular docking against multiple InhA conformations show variation in ligand binding affinity and suggest that Ser94, Gly96, Lys165 and Ile194 amino acids play critical role on strong drug-InhA interaction. Modified drug N1 showed greater binding affinity compared to EN in most conformations. Structure of PDB ID: 2NSD and snapshot conformer at 5.5ns show most favorable binding with N1 compared to other conformers. Fluorine participates in forming fluorine bonds and contributes significantly in increasing binding affinity. Our study reveal that addition of trifluoromethyl group explicitly shows promise in improving thermodynamic properties and in enhancing hydrogen bonding and non-bonded interactions. Molecular dynamics (MD) simulation show that EN and N1 remained in the binding pocket similar to the docked pose of EN-InhA and E1-InhA complexes and also suggested that InhA binds to its inhibitor in inhibitor-induced folding manner. ADMET calculations predict modified drugs to have improved pharmacokinetic properties. Our study concludes that multiple receptor conformers based

  17. A conformational study of protonated noradrenaline by UV-UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method.

    Science.gov (United States)

    Wako, Hiromichi; Ishiuchi, Shun-Ichi; Kato, Daichi; Féraud, Géraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe; Fujii, Masaaki

    2017-05-03

    The conformer-selected ultraviolet (UV) and infrared (IR) spectra of protonated noradrenaline were measured using an electrospray/cryogenic ion trap technique combined with photo-dissociation spectroscopy. By comparing the UV photo dissociation (UVPD) spectra with the UV-UV hole burning (HB) spectra, it was found that five conformers coexist under ultra-cold conditions. Based on the spectral features of the IR dip spectra of each conformer, two different conformations on the amine side chain were identified. Three conformers (group I) were assigned to folded and others (group II) to extended structures by comparing the observed IR spectra with the calculated ones. Observation of the significantly less-stable extended conformers strongly suggests that the extended structures are dominant in solution and are detected in the gas phase by kinetic trapping. The conformers in each group are assignable to rotamers of OH orientations in the catechol ring. By comparing the UV-UV HB spectra and the calculated Franck-Condon spectra obtained by harmonic vibrational analysis of the S1 state, with the aid of relative stabilization energies of each conformer in the S0 state, the absolute orientations of catechol OHs of the observed five conformers were successfully determined. It was found that the 0-0 transition of one folded conformer is red-shifted by about 1000 cm(-1) from the others. The significant red-shift was explained by a large contribution of the πσ* state to S1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.

  18. X-ray and 1H-NMR spectroscopic studies of the structures and conformations of the new nootropic agents RU-35929, RU-47010 and RU-35965

    Science.gov (United States)

    Amato, Maria E.; Bandoli, Giuliano; Casellato, Umberto; Pappalardo, Giuseppe C.; Toja, Emilio

    1990-10-01

    The crystal and molecular structures of the nootropics (±)1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine ( 1), (±)1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine ( 2) and (±)1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine ( 3) have been determined by X-ray analysis. The solution conformation of 1, 2 and 3 has been investigated by 1H NMR spectroscopy. In the solid state, the main feature consists of the similar structural parameters and conformations, with the exception of the conformation adopted by the 5-ethoxy moiety which changes on passing from 1 to 2. The solid state overall enveloped conformation of the 2-pyrrolidinone ring for the three nootropics is found to be retained in solution on the basis of NMR evidence. Comparison between calculated and experimental coupling constant values shows that one of the two possible puckered opposite conformational isomers (half-chair shapes) occurs in solution. The relative pharmacological potencies of 1, 2 and 3 cannot therefore be interpreted in terms of the different conformation features presently detectable by available experimental methods.

  19. 5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

    Science.gov (United States)

    Jarmuła, Adam; Cieplak, Piotr; Montfort, William R.

    2005-02-01

    We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

  20. On New Families of Integrals in Analytical Studies of Superconductors within the Conformal Transformation Method

    Directory of Open Access Journals (Sweden)

    Ryszard Gonczarek

    2015-01-01

    Full Text Available We show that, by applying the conformal transformation method, strongly correlated superconducting systems can be discussed in terms of the Fermi liquid with a variable density of states function. Within this approach, it is possible to formulate and carry out purely analytical study based on a set of fundamental equations. After presenting the mathematical structure of the s-wave superconducting gap and other quantitative characteristics of superconductors, we evaluate and discuss integrals inherent in fundamental equations describing superconducting systems. The results presented here extend the approach formulated by Abrikosov and Maki, which was restricted to the first-order expansion. A few infinite families of integrals are derived and allow us to express the fundamental equations by means of analytical formulas. They can be then exploited in order to find quantitative characteristics of superconducting systems by the method of successive approximations. We show that the results can be applied in studies of high-Tc superconductors and other superconducting materials of the new generation.

  1. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred [Univ. of California, Berkeley, CA (United States)

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  2. Atropisomerism at C ̶ N bonds: Structural conformations and vibrational spectral study of Iminothiazoline Derivatives with density functional theoretical optimizations

    Directory of Open Access Journals (Sweden)

    F.Z. MIMOUNI

    2013-03-01

    Full Text Available The isolation of the pair atropisomers of the both iminothiazoline derivatives and the spectroscopic analytical of the compound have been computed using B3LYP/6-31G(d,p level to derive the equilibrium geometry, conformational stability, molecular orbital energies and vibrational frequencies was studied in this paper.

  3. Integrability of conformal fishnet theory

    Science.gov (United States)

    Gromov, Nikolay; Kazakov, Vladimir; Korchemsky, Gregory; Negro, Stefano; Sizov, Grigory

    2018-01-01

    We study integrability of fishnet-type Feynman graphs arising in planar four-dimensional bi-scalar chiral theory recently proposed in arXiv:1512.06704 as a special double scaling limit of gamma-deformed N = 4 SYM theory. We show that the transfer matrix "building" the fishnet graphs emerges from the R-matrix of non-compact conformal SU(2 , 2) Heisenberg spin chain with spins belonging to principal series representations of the four-dimensional conformal group. We demonstrate explicitly a relationship between this integrable spin chain and the Quantum Spectral Curve (QSC) of N = 4 SYM. Using QSC and spin chain methods, we construct Baxter equation for Q-functions of the conformal spin chain needed for computation of the anomalous dimensions of operators of the type tr( ϕ 1 J ) where ϕ 1 is one of the two scalars of the theory. For J = 3 we derive from QSC a quantization condition that fixes the relevant solution of Baxter equation. The scaling dimensions of the operators only receive contributions from wheel-like graphs. We develop integrability techniques to compute the divergent part of these graphs and use it to present the weak coupling expansion of dimensions to very high orders. Then we apply our exact equations to calculate the anomalous dimensions with J = 3 to practically unlimited precision at any coupling. These equations also describe an infinite tower of local conformal operators all carrying the same charge J = 3. The method should be applicable for any J and, in principle, to any local operators of bi-scalar theory. We show that at strong coupling the scaling dimensions can be derived from semiclassical quantization of finite gap solutions describing an integrable system of noncompact SU(2 , 2) spins. This bears similarities with the classical strings arising in the strongly coupled limit of N = 4 SYM.

  4. Molecular structure, vibrational spectral analysis, NBO, HOMO-LUMO and conformational studies of ninhydrin

    Science.gov (United States)

    Arivazhagan, M.; Anitha Rexalin, D.

    2013-03-01

    The FT-IR and FT-Raman vibrational spectra of ninhydrin have been recorded in the range 4000-400 cm-1and 3600-50 cm-1, respectively. A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry, vibrational frequencies, atomic charges, dipole moment, rotational constants and several thermodynamic parameters in the ground state are calculated using ab initio HF and density functional B3LYP methods with 6-311++G(d,p) basis set combination. In order to find the most optimized geometry, the energy calculations are carried out for various possible conformers. Keto and enol forms of ninhydrin are also studied. The condensed summary of the principal NBOs shows the occupancy, orbital energy and the qualitative pattern of delocalization interactions of ninhydrin. The calculated HOMO-LUMO energies reveal that charge transfer occurs within the molecule. The predicted first hyperpolarizability also shows that the ninhydrin molecule have good optical quality and nonlinear optical (NLO) behavior. With the help of specific scaling procedures, the observed vibrational wave numbers in FT-IR and FT-Raman spectra are analyzed and assigned to different normal modes of the molecule.

  5. The tertiary origin of the allosteric activation of E. coli glucosamine-6-phosphate deaminase studied by sol-gel nanoencapsulation of its T conformer.

    Directory of Open Access Journals (Sweden)

    Sergio Zonszein

    Full Text Available The role of tertiary conformational changes associated to ligand binding was explored using the allosteric enzyme glucosamine-6-phosphate (GlcN6P deaminase from Escherichia coli (EcGNPDA as an experimental model. This is an enzyme of amino sugar catabolism that deaminates GlcN6P, giving fructose 6-phosphate and ammonia, and is allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P. We resorted to the nanoencapsulation of this enzyme in wet silica sol-gels for studying the role of intrasubunit local mobility in its allosteric activation under the suppression of quaternary transition. The gel-trapped enzyme lost its characteristic homotropic cooperativity while keeping its catalytic properties and the allosteric activation by GlcNAc6P. The nanoencapsulation keeps the enzyme in the T quaternary conformation, making possible the study of its allosteric activation under a condition that is not possible to attain in a soluble phase. The involved local transition was slowed down by nanoencapsulation, thus easing the fluorometric analysis of its relaxation kinetics, which revealed an induced-fit mechanism. The absence of cooperativity produced allosterically activated transitory states displaying velocity against substrate concentration curves with apparent negative cooperativity, due to the simultaneous presence of subunits with different substrate affinities. Reaction kinetics experiments performed at different tertiary conformational relaxation times also reveal the sequential nature of the allosteric activation. We assumed as a minimal model the existence of two tertiary states, t and r, of low and high affinity, respectively, for the substrate and the activator. By fitting the velocity-substrate curves as a linear combination of two hyperbolic functions with Kt and Kr as KM values, we obtained comparable values to those reported for the quaternary conformers in solution fitted to MWC model. These results are discussed in the

  6. mtsslSuite: Probing Biomolecular Conformation by Spin-Labeling Studies.

    Science.gov (United States)

    Hagelueken, Gregor; Abdullin, Dinar; Schiemann, Olav

    2015-01-01

    EPR long-range distance measurements on spin-labeled macromolecules have recently become a popular tool in structural biology. The method can be used to obtain coarse-grained structures of biomolecules, to track conformational changes and dynamics, to dock macromolecular complexes, or to localize spin centers within macromolecules using trilateration. Because the conformation of the spin label is usually unknown, it is often necessary to construct conformational models of the spin label on the macromolecules for data interpretation. For this purpose, so-called in silico spin-labeling approaches have been developed. In this chapter, a comprehensive summary of the mtsslSuite is provided, one of the in silico spin-labeling software packages. The package currently contains three programs: mtsslWizard, mtsslDock, and mtsslTrilaterate. Worked examples for the usage of all three programs during the planning- and interpretation stages of the EPR experiment are given. © 2015 Elsevier Inc. All rights reserved.

  7. Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

    Science.gov (United States)

    Zhang, Hao; Liu, Haijun; Blankenship, Robert E.; Gross, Michael L.

    2016-01-01

    We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded "heavy" and "light" GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the "heavy" and "light" peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

  8. High electric field dielectric studies of aqueous myoglobin solutions.

    Science.gov (United States)

    Jones, G P; Davies, A E; van der Sluijs, M J

    1979-01-01

    High field dielectric measurements of the Piekara factor deltaepsilon/E2 have been carried out for a range of concentrations of horse heart myoglobin in water at 293K. Using the literature value for the dipole moment of myoglobin and the established theory for the classical orientational dipolar non-linear effect predicts a value of deltaepsilon/E2 one order of magnitude greater than that for water. The measured effect, however, was found to be one order of magnitude less than for water. This difference is explained as being most probably due to the existence of antiparallel molecular dipole pairs in the myoglobin solution. The possibility of a positive deltaepsilon due to a field induced conformational change of the myoglobin cannot, however, be ruled out.

  9. Theoretical studies on the molecular structure, conformational preferences, topological and vibrational analysis of allicin

    Science.gov (United States)

    Durlak, Piotr; Berski, Sławomir; Latajka, Zdzisław

    2016-01-01

    The molecular structure, conformational preferences, topological and vibrational analysis of allicin has been investigated at two different approaches. Calculations have been carried out on static (DFT and MP2) levels with an assortment of Dunning's basis sets and dynamic CPMD simulations. In this both case within the isolated molecule approximation. The results point out that at least twenty different conformers coexist on the PES as confirmed by the flexible character of this molecule. The topological analysis of ELF showed very similar nature of the Ssbnd S and Ssbnd O bonds. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed.

  10. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

    Science.gov (United States)

    van der Vaart, Arjan

    2015-05-01

    Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  11. Experimental and theoretical study of dilute polyacrylamide solutions: effect of salt concentration.

    Science.gov (United States)

    Chen, Panke; Yao, Lin; Liu, Yanyan; Luo, Jianhui; Zhou, Ge; Jiang, Bo

    2012-07-01

    The structure and intrinsic viscosity of the partially hydrolyzed polyacrylamide (HAPM) and polyacrylamide (PAM) in aqueous solution were investigated by comparative studies of molecular dynamics simulation over a wide range of the NaCl concentration. The radius of gyration (R(g)), the hydrodynamic radius (R(h)) and the ratio of the radius gyration and the hydrodynamic radius (ρ) were calculated for the PAM or HPAM in solutions with different NaCl concentrations at 298 K. The conformational changes of the polymer chain in different aqueous solution were discussed according to the molecular shapes. It was found that the change of the R(h) or the R(g) can reflect the change in the [η]. And the changes in the structure of the polymer chain with different NaCl concentrations were discussed via the ρ which can predict [η] changes. The results showed that behavior of the polymer solution calculated from the simulation agreed with the experimental measurements. Furthermore, the radial distribution functions for the HPAM solutions were investigated, which verified the micro-mechanism for the change of the structure. The results of this research showed that the computational method used in this work has practical applicability.

  12. Conformal Janus on Euclidean sphere

    Energy Technology Data Exchange (ETDEWEB)

    Bak, Dongsu [Physics Department, University of Seoul,Seoul 02504 (Korea, Republic of); B.W. Lee Center for Fields, Gravity & Strings, Institute for Basic Sciences,Daejeon 34047 (Korea, Republic of); Gustavsson, Andreas [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of); Rey, Soo-Jong [School of Physics & Astronomy and Center for Theoretical Physics,Seoul National University,Seoul 08826 (Korea, Republic of); Center for Theoretical Physics, College of Physical Sciences, Sichuan University,Chengdu 610064 P.R. (China); B.W. Lee Center for Fields, Gravity & Strings, Institute for Basic Sciences,Daejeon 34047 (Korea, Republic of)

    2016-12-07

    We interpret Janus as an interface in a conformal field theory and study its properties. The Janus is created by an exactly marginal operator and we study its effect on the interface conformal field theory on the Janus. We do this by utilizing the AdS/CFT correspondence. We compute the interface free energy both from leading correction to the Euclidean action in the dual gravity description and from conformal perturbation theory in the conformal field theory. We find that the two results agree each other and that the interface free energy scales precisely as expected from the conformal invariance of the Janus interface.

  13. Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

    Energy Technology Data Exchange (ETDEWEB)

    Asadinezhad, Ahmad, E-mail: asadinezhad@cc.iut.ac.ir; Kelich, Payam

    2017-01-15

    Highlights: • Poly (trimethylene terephthalate) (PTT) conformation adopts a folded shape near nanofiller surface. • Graphene and carbon nanotube with different size and chemistry were simulated. • Graphene functionalization induces stronger confinement on PTT chain conformation. • PTT chain motion alters in dynamics mode as it becomes adsorbed onto nanofillers. • PTT reveals further changes near graphene than carbon nanotube surface. - Abstract: The effects of nanofiller chemistry and geometry on static and dynamic properties of an aromatic polyester, poly (trimethylene terephthalate), were addressed thanks to long-run classical molecular dynamics simulation. Two carbon nanofillers, graphene and carbon nanotube, were employed, where graphene was used in pristine and functionalized forms and carbon nanotube was used in two different diameters. The nanofiller geometry and chemistry were found to exert significant effects on conformation and dynamic behavior of PTT chain at the interface within the time scale the simulation was performed. It was found that PTT chain underwent interaction of van der Waals type with nanofiller via two subsequent phases, adsorption and orientation. The former stage, with definite characteristic time, involved translation of polymer chain toward interface while the latter was controlled by vibrational motions of chain atoms. The consequence of interaction was an increase in conformational order of polymer chain by transition to folded shape being favorable for any subsequent structural ordering (crystallization). The interaction of polymer with nanofiller gave rise to a reduction in overall mobility of polymer chain characterized by crossover from normal diffusive motion to subdiffusive mode.

  14. Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and 3JHH coupling constant analyses.

    Science.gov (United States)

    Silva, Weslley G D P; Braga, Carolyne B; Rittner, Roberto

    2017-01-01

    The understanding of the conformational behavior of amino acids and their derivatives is a challenging task. Here, the conformational analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of 1H NMR and electronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into account the implicit solvent effects, according to the integral equation formalism polarizable continuum model (IEF-PCM), were obtained at the ωB97X-D/aug-cc-pVTZ level. The conformational preferences of the compounds in solution were also determined from experimental and theoretical 3JHH coupling constants analysis in different aprotic solvents. The results showed that the conformational stability of the esterified derivatives is not very sensitive to solvent effects, whereas the conformational equilibrium of the N-acetylated derivatives changes in the presence of solvent. According to the natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects.

  15. Rigid supersymmetry from conformal supergravity in five dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Pini, Alessandro [Department of Physics, Universidad de Oviedo, Avda. Calvo Sotelo 18, 33007, Oviedo (Spain); Centre for Research in String Theory, School of Physics, Queen Mary University of London,Mile End Road, London, E1 4NS (United Kingdom); Rodriguez-Gomez, Diego; Schmude, Johannes [Department of Physics, Universidad de Oviedo, Avda. Calvo Sotelo 18, 33007, Oviedo (Spain)

    2015-09-17

    We study the rigid limit of 5d conformal supergravity with minimal supersymmetry on Riemannian manifolds. The necessary and sufficient condition for the existence of a solution is the existence of a conformal Killing vector. Whenever a certain SU(2) curvature becomes abelian the backgrounds define a transversally holomorphic foliation. Subsequently we turn to the question under which circumstances these backgrounds admit a kinetic Yang-Mills term in the action of a vector multiplet. Here we find that the conformal Killing vector has to be Killing. We supplement the discussion with various appendices.

  16. Conformational and dynamical properties of disaccharides in water: a molecular dynamics study.

    Science.gov (United States)

    Pereira, Cristina S; Kony, David; Baron, Riccardo; Müller, Martin; van Gunsteren, Wilfred F; Hünenberger, Philippe H

    2006-06-15

    Explicit-solvent molecular dynamics simulations (50 ns, 300 K) of the eight reducing glucose disaccharides (kojibiose, sophorose, nigerose, laminarabiose, maltose, cellobiose, isomaltose, and gentiobiose) have been carried out using the GROMOS 45A4 force field (including a recently reoptimized carbohydrate parameter set), to investigate and compare their conformational preferences, intramolecular hydrogen-bonding patterns, torsional dynamics, and configurational entropies. The calculated average values of the glycosidic torsional angles agree well with available experimental data, providing validation for the force field and simulation methodology employed in this study. These simulations show in particular that: 1) (1-->6)-linked disaccharides are characterized by an increased flexibility, the absence of any persistent intramolecular hydrogen bond and a significantly higher configurational entropy (compared to the other disaccharides); 2) cellobiose presents a highly persistent interresidue hydrogen bond and a significantly lower configurational entropy (compared to the other disaccharides); 3) persistent hydrogen bonds are observed for all disaccharides (except (1-->6)-linked) and typically involve a hydrogen donor in the reducing residue and an acceptor in the nonreducing one; 4) the probability distributions associated with the glycosidic dihedral angles and psi are essentially unimodal for all disaccharides, and full rotation around these angles occurs at most once or twice for (never for psi) on the 50-ns timescale; and 5) the timescales associated with torsional transitions (except around and psi) range from approximately 30 ps (rotation of hydroxyl groups) to the nanosecond range (rotation of the lactol and hydroxymethyl groups, and around the omega-glycosidic dihedral angle in (1-->6)-linked disaccharides).

  17. Net ZEB case study buildings, measures and solution sets

    DEFF Research Database (Denmark)

    Aelenei, Laura; Waldren, David; Aelenei, Daniel

    2017-01-01

    The chapter summarises techniques - combined in solution sets - used in the case studied buildings to achieve buildings with net zero energy or energy neutral standard.......The chapter summarises techniques - combined in solution sets - used in the case studied buildings to achieve buildings with net zero energy or energy neutral standard....

  18. Group Size and Conformity

    OpenAIRE

    Bond, Rod

    2005-01-01

    Abstract This paper reviews theory and research on the relationship between group size and conformity and presents a meta-analysis of 125 Asch-type conformity studies. It questions the assumption of a single function made in formal models of social influence and proposes instead that the function will vary depending on which social influence process predominates. It is argued that normative influence is lik...

  19. Conformal expansions and renormalons

    CERN Document Server

    Brodsky, S J; Grunberg, G; Rathsman, J; Brodsky, Stanley J.; Gardi, Einan; Grunberg, Georges; Rathsman, Johan

    2001-01-01

    The coefficients in perturbative expansions in gauge theories are factoriallyincreasing, predominantly due to renormalons. This type of factorial increaseis not expected in conformal theories. In QCD conformal relations betweenobservables can be defined in the presence of a perturbative infraredfixed-point. Using the Banks-Zaks expansion we study the effect of thelarge-order behavior of the perturbative series on the conformal coefficients.We find that in general these coefficients become factorially increasing.However, when the factorial behavior genuinely originates in a renormalonintegral, as implied by a postulated skeleton expansion, it does not affect theconformal coefficients. As a consequence, the conformal coefficients willindeed be free of renormalon divergence, in accordance with previousobservations concerning the smallness of these coefficients for specificobservables. We further show that the correspondence of the BLM method with theskeleton expansion implies a unique scale-setting procedure. Th...

  20. Conformational analysis, UV-VIS, MESP, NLO and NMR studies of 6-methoxy-1,2,3,4-tetrahydronaphthalene.

    Science.gov (United States)

    Arivazhagan, M; Kavitha, R; Subhasini, V P

    2014-07-15

    The detailed HF and B3LYP/6-311++G(d,p) comparative studies on the complete FT-IR and FT-Raman spectra of 6-methoxy-1,2,3,4-tetrahydronaphthalene [MTHN] have been studied. In view of the special properties and uses, the present investigation has been undertaken to provide a satisfactorily vibrational analysis of 6-methoxy-1,2,3,4-tetrahydronaphthalene. Therefore, a thorough Raman, IR, molecular electrostatic potential (MESP), non-linear optical (NLO) properties, UV-VIS, HOMO-LUMO and NMR spectroscopic investigation are reported complemented by B3LYP theoretical predictions with basis set 6-311++G(d,p) to provide novel insight on vibrational assignments and conformational stability of MTHN. Potential energy surface scans (PES) of the CH3 group are undertaken to shed light on the rather complicated conformational interchanges in the compound under investigation. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Study of conformation and thermodynamics of α-amylase interaction with ethylene in vitro.

    Science.gov (United States)

    Hu, Yiwei; Zhang, Guangxian; Zhang, Fengxiu

    2016-10-01

    In this article, the conformation and thermodynamics of α-amylase interaction with ethylene in vitro were investigated. The ultraviolet (UV) absorption showed a strong peak of α-amylase treated with 6.04, 29.32 and 262.11μmolL(-1) ethylene appears at ~222nm and a weak peak at 278nm blue-shifted 1nm. Circular dichroism (CD) spectra indicated that the conformations of α-amylase treated with 29.32 and 262.11μmolL(-1) ethylene were obviously changed in which α-helix content were decreased by 20 and 31% respectively, and β-sheet, β-turn and random coil contents were increased by contrast. Fluorescence spectra suggested that the peak intensities of α-amylase at 342nm were obviously increased with the ethylene increase from 6.04 to 525.75μmolL(-1) and more than control group. The binding constants K between ethylene and α-amylase were 3.318×10(6), 4.407×10(6) and 5.125×10(6)Lmol(-1) at 288, 298 and 308K, respectively. And the calculated values of ΔH(0) and ΔS(0) are positive, which suggests that the interaction between ethylene and α-amylase is an endothermic reaction. The negative ΔG(0) values implied that the direct effect of ethylene on α-amylase conformation was spontaneous. The possible reason is that ethylene molecules were easily embedded into the interior of α-amylase in term of the hydrophobic force between α-amylase and ethylene, causing the conformation and thermodynamics changes of α-amylase. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Molecular Docking Study of Conformational Polymorph: Building Block of Crystal Chemistry

    Directory of Open Access Journals (Sweden)

    Rashmi Dubey

    2013-01-01

    Full Text Available Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2 receptor than the standard (Nimesulide.

  3. Synthesis and spectroscopic conformational studies of Ac-Nit-NHMe dipeptide model

    Czech Academy of Sciences Publication Activity Database

    Brichtová, Eva; Niederhafner, Petr; Šebestík, Jaroslav

    2017-01-01

    Roč. 15, č. 1 (2017), s. 7 ISSN 2336-7202. [Mezioborové setkání mladých biologů, biochemiků a chemiků /17./. 30.05.2017-01.06.2017, Milovy] R&D Projects: GA ČR(CZ) GA17-00121S Institutional support: RVO:61388963 Keywords : nitrotyrosin * conformational space * spectra simulation Subject RIV: CF - Physical ; Theoretical Chemistry

  4. Thermodynamic Studies of Levitated Microdroplets of Highly Supersaturated Electrolyte Solutions

    Science.gov (United States)

    Myerson, Allan S.; Izmailov, Alexander F.; Na, Han-Soo

    1996-01-01

    Highly supersaturated electrolyte solutions are studied by employing an electrodynamic levitator trap (ELT) technique. The ELT technique involves containerless suspension of a microdroplet thus eliminating dust, dirt, and container walls which normally cause heterogeneous nucleation. This allows very high supersaturations to be achieved. A theoretical study of the experimental results obtained for the water activity in microdroplets of various electrolyte solutions is based on the development of the Cahn-Hilliard formalism for electrolyte solutions. A correspondence of 96-99% between the theory and experiment for the all solutions studied was achieved and allowed the determination of an analytical expression for the spinodal concentration n(sub spin) and its calculation for various electrolyte solutions at 298 K.

  5. Thermodynamic studies of levitated microdroplets of highly supersaturated electrolyte solutions

    Science.gov (United States)

    Myerson, Allan S.; Izmailov, Alexander F.; Na, Han-Soo

    1996-09-01

    Highly supersaturated electrolyte solutions are studied by employing an electrodynamic levitator trap (ELT) technique. The ELT technique involves containerless suspension of a microdroplet thus eliminating dust, dirt, and container walls which normally cause heterogeneous nucleation. This allows very high supersaturations to be achieved. A theoretical study of the experimental results obtained for the water activity in microdroplets of various electrolyte solutions is based on the development of the Cahn-Hilliard formalism for electrolyte solutions. A correspondence of 96-99% between the theory and experiment for the all solutions studied was achieved and allowed the determination of an analytical expression for the spinodal concentration nspin and its calculation for various electrolyte solutions at 298 K.

  6. Study of High Beta Optics Solution for TOTEM

    OpenAIRE

    Burkhardt, H; White, S; Levinsen, Y

    2009-01-01

    The TOTEM experiment requires special high beta optics solutions. We report on studies of optics for an intermediate β* = 90m, as well as a solutions for a very high β* of 1535 m, which respect all known constraints. These optics are rather different from the normal physics optics and will require global tune changes or adjustments.

  7. Examples for Non-Ideal Solution Thermodynamics Study

    Science.gov (United States)

    David, Carl W.

    2004-01-01

    A mathematical model of a non-ideal solution is presented, where it is shown how and where the non-ideality manifests itself in the standard thermodynamics tableau. Examples related to the non-ideal solution thermodynamics study are also included.

  8. Jatrophidin I, a cyclic peptide from Brazilian Jatropha curcas L.: isolation, characterization, conformational studies and biological activity.

    Science.gov (United States)

    Altei, Wanessa F; Picchi, Douglas G; Abissi, Barbara M; Giesel, Guilherme M; Flausino, Otavio; Reboud-Ravaux, Michèle; Verli, Hugo; Crusca, Edson; Silveira, Edilberto R; Cilli, Eduardo M; Bolzani, Vanderlan S

    2014-11-01

    A cyclic peptide, jatrophidin I, was isolated from the latex of Jatropha curcas L. Its structure was elucidated by extensive 2D NMR spectroscopic analysis, with additional conformational studies performed using Molecular Dynamics/Simulated Annealing (MD/SA). Jatrophidin I had moderate protease inhibition activity when compared with pepstatin A; however, the peptide was inactive in antimalarial, cytotoxic and antioxidant assays. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. A computational and spectroscopic study of the gas-phase conformers of adrenaline

    Science.gov (United States)

    Çarçabal, P.; Snoek, L. C.; van Mourik, T.

    The conformational landscapes of the neurotransmitter l-adrenaline (l-epinephrine) and its diastereoisomer pseudo-adrenaline, isolated in the gas phase and un-protonated, have been investigated by using a combination of mass-selected ultraviolet and infrared holeburn spectroscopy, following laser desorption of the sample into a pulsed supersonic argon jet, and DFT and ab initio computation (at the B3LYP/6-31+G*, MP2/6-31+G* and MP2/aug-cc-pVDZ levels of theory). Both for adrenaline and its diastereoisomer, pseudo-adrenaline, one dominant molecular conformation, very similar to the one seen in noradrenaline, has been observed. It could be assigned to an extended side-chain structure (AG1a) stabilized by an OH → N intramolecular hydrogen bond. An intramolecular hydrogen bond is also formed between the neighbouring hydroxyl groups on the catechol ring. The presence of further conformers for both diastereoisomers could not be excluded, but overlapping electronic spectra and low ion signals prevented further assignments.

  10. Application of conformal map theory for design of 2-D ultrasonic array structure for NDT imaging application: a feasibility study.

    Science.gov (United States)

    Ramadas, Sivaram N; Jackson, Joseph C; Dziewierz, Jerzy; O'Leary, Richard; Gachagan, Anthony

    2014-03-01

    Two-dimensional ultrasonic phased arrays are becoming increasingly popular in nondestructive evaluation (NDE). Sparse array element configurations are required to fully exploit the potential benefits of 2-D phased arrays. This paper applies the conformal mapping technique as a means of designing sparse 2-D array layouts for NDE applications. Modeling using both Huygens' field prediction theory and 2-D fast Fourier transformation is employed to study the resulting new structure. A conformal power map was used that, for fixed beam width, was shown in simulations to have a greater contrast than rectangular or random arrays. A prototype aperiodic 2-D array configuration for direct contact operation in steel, with operational frequency ~3 MHz, was designed using the array design principle described in this paper. Experimental results demonstrate a working sparse-array transducer capable of performing volumetric imaging.

  11. Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics.

    Science.gov (United States)

    Hammond, Philip S; Wu, Yudong; Harris, Rebecca; Minehardt, Todd J; Car, Roberto; Schmitt, Jeffrey D

    2005-01-01

    A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

  12. Conformational study of (8alpha,8'beta)-bis(substituted phenyl)-lignano-9,9'-lactones by means of combined computational, database mining, NMR, and chemometric approaches.

    Science.gov (United States)

    Kiralj, Rudolf; Ferreira, Marcia M C; Donate, Paulo M; da Silva, Rosangela; Albuquerque, Sergio

    2007-07-19

    Beta-(3,4-Methylenedioxybenzyl)-gamma-butyrolactone (MDBL) and (-)-hinokinin (HK) were obtained by partial synthesis and characterized by 1H NMR and computational methods (conformational analysis, molecular modeling, structural data mining and chemometrics). Three conformers were detected for MDBL and nine were found for HK. The energy differences are around 1 and 2 kcal mol(-1) and rotation barriers are less than 3 and 5 kcal mol(-1) for MDBL and HK conformers, respectively. The geometries of these conformers, obtained from semiempirical PM3 and density functional theory (DFT) B3LYP 6-31G** calculations agree satisfactorily with 1H NMR data (vicinal proton-proton coupling constants) and structures retrieved from the Cambridge Structural Database (torsion angles). DFT combined with some variants of the Haasnoot-de Leeuuw-Altona equations gives the best predictions for the coupling constants. The molecular conformation of MDBL, of HK, and of related systems depends not only on intramolecular interactions but also on crystal packing forces and solvent-solute interactions, in particular hydrogen bonds and polar interactions. Hydration favors more stable HK conformers, which can be important for their behavior in chemical and biological systems.

  13. Vitamin E Circular Dichroism Studies: Insights into Conformational Changes Induced by the Solvent’s Polarity

    Directory of Open Access Journals (Sweden)

    Drew Marquardt

    2016-12-01

    Full Text Available We used circular dichroism (CD to study differences in CD spectra between α-, δ-, and methylated-α-tocopherol in solvents with different polarities. CD spectra of the different tocopherol structures differ from each other in intensity and peak locations, which can be attributed to chromanol substitution and the ability to form hydrogen bonds. In addition, each structure was examined in different polarity solvents using the Reichardt index—a measure of the solvent’s ionizing ability, and a direct measurement of solvent–solute interactions. Differences across solvents indicate that hydrogen bonding is a key contributor to CD spectra at 200 nm. These results are a first step in examining the hydrogen bonding abilities of vitamin E in a lipid bilayer.

  14. Open science grid study of the coupling between conformation and water content in the interior of a protein.

    Science.gov (United States)

    Damjanović, Ana; Miller, Benjamin T; Wenaus, Torre J; Maksimović, Petar; García-Moreno E, Bertrand; Brooks, Bernard R

    2008-10-01

    Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.

  15. Formal consensus method to evaluate the conformity of prescription of a recently approved chemotherapy treatment in an observatory study.

    Directory of Open Access Journals (Sweden)

    Nadine Houédé

    Full Text Available Cabazitaxel is a second line chemotherapy drug recently approved for the treatment of metastatic castration-resistant prostate cancer. A first panel of French experts and a second independent panel of European experts were convened to assess the conformity of prescription of cabazitaxel with a Delphi consensus method. A two-round modified Delphi consensus process was conducted. This methodology is based on experts' opinion obtained in a systematic manner. The process was divided into five steps: (i elaboration of the questionnaire, (ii rating, (iii analysis, (iv discussion of the points with absence of consensus following rating of the questionnaire, and (v final reporting. Consensus was defined according to RAND method and all analyses were conducted according to the same methodology. At the end of the two rounds of rating and a synthesis meeting, of the 26 items included in the Summary of Product Characteristics (SPC, 11 items were judged appropriate with strong consensus by the two independent panels of experts. These items can therefore be considered of prime importance to evaluate conformity of cabazitaxel prescription in the context of observatory studies as well as in further clinical trials using this new taxane. Our findings further provide important evidence about the value of the Delphi consensus and highlight a requirement for "conformity" standards to assist practitioners in a safe chemotherapy drug prescription.

  16. A STUDY OF THE EDGE FIELD EFFECT USING MAFIA SIMULATIONS CONFORMAL MAPPING

    Energy Technology Data Exchange (ETDEWEB)

    ZHAO,Y.

    1999-10-01

    It was found that the measured Q value of a tape resonator has a large difference with that calculated with MAFIA. This difference is recognized to be mainly due to the error in the simulation, which is unable to handle a sharp edge. This note addresses the 2-dimensional MAFIA simulation and conformal mapping. It shows the error could be as high as 60 %. Reasonable caution should be exercised in the use of MAFIA, and other codes as well, in calculating Q value if a sharp edge exists in the problem.

  17. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Olsen, Jógvan Magnus Haugaard; Aidas, Kestutis

    2011-01-01

    In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers...... using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior...... to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations...

  18. Conformational relaxations of human serum albumin studied by molecular dynamics simulations with pressure jumps

    Directory of Open Access Journals (Sweden)

    Yesylevskyy S. O.

    2012-12-01

    Full Text Available Aim. In this work we developed a novel technique of obtaining the spectrum of conformational relaxations in a solvated protein using non-equilibrium molecular dynamics simulation. Methods. Structural relaxations in the protein are initiated by the abrupt jump of pressure in the NPT simulations. The change of the protein volume after the jump is monitored and the Maximum Entropy Method is used for spectral decomposition of the volume relaxation curve. The human serum albumin (HSA is used as a test case. Results. The obtained relaxation spectrum of HSA contains one component attributed to the bulk water and five components caused by the relaxations of the protein globule and its hydration shell. All relaxation components are in good agreement with the available experimental data obtained by the time-resolved spectroscopy and the broadband acoustic spectroscopy of HSA. Conclusions. The developed technique allows obtaining spectra of conformational relaxations of soluble proteins in a range of time scales from ~0.1 ps to ~50 ns utilizing single non-equilibrium molecular dynamics simulation.

  19. Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

    Science.gov (United States)

    Asadinezhad, Ahmad; Kelich, Payam

    2017-01-01

    The effects of nanofiller chemistry and geometry on static and dynamic properties of an aromatic polyester, poly (trimethylene terephthalate), were addressed thanks to long-run classical molecular dynamics simulation. Two carbon nanofillers, graphene and carbon nanotube, were employed, where graphene was used in pristine and functionalized forms and carbon nanotube was used in two different diameters. The nanofiller geometry and chemistry were found to exert significant effects on conformation and dynamic behavior of PTT chain at the interface within the time scale the simulation was performed. It was found that PTT chain underwent interaction of van der Waals type with nanofiller via two subsequent phases, adsorption and orientation. The former stage, with definite characteristic time, involved translation of polymer chain toward interface while the latter was controlled by vibrational motions of chain atoms. The consequence of interaction was an increase in conformational order of polymer chain by transition to folded shape being favorable for any subsequent structural ordering (crystallization). The interaction of polymer with nanofiller gave rise to a reduction in overall mobility of polymer chain characterized by crossover from normal diffusive motion to subdiffusive mode.

  20. SOLUTIONING

    Directory of Open Access Journals (Sweden)

    Maria de Hoyos Guajardo, Ph.D. Candidate, M.Sc., B.Eng.

    2004-11-01

    Full Text Available The theory that is presented below aims to conceptualise how a group of undergraduate students tackle non-routine mathematical problems during a problem-solving course. The aim of the course is to allow students to experience mathematics as a creative process and to reflect on their own experience. During the course, students are required to produce a written ‘rubric’ of their work, i.e., to document their thoughts as they occur as well as their emotionsduring the process. These ‘rubrics’ were used as the main source of data.Students’ problem-solving processes can be explained as a three-stage process that has been called ‘solutioning’. This process is presented in the six sections below. The first three refer to a common area of concern that can be called‘generating knowledge’. In this way, generating knowledge also includes issues related to ‘key ideas’ and ‘gaining understanding’. The third and the fourth sections refer to ‘generating’ and ‘validating a solution’, respectively. Finally, once solutions are generated and validated, students usually try to improve them further before presenting them as final results. Thus, the last section deals with‘improving a solution’. Although not all students go through all of the stages, it may be said that ‘solutioning’ considers students’ main concerns as they tackle non-routine mathematical problems.

  1. Charged C-metric in conformal gravity

    CERN Document Server

    Lim, Yen-Kheng

    2016-01-01

    Using a C-metric-type ansatz, we obtain an exact solution to conformal gravity coupled to a Maxwell electromagnetic field. The solution resembles a C-metric spacetime carrying an electromagnetic charge. The metric is cast in a factorised form which allows us to study the domain structure of its static coordinate regions. This metric reduces to the well-known Mannheim-Kazanas metric under an appropriate limiting procedure, and also reduces to the (Anti-)de Sitter C-metric of Einstein gravity for a particular choice of parameters.

  2. Studies on the Use of Oyster, Snail and Periwinkle Shells as Adsorbents for the Removalof Pb2+ Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Stevens A. Odoemelam

    2009-01-01

    Full Text Available In view of increasing rate of lead pollution resulting from discharge of lead containing effluents by industries into the environment, this study was carried out to investigate the removal of Pb2+ from aqueous solutions by oyster, snail and periwinkle shells. The effects of contact time and concentration on adsorption, thermodynamics of sorption and distribution coefficients of the adsorbents were examined to optimize the conditions to be utilized for decontamination of effluents containing Pb2+. The study revealed that these materials are good adsorbents that can be used for the removal of Pb2+ from aqueous solution. Adsorption of Pb2+ by oyster, snail and periwinkle shells were found to conform to the classical models of Langmuir, Freundlich and Temkin adsorption isotherms. Thermodynamic consideration revealed that adsorption of Pb2+ by these materials was spontaneous and proceeded via chemical adsorption. The use of these materials for the removal of lead ion from aqueous solution is therefore advocated

  3. Experimental and theoretical study of the CD spectra and conformational properties of axially chiral 2,2'-, 3,3'-, and 4,4'-biphenol ethers.

    Science.gov (United States)

    Mori, Tadashi; Inoue, Yoshihisa; Grimme, Stefan

    2007-05-24

    New chiral biphenol ethers (Biph22, Biph33, and Biph44), carrying (R)-methylpropyloxy groups at 2,2'-, 3,3'-, and 4,4'-positions of biphenyl, were prepared. The introduced peripheral chiral groups in these biphenol ethers induce an (averaged) axial chirality to give predominant aR- or aS-rotamers. The chiroptical properties of these axially chiral biphenol ethers in polar and nonpolar solvents were determined experimentally and were compared with the corresponding theoretical values to determine their conformational behavior in solution. Geometry optimization at the DFT-D/TZV2P level and subsequent time-dependent density functional theory (TD-DFT) at the BH-LYP/TZV2P level treatments to obtain rotatory strengths revealed that 6 out of 18 conformers (aR-Tg-, aR-Tg+, aR-G+t, aS-Tg-, aS-Tg+, and aS-G+t) are crucial to reproduce the experimental circular dichroism (CD) spectra and optical rotations. Although biphenyl molecules are in conformational equilibrium with varying interplanar angles in solution, our static approach to the prediction of the experimental CD spectra is simply based on pairs of thermally populated, local-minimum structures, that is, the dynamic behavior of the systems or the vibrational wave functions are not considered. The relative energies computed at the SCS-MP2/TZVPP level in the gas phase or in acetonitrile solution using the conductor-like screening model (COSMO) were found to be accurate enough to calculate the thermal population of the relevant conformers. Although most of the CD signals mutually cancel out each other between a pair of aR- and aS-rotamers, the remaining Cotton effects due to a small preference for a single rotamer produce characteristic CD spectra. In general (and somewhat unexpectedly), the delicate cancellation effects in the CD spectra are accurately described by the theoretical approach, and the simulated CD spectra are in excellent agreement with the experimental ones though observed rotatory strengths being always

  4. Scattering Study of a Modified Cusp Potential in Conformable Fractional Formalism

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Won Sang [Gyeongsang National University, Jinju (Korea, Republic of); Zarrinkamar, Saber [Islamic Azad University, Garmsar (Iran, Islamic Republic of); Zare, Soroush [Islamic Azad University North Tehran Branch, Tehran (Iran, Islamic Republic of); Hassanabadi, Hassan [Shahrood University of Technology, Shahrood (Iran, Islamic Republic of)

    2017-02-15

    The fractional Schr¨odinger equation is considered with a cusp interaction. Exact analytical solutions are obtained and thereby the scattering states as well as transmission and reflection coefficients are determined.

  5. Scattering study of a modified cusp potential in conformable fractional formalism

    Science.gov (United States)

    Chung, Won Sang; Zarrinkamar, Saber; Zare, Soroush; Hassanabadi, Hassan

    2017-02-01

    The fractional Schrödinger equation is considered with a cusp interaction. Exact analytical solutions are obtained and thereby the scattering states as well as transmission and reflection coefficients are determined.

  6. Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection.

    Science.gov (United States)

    Buscaglia, Robert; Miller, M Clarke; Dean, William L; Gray, Robert D; Lane, Andrew N; Trent, John O; Chaires, Jonathan B

    2013-09-01

    Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the 'hybrid' conformation to an all-parallel 'propeller' conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation.

  7. Vibrational spectra, NBO, HOMO-LUMO and conformational stability studies of 4-hydroxythiobenzamide

    Science.gov (United States)

    Sambathkumar, Kuppusamy

    2015-08-01

    In this work, the experimental and theoretical study on molecular structure, vibrational spectral analysis of 4-hydroxythiobenzamide (HTB) have been reported. The solid phase FTIR (4000-400 cm-1) and FT-Raman spectra (3500-50 cm-1) were recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of HTB in the ground-state have been calculated by the density functional method (B3LYP) with 6-311+G(d,p) and 6-311++G(d,p) as basis sets. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Stability of the molecule arising from hyperconjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that the value of electron density (ED) in the σ∗ antibonding orbitals and E(2) energies confirms the occurrence of ICT (intra-molecular charge transfer) within the molecule. The UV spectrum was measured in ethanol solution. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) correlates with the experimental findings. The calculated molecular electrostatic potential (MESP), HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides, the simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra.

  8. Study of conformational stability, structural, electronic and charge transfer properties of cladrin using vibrational spectroscopy and DFT calculations.

    Science.gov (United States)

    Singh, Swapnil; Singh, Harshita; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Bharti, Purnima; Kumar, Sudhir; Kumar, Padam; Maurya, Rakesh

    2014-11-11

    In the present work, a detailed conformational study of cladrin (3-(3,4-dimethoxy phenyl)-7-hydroxychromen-4-one) has been done by using spectroscopic techniques (FT-IR/FT-Raman/UV-Vis/NMR) and quantum chemical calculations. The optimized geometry, wavenumber and intensity of the vibrational bands of the cladrin in ground state were calculated by density functional theory (DFT) employing 6-311++G(d,p) basis sets. The study has been focused on the two most stable conformers that are selected after the full geometry optimization of the molecule. A detailed assignment of the FT-IR and FT-Raman spectra has been done for both the conformers along with potential energy distribution for each vibrational mode. The observed and scaled wavenumber of most of the bands has been found to be in good agreement. The UV-Vis spectrum has been recorded and compared with calculated spectrum. In addition, 1H and 13C nuclear magnetic resonance spectra have been also recorded and compared with the calculated data that shows the inter or intramolecular hydrogen bonding. The electronic properties such as HOMO-LUMO energies were calculated by using time-dependent density functional theory. Molecular electrostatic potential has been plotted to elucidate the reactive part of the molecule. Natural bond orbital analysis was performed to investigate the molecular stability. Non linear optical property of the molecule have been studied by calculating the electric dipole moment (μ) and the first hyperpolarizability (β) that results in the nonlinearity of the molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Crises Solutions for SMEs Case Study: ERP Cloud vs Classic Solution

    Directory of Open Access Journals (Sweden)

    Gabriela GHEORGHE

    2012-11-01

    Full Text Available Information Technology has responded to the crisis by change and innovation. The phenomenon of cloud computing represents a huge chance for a country like Romania, as a technologically low economy has, from the start, a handicap. Cloud technologies redefine concepts such as saving time and money, flexibility, scalability and global access, transforming them into business advantages. This case study wishes to argument the software provider’s decision to change his strategy, choosing an “all inclusive” solution.

  10. Non-Catalyzed Click Reactions of ADIBO Derivatives with 5-Methyluridine Azides and Conformational Study of the Resulting Triazoles

    Science.gov (United States)

    Smyslova, Petra; Popa, Igor; Lyčka, Antonín; Tejral, Gracian; Hlavac, Jan

    2015-01-01

    Copper-free click reactions between a dibenzoazocine derivative and azides derived from 5-methyluridine were investigated. The non-catalyzed reaction yielded both regioisomers in an approximately equivalent ratio. The NMR spectra of each regioisomer revealed conformational isomery. The ratio of isomers was dependent on the type of regioisomer and the type of solvent. The synthesis of various analogs, a detailed NMR study and computational modeling provided evidence that the isomery was dependent on the interaction of the azocine and pyrimidine parts. PMID:26673606

  11. Solution NMR studies of amphibian antimicrobial peptides: linking structure to function?

    Science.gov (United States)

    Haney, Evan F; Hunter, Howard N; Matsuzaki, Katsumi; Vogel, Hans J

    2009-08-01

    The high-resolution three-dimensional structure of an antimicrobial peptide has implications for the mechanism of its antimicrobial activity, as the conformation of the peptide provides insights into the intermolecular interactions that govern the binding to its biological target. For many cationic antimicrobial peptides the negatively charged membranes surrounding the bacterial cell appear to be a main target. In contrast to what has been found for other classes of antimicrobial peptides, solution NMR studies have revealed that in spite of the wide diversity in the amino acid sequences of amphibian antimicrobial peptides (AAMPs), they all adopt amphipathic alpha-helical structures in the presence of membrane-mimetic micelles, bicelles or organic solvent mixtures. In some cases the amphipathic AAMP structures are directly membrane-perturbing (e.g. magainin, aurein and the rana-box peptides), in other instances the peptide spontaneously passes through the membrane and acts on intracellular targets (e.g. buforin). Armed with a high-resolution structure, it is possible to relate the peptide structure to other relevant biophysical and biological data to elucidate a mechanism of action. While many linear AAMPs have significant antimicrobial activity of their own, mixtures of peptides sometimes have vastly improved antibiotic effects. Thus, synergy among antimicrobial peptides is an avenue of research that has recently attracted considerable attention. While synergistic relationships between AAMPs are well described, it is becoming increasingly evident that analyzing the intermolecular interactions between these peptides will be essential for understanding the increased antimicrobial effect. NMR structure determination of hybrid peptides composed of known antimicrobial peptides can shed light on these intricate synergistic relationships. In this work, we present the first NMR solution structure of a hybrid peptide composed of magainin 2 and PGLa bound to SDS and DPC

  12. Theoretical study on conformation dynamics of three-station molecular shuttle in different environments and its influence on NMR chemical shifts and binding interactions.

    Science.gov (United States)

    Liu, Pingying; Li, Wei; Liu, Li; Wang, Leyong; Ma, Jing

    2014-10-02

    Microscopic information on conformational flexibility and macrocycle-thread binding interactions is helpful in rational design of novel multistation molecular shuttles with interesting topology and functions. Molecular dynamics (MD) was applied to simulate conformational changes of thread and macrocycle of a three-station molecular shuttle in different chemical environments (vacuum, CD3CN-CDCl3 solution, and crystal). In contrast with the highly distorted thread conformation in the gas phase and nonpolar CDCl3 solution, the solvated thread in CD3CN-CDCl3 (1:1) mix solvents exhibited a relatively rigid structure. Experimental observations of preferential binding at the protonated dibenzylammonium group (station I) were rationalized by quantum chemical calculations of macrocycle-thread binding energies at three different stations. The orthogonality of site-specific binding interactions at three different stations was also revealed by the nearly constant binding energy obtained at each specific recognition center with the replacement of different neighboring groups and terminal stoppers on the thread. Conformational flexibility has little effect on NMR signals of binding sites, but for some protons that are close to the solvent molecules in the first solvent shell, their chemical shifts are sensitive to the local electrostatic environment caused by nearby solvents. In crystal, π stacking induced evident upfield shifts of NMR signals in comparison with the isolated monomer.

  13. Effects of Shapes of Solute Molecules on Diffusion: A Study of Dependences on Solute Size, Solvent, and Temperature.

    Science.gov (United States)

    Chan, T C; Li, H T; Li, K Y

    2015-12-24

    Diffusivities of basically linear, planar, and spherical solutes at infinite dilution in various solvents are studied to unravel the effects of solute shapes on diffusion. On the basis of the relationship between the reciprocal of diffusivity and the molecular volume of solute molecules with similar shape in a given solvent at constant temperature, the diffusivities of solutes of equal molecular volume but different shapes are evaluated and the effects due to different shapes of two equal-sized solute molecules on diffusion are determined. It is found that the effects are dependent on the size of the solute pairs studied. Evidence of the dependence of the solute-shape effects on solvent properties is also demonstrated and discussed. Here, some new diffusion data of aromatic compounds in methanol at different temperatures are reported. The result for methanol in this study indicates that the effects of solute shape on diffusivity are only weakly dependent on temperature.

  14. Spectroscopic studies of oligodiacetylenes in solution and polymer film

    NARCIS (Netherlands)

    Hendrikx, C.C.J.; Polhuis, M.; Pul-Hootsen, A.; Koehorst, R.B.M.; Hoek, van A.; Zuilhof, H.; Sudhölter, E.J.R.

    2005-01-01

    The photophysical properties of a series of monomeric, dimeric and trimeric oligodiacetylenes (ODAs; oligoenynes) bearing trimethylsilyl, t-butyl and n-octyl end-capping substituents were studied in solution and in a polymer film. Emission studies show a significant emission of oligodiacetylenes in

  15. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

    Although member states are obliged to transpose directives into domestic law in a conformable manner and receive considerable time for their transposition activities, we identify three levels of transposition outcomes for EU directives: conformable, partially conformable and non-conformable...... and the Commission regarding a directive’s outcome, play a much more strategic role than has to date acknowledged in the transposition literature. Whereas disagreement of a member state delays conformable transposition, it speeds up non-conformable transposition. Disagreement of the Commission only prolongs...

  16. [Non-conformities management in laboratory of medical biology: application to non-conformities of biological samples during 2009].

    Science.gov (United States)

    Annaix, Véronique; Rogowski, Julien; Joyau, Mireille; Jaouën, Edtih

    2011-01-01

    The non-conformity management is required for the ISO 15189 standard. The laboratory of medical biology has to carry out suitable acts and procedures to exploit different indicators through the framework of continuous improvement. We particularly study the indicator of biological samples nonconformities and we report 2009 results to the nurses' team managers to find solutions for quality of care to the patient.

  17. CONFORMATIONAL FLEXIBILITY OF AQUEOUS MONOMERIC AND DIMERIC INSULIN - A MOLECULAR-DYNAMICS STUDY

    NARCIS (Netherlands)

    MARK, AE; BERENDSEN, HJC; VANGUNSTEREN, WF

    1991-01-01

    A series of molecular dynamics simulations have been used to investigate the nature of monomeric and dimeric insulin in aqueous solution. It is shown that in the absence of crystal contacts both monomeric and dimeric insulin have a high degree of intrinsic flexibility. Neither of the two monomer

  18. Effects of Anesthetic Membrane Solutes on Orientational Order in Lecithin Bilayer Membranes: a Deuterium NMR Study.

    Science.gov (United States)

    Phonphok, Nason

    The interaction of eight n-alkanols and three volatile anesthetics with bilayers of dimyristoylphosphatidylcholine (DMPC) has been studied by deuterium nuclear magnetic resonance (^2H NMR). At comparable temperatures and concentrations of solute in the bilayer, order parameters measured at the 1-methylene segment of the n-alkanols, and average order parameters for the whole alkyl chain, show a maximum for n-dodecanol. This maximum in orientational ordering also occurs for n-dodecanol at the much lower levels of solute concentration which produce anesthesia. For both n-dodecanol and n-tetradecanol, orientational ordering shows a maximum at the C-4 to C-7 methylene segments, with labels at both ends of the n-alkanol exhibiting reduced order. Unlike the longer chain n-alkanols, ordering in n-butanol decreases from the hydroxyl group end to the methyl group end of the molecule. The quadrupole splittings observed in DMPC-water systems containing perdeuterated ether, chloroform and n-hexane show that these volatile anesthetics are also ordered in the bilayer in the L _{alpha} phase. The temperature dependence of the quadrupole splitting ^2H_2O in DMPC bilayers at low hydration indicates that both the n-alkanols and volatile anesthetics do not affect water structure in the L_alpha phase, but they do so below the main phase transition. Orientational ordering at nine inequivalent sites in the headgroup region of DMPC, as well as the acyl chains, has also been measured. Every anesthetic produces a disordering at the beta-methylene of the choline, the 3-methylene segment and the 1-R site (except chloroform) of the glycerol backbone. Molecular and conformational ordering at the interfacial region of DMPC in the L _alpha phase have been examined by analysing ^2H-NMR data from multiple sites in the most rigid region of the DMPC molecule. It was found that these anesthetics change the conformation at the glycerol moiety of DMPC without changing the molecular order parameter rm S

  19. SU-E-T-562: Motion Tracking Optimization for Conformal Arc Radiotherapy Plans: A QUASAR Phantom Based Study

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Z; Wang, I; Yao, R; Podgorsak, M [Roswell Park Cancer Institute, Buffalo, NY (United States)

    2015-06-15

    Purpose: This study is to use plan parameters optimization (Dose rate, collimator angle, couch angle, initial starting phase) to improve the performance of conformal arc radiotherapy plans with motion tracking by increasing the plan performance score (PPS). Methods: Two types of 3D conformal arc plans were created based on QUASAR respiratory motion phantom with spherical and cylindrical targets. Sinusoidal model was applied to the MLC leaves to generate motion tracking plans. A MATLAB program was developed to calculate PPS of each plan (ranges from 0–1) and optimize plan parameters. We first selected the dose rate for motion tracking plans and then used simulated annealing algorithm to search for the combination of the other parameters that resulted in the plan of the maximal PPS. The optimized motion tracking plan was delivered by Varian Truebeam Linac. In-room cameras and stopwatch were used for starting phase selection and synchronization between phantom motion and plan delivery. Gaf-EBT2 dosimetry films were used to measure the dose delivered to the target in QUASAR phantom. Dose profiles and Truebeam trajectory log files were used for plan delivery performance evaluation. Results: For spherical target, the maximal PPS (PPSsph) of the optimized plan was 0.79: (Dose rate: 500MU/min, Collimator: 90°, Couch: +10°, starting phase: 0.83π). For cylindrical target, the maximal PPScyl was 0.75 (Dose rate: 300MU/min, Collimator: 87°, starting phase: 0.97π) with couch at 0°. Differences of dose profiles between motion tracking plans (with the maximal and the minimal PPS) and 3D conformal plans were as follows: PPSsph=0.79: %ΔFWHM: 8.9%, %Dmax: 3.1%; PPSsph=0.52: %ΔFWHM: 10.4%, %Dmax: 6.1%. PPScyl=0.75: %ΔFWHM: 4.7%, %Dmax: 3.6%; PPScyl=0.42: %ΔFWHM: 12.5%, %Dmax: 9.6%. Conclusion: By achieving high plan performance score through parameters optimization, we can improve target dose conformity of motion tracking plan by decreasing total MLC leaf travel distance

  20. Silicon-Containing Amino Acids: Synthetic Aspects, Conformational Studies, and Applications to Bioactive Peptides.

    Science.gov (United States)

    Rémond, Emmanuelle; Martin, Charlotte; Martinez, Jean; Cavelier, Florine

    2016-10-12

    Unnatural α-amino acids form a family of essential molecules used for, among other applications, the synthesis of modified peptides, to improve resistance to proteolytic enzyme degradation, and to modulate physico- and biochemical properties of bioactive peptides as well as chiral inducers in asymmetric synthesis. Among them, silicon-containing unnatural amino acids are becoming an interesting new class of building blocks. The replacement of carbon atoms in bioactive substances with silicon is becoming increasingly popular. Peptides containing silyl amino acids hold great promise for maintaining or reinforcing the biological activity of active compounds, while they simultaneously enhance their resistance to enzyme degradation. In addition, the lipophilicity of the silicon atom facilitates their membrane crossing and their bioavailability. Nowadays, the interest of the pharmaceutical industry in peptide- and protein-based therapies is increasing. In this respect, silicon-containing amino acids and peptides are likely to be a significant part of future innovations in this area, and more generally in the area of biomolecules. In this process, commercial availability of silicon-containing amino acids is necessary: new syntheses have been developed, and work in this area is ongoing. This review aims to be a comprehensive and general summary of the different methods used to prepare silicon-containing amino acids and their implications on conformational structures and biological applications when they are incorporated into bioactive molecules.

  1. Dehydration-induced conformational changes of poly-L-lysine as influenced by drying rate and carbohydrates.

    NARCIS (Netherlands)

    Wolkers, W.F.; Kilsdonk, van M.G.; Hoekstra, F.A.

    1998-01-01

    The conformation of hydrated and air-dried poly-L-lysine in thin films was studied using Fourier transform IR spectroscopy in the amide-I region. Hydrated poly-L-lysine has a random coil conformation. Upon slow drying of small droplets of the polypeptide solution over a period of several hours, an

  2. Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.

    Science.gov (United States)

    Machado, Agnes Thiane Pereira; Fonseca, Emanuella Maria Barreto; Reis, Marcelo Augusto Dos; Saraiva, Antonio Marcos; Santos, Clelton Aparecido Dos; de Toledo, Marcelo Augusto Szymanski; Polikarpov, Igor; de Souza, Anete Pereira; Aparicio, Ricardo; Iulek, Jorge

    2017-10-01

    Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein. © 2017 Wiley Periodicals, Inc.

  3. Challenges of Agro-Food Standards Conformity

    DEFF Research Database (Denmark)

    Bolwig, Simon; Riisgaard, Lone; Gibbon, Peter

    2013-01-01

    a variety of programmes and projects aimed at supporting standards development and conformity. This article contributes to the critical literature discussing the challenges and potentials of standards conformity and supplies policy recommendations for future interventions. It reports the results...... of a research programme on standards conformity in East Africa. These demonstrate that most interventions underestimate the nature of the challenges faced and that significant impacts are achieved only under rather restricted conditions. The solutions lay not only in more selective support to standard...

  4. Conformal gravity and "gravitational bubbles"

    CERN Document Server

    Berezin, V A; Eroshenko, Yu N

    2015-01-01

    We describe the general structure of the spherically symmetric solutions in the Weyl conformal gravity. The corresponding Bach equations are derived for the special type of metrics, which can be considered as the representative of the general class. The complete set of the pure vacuum solutions, consisting of two classes, is found. The first one contains the solutions with constant two-dimensional curvature scalar, and the representatives are the famous Robertson--Walker metrics. We called one of them the "gravitational bubbles", which is compact and with zero Weyl tensor. These "gravitational bubbles" are the pure vacuum curved space-times (without any material sources, including the cosmological constant), which are absolutely impossible in General Relativity. This phenomenon makes it easier to create the universe from "nothing". The second class consists of the solutions with varying curvature scalar. We found its representative as the one-parameter family, which can be conformally covered by the thee-para...

  5. Effect of graphene oxide on the conformational transitions of amyloid beta peptide: A molecular dynamics simulation study.

    Science.gov (United States)

    Baweja, Lokesh; Balamurugan, Kanagasabai; Subramanian, Venkatesan; Dhawan, Alok

    2015-09-01

    The interactions between nanomaterials (NMs) and amyloid proteins are central to the nanotechnology-based diagnostics and therapy in neurodegenerative disorders such as Alzheimer's and Parkinson's. Graphene oxide (GO) and its derivatives have shown to modulate the aggregation pattern of disease causing amyloid beta (Aβ) peptide. However, the mechanism is still not well understood. Using molecular dynamics simulations, the effect of graphene oxide (GO) and reduced graphene oxide (rGO) having carbon:oxygen ratio of 4:1 and 10:1, respectively, on the conformational transitions (alpha-helix to beta-sheet) and the dynamics of the peptide was investigated. GO and rGO decreased the beta-strand propensity of amino acid residues in Aβ. The peptide displayed different modes of adsorption on GO and rGO. The adsorption on GO was dominated by electrostatic interactions, whereas on rGO, both van der Waals and electrostatic interactions contributed in the adsorption of the peptide. Our study revealed that the slight increase in the hydrophobic patches on rGO made it more effective inhibitor of conformational transitions in the peptide. Alpha helix-beta sheet transition in Aβ peptide could be one of the plausible mechanism by which graphene oxide may inhibit amyloid fibrillation. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. A Longitudinal Study of non-Conforming Social Reputation and Violence in Adolescents From the Gender Perspective

    Directory of Open Access Journals (Sweden)

    David Moreno Ruiz

    2011-12-01

    Full Text Available The aim of the current study was to analyze the relationship between non-conformist social reputation (perceived and ideal and instrumental violence (overt and relational in adolescents from the gender perspective. The sample was composed of 1319 adolescents -T1- aged from 11 to 16 years old (Mean 13.5; S.D. 1.5 and both sexes (53 % girls and 47 % boys in secondary school, and 554 students -T2- (54 % girls and 46 % boys. Measures were Non-conformist social reputation scale (Carroll, Houghton, Hattie and Durkin, 1999 and Instrumental violence behavior scale (Little, Henrich, Jones and Hawley, 2003. From structural equation models it was found that the non-conforming social reputation –ideal and perceived- (T1 was related with non-conforming social reputation (T2. An indirect relation was also observed between perceived reputation (T1 and perceived reputation (T2 through overt instrumental violence. Results were analyzed from a gender perspective.

  7. Volumetric studies of some amino acids in binary aqueous solutions ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 117; Issue 3. Volumetric studies of some amino acids in binary aqueous solutions of MgCl2.6H2O at 288.15, and 308.15 K. Amalendu Pal Suresh Kumar. Volume 117 Issue 3 May 2005 pp 267-273 ...

  8. Synthetic, spectral and solution studies on imidazolate-bridged ...

    Indian Academy of Sciences (India)

    Synthesis, spectral and solution studies on 2-ethyl imidazolate-bridged (2-EtIm) homo-binuclear copper(II)-copper(II) and hetero-binuclear copper(II)-zinc(II) homologue are described. Magnetic moment values of homo-binuclear complexes indicate that the imidazolate group can mediate antiferromagnetic interactions.

  9. Carbon Market and Integrated Waste Solutions : a Case Study of ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Carbon Market and Integrated Waste Solutions : a Case Study of Indonesia. The Kyoto Protocol's Clean Development Mechanism (CDM) was established in 1997 with the dual purpose of helping developing countries achieve sustainable development (as defined nationally) and industrialized countries achieve compliance ...

  10. Spectrochemistry of Solutions: A Vibrational Spectroscopic Study of ...

    African Journals Online (AJOL)

    Ion pairing and upper stage transition of magnesium (II) and calcium (II) with thiocyanate ion has been studied by Infrared and Raman spectroscopy. A complete picture of species present in thiocyanate solutions has been established. The spectral profile consists of five thiocyanate species namely; a triple-ion, [SCN - M ...

  11. Kinetic Uptake Studies of Powdered Materials in Solution

    Directory of Open Access Journals (Sweden)

    Mohamed H. Mohamed

    2015-06-01

    Full Text Available Challenges exist for the study of time dependent sorption processes for heterogeneous systems, especially in the case of dispersed nanomaterials in solvents or solutions because they are not well suited to conventional batch kinetic experiments. In this study, a comparison of batch versus a one-pot setup in two variable configurations was evaluated for the study of uptake kinetics in heterogeneous (solid/solution systems: (i conventional batch method; (ii one-pot system with dispersed adsorbent in solution with a semi-permeable barrier (filter paper or dialysis tubing for in situ sampling; and (iii one-pot system with an adsorbent confined in a semi-permeable barrier (dialysis tubing or filter paper barrier with ex situ sampling. The sorbent systems evaluated herein include several cyclodextrin-based polyurethane materials with two types of phenolic dyes: p-nitrophenol and phenolphthalein. The one-pot kinetics method with in situ (Method ii or ex situ (Method iii sampling described herein offers significant advantages for the study of heterogeneous sorption kinetics of highly dispersed sorbent materials with particles sizes across a range of dimensions from the micron to nanometer scale. The method described herein will contribute positively to the development of advanced studies for heterogeneous sorption processes where an assessment of the relative uptake properties is required at different experimental conditions. The results of this study will be advantageous for the study of nanomaterials with significant benefits over batch kinetic studies for a wide range of heterogeneous sorption processes.

  12. Recent advancements in conformal gravity

    Science.gov (United States)

    O'Brien, James G.; Chaykov, Spasen S.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian; Moss, Robert J.

    2017-05-01

    In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing.

  13. Asymptotic symmetry algebra of conformal gravity

    Science.gov (United States)

    Irakleidou, Maria; Lovrekovic, Iva

    2017-11-01

    We compute asymptotic symmetry algebras of conformal gravity. Due to more general boundary conditions allowed in conformal gravity in comparison to those in Einstein gravity, we can classify the corresponding algebras. The highest algebra for nontrivial boundary conditions is five dimensional and it leads to global geon solution with nonvanishing charges.

  14. Effects of solute-solute interactions on protein stability studied using various counterions and dendrimers.

    Directory of Open Access Journals (Sweden)

    Curtiss P Schneider

    Full Text Available Much work has been performed on understanding the effects of additives on protein thermodynamics and degradation kinetics, in particular addressing the Hofmeister series and other broad empirical phenomena. Little attention, however, has been paid to the effect of additive-additive interactions on proteins. Our group and others have recently shown that such interactions can actually govern protein events, such as aggregation. Here we use dendrimers, which have the advantage that both size and surface chemical groups can be changed and therein studied independently. Dendrimers are a relatively new and broad class of materials which have been demonstrated useful in biological and therapeutic applications, such as drug delivery, perturbing amyloid formation, etc. Guanidinium modified dendrimers pose an interesting case given that guanidinium can form multiple attractive hydrogen bonds with either a protein surface or other components in solution, such as hydrogen bond accepting counterions. Here we present a study which shows that the behavior of such macromolecule species (modified PAMAM dendrimers is governed by intra-solvent interactions. Attractive guanidinium-anion interactions seem to cause clustering in solution, which inhibits cooperative binding to the protein surface but at the same time, significantly suppresses nonnative aggregation.

  15. Assignments of /sup 1/H nuclear magnetic resonances of the cystyl, asparaginyl, and aromatic residues of arginine vasopressin in D/sub 2/O. A comparison with lysine vasopressin and oxytocin in terms of solution conformation

    Energy Technology Data Exchange (ETDEWEB)

    Wyssbrod, H.R.; Fischman, A.J.; Live, D.H.; Hruby, V.J.; Agarwal, N.S.; Upson, D.A.

    1979-07-18

    The resonances of the C/sup ..cap alpha../ and C/sup ..beta../ protons of the cystyl, asparaginyl, and aromatic residues of (8-arginine)vasopressin (AVP) in D/sub 2/O at pD 3.8 and 20/sup 0/C were assigned in a rigorous manner by the use of isotopic isomers of AVP that contain specific replacements of protons by deuterons and by comparison of /sup 1/H NMR characteristics of AVP to those of (8-lysine)vasopressin (LVP) and oxytocin (OT). Although there is extensive overlap of resonances of C/sup ..beta../ protons even at 360 MHz, all of the chemical shifts of these protons and most of the couplings between them and their vicinal C/sup ..cap alpha../ protons could be determined, at least to a first approximation. It was concluded that the cyclic moieties (residues 1-6) of AVP, LVP, and OT possess essentially the same overall backbone conformation, and that the side-chain conformation - or rotamer populations - about the C/sup ..cap alpha../-C/sup ..beta../ bonds of the cystyl residue (positions 1 and 6), the tyrosyl residue (position 2), and the asparaginyl residue (position 5) are similar. This study indicates that selective replacements of C/sup ..beta../ protons by deuterons are necessary to improve the accuracy of coupling constants extracted from 360-MHz spectra of a AVP for use in conformational analysis.

  16. NMR spectra and potentiometry studies of aluminum(III) binding with coenzyme NAD+ in acidic aqueous solutions.

    Science.gov (United States)

    Yang, Xiaodi; Bi, Shuping; Yang, Xiaoliang; Yang, Li; Hu, Jun; Liu, Jian; Yang, Zhengbiao

    2003-06-01

    Complexation and conformational studies of coenzyme NAD+ with aluminum were conducted in acidic aqueous solutions (pH 2-5) by means of potentiometry as well as multinuclear (1H, 13C, 31P, 27Al) and two-dimensional (1H, 1H-NOESY) NMR spectroscopy. These led to the following results: (1) Al could coordinate with NAD+ through the following binding sites: N7' of adenine and pyrophosphate free oxygen (O(A)1, O(N)1,O(A)2) to form various mononuclear 1:1 (AlLH23+, AlLH2+) and 2:1 (AlL2-) species, and dinuclear 2:2 (Al2L22+) species. (2) The conformations of NAD+ and Al-NAD+ depended on the solvents and different species in the complexes. The results suggest the occurrence of an Al-linked complexation, which causes structural changes at the primary recognition sites and secondary conformational alterations for coenzymes. This finding will help us to understand role of Al in biological enzyme reaction systems.

  17. The comparative study on analytical solutions and numerical solutions of displacement in transversely isotropic rock mass

    Science.gov (United States)

    Zhang, Zhizeng; Zhao, Zhao; Li, Yongtao

    2016-06-01

    This paper attempts to verify the correctness of the analytical displacement solution in transversely isotropic rock mass, and to determine the scope of its application. The analytical displacement solution of a circular tunnel in transversely isotropic rock mass was derived firstly. The analytical solution was compared with the numerical solution, which was carried out by FLAC3D software. The results show that the expression of the analytical displacement solution is correct, and the allowable engineering range is that the dip angle is less than 15 degrees.

  18. Replacement between conformity and counter-conformity in consumption decisions.

    Science.gov (United States)

    Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

    2013-02-01

    This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

  19. Theoretical study on the adsorption and relative stability of conformers of L-ascorbic acid on γ - alumina (100) surface

    Science.gov (United States)

    Mozaffari Majd, M.; Dabbagh, H. A.; Farrokhpour, H.; Najafi Chermahini, A.

    2017-11-01

    The adsorption energies (Eads) and relative stabilities of selected conformers of the most stable tautomer of L-ascorbic acid (vitamin C) on the dehydroxylated γ-alumina (100) surface were calculated in both gas phase and solvent (water) using the density functional theory (DFT) method. The selected conformers were related to the different rotational angles of OH groups of L-ascorbic acid. The conformational analysis of bare tautomer in both gas and water showed that the conformer No.20 (conf. 20) and 13 (conf. 13) with the dihedral angles of H15sbnd O10sbnd C11sbnd C9 (-73°) and H20sbnd O19sbnd C9sbnd C11 (-135°) were the most stable and unstable conformers, respectively. The performed calculations in the presence of surface showed that the interaction of the conformers with the surface changes their relative stabilities and structures in both gas phase and water. The Ead of each conformer was calculated and it was determined that conf. 8 and conf. 16 have the highest value of Ead in the gas phase (-62.56 kcal/mol) and water (-54.44 kcal/mol), respectively. The optimized structure of each conformer on the surface and the number of hydrogen bonds between it and surface along with their bond lengths were determined.

  20. Conformational analysis of oleandomycin and its 8-methylene-9-oxime derivative by NMR and molecular modelling.

    Science.gov (United States)

    Novak, Predrag; Tomisić, Zrinka Banić; Tepes, Predrag; Lazarevski, Gorjana; Plavec, Janez; Turkalj, Gordana

    2005-01-07

    Conformations of the 14-membered macrolide antibiotic oleandomycin and its 8-methylene-9-oxime derivative were determined in various solvents. The experimental NMR data--coupling constants and NOE contacts--were compared with the results of molecular modelling--molecular mechanics calculations and molecular dynamics simulations. The conformational changes, on the right-hand side of the 14-membered ring, affected mostly the 3JH2,H3 values and NOE crosspeaks H3 or H4 to H11. Oleandomycin was found to be present predominantly in the C3-C5 folded-in conformations in DMSO-d6 solution, whereas in buffered D2O, acetone-d6 and CDCl3, there was a mixture of folded-in and folded-out conformational families. The predominant conformation of the 8-methylene-oleandomycin-9-oxime derivative in solution was a folded-out one although different amounts of folded-in conformation were also present depending on the solvent. Oleandrose and desosamine sugar moieties adopted the usual and expected chair conformation. The conformation around the glycosidic bonds, governing the relative orientation of sugars vs. the lactone ring, showed a certain flexibility within two conformationally close families. We believe that by combining the experimental NMR data and the molecular modelling techniques, as reported in this paper, we have made significant progress in understanding the conformational behaviour and properties of macrolides. Our belief is based on our own current studies on oleandomycins as well as on the previously reported results and best practices concerning other macrolides. A rational for macrolide conformational studies and advances in methodology has been suggested accordingly.

  1. (R,R-Tartaric Acid Dimethyl Diester from X-Ray and Ab Initio Studies: Factors Influencing Its Conformation and Packing

    Directory of Open Access Journals (Sweden)

    J. Rychlewski

    1997-07-01

    Full Text Available The conformation of dimethyl (R,R-tartrate has been analyzed on the basis of the single crystal X-ray diffraction method as well as by ab-initio quantum chemical studies. The results showed that the extended T conformation containing two planar hydroxyester moieties predominates in both ab-initio and X-ray studies. The lowest energy conformer in ab-initio calculations has C2 symmetry and hydrogen bonds between a hydroxyl group and the nearest carbonyl oxygen. The second in energetical sequence, with an energy difference of only 1.2 kcal/mol, is the asymmetrical conformer, which differs from the lowest energy form by the rotation of one of the ester groups by 180°. Intramolecular OH...O hydrogen bonds observed in this rotamer again involve only proximal functional groups. This conformer is present in the crystal structure of the studied compound, although its conformation in the solid state is no longer stabilized by intramolecular hydrogen bonds of the type mentioned above. In the crystal, hydroxyl groups are mostly involved in intermolecular hydrogen bonds and form only a weak intramolecular hydrogen bond with each other. The planar arrangement of the α-hydroxyester moieties combined with the extended conformation of the carbon chain seems to be stabilized by the intramolecular hydrogen bonds between neighboring functional groups and by the long range dipole-dipole interactions between two pairs of CO and (βC-H bonds.

  2. Synthesis, properties, and NMR studies of a C8-phenylguanine modified oligonucleotide that preferentially adopts the Z DNA conformation.

    Science.gov (United States)

    Gannett, Peter M; Heavner, Sue; Daft, Jonathan R; Shaughnessy, Kevin H; Epperson, Jon D; Greenbaum, Nancy L

    2003-10-01

    Carcinogenic aryl hydrazines produce C8-arylated purine adducts. The effect of these adducts on DNA conformation and their role in hydrazine carcinogenesis are unknown. Here, we describe a new synthetic route to produce these adducts that is also compatible with the synthesis of the corresponding phosphoramidites needed for oligonucleotide synthesis. Two oligonucleotides were prepared, an unmodified oligonucleotide, d((5)(')CGCGCGCGCG(3)(')), and a C8-phenylguanine modified oligonucleotide, d((5)(')CGCGCGCGCG(3)(')) (G = 8-phenylguanine). These oligonucleotides were compared using thermal denaturation, circular dichroism, NMR, and molecular modeling. The phenyl modification destabilizes the B DNA form and stabilizes the Z DNA form such that the B:Z ratio is near one under physiological conditions. In light of recent studies that show a role for Z DNA in gene expression and cell transformation, Z DNA stabilization by C8-arylguanine formation from aryl hydrazines may be relevant to their role in carcinogenesis.

  3. Novel conformation of an RNA structural switch.

    Science.gov (United States)

    Kennedy, Scott D; Kierzek, Ryszard; Turner, Douglas H

    2012-11-20

    The RNA duplex, (5'GACGAGUGUCA)(2), has two conformations in equilibrium. The nuclear magnetic resonance solution structure reveals that the major conformation of the loop, 5'GAGU/3'UGAG, is novel and contains two unusual Watson-Crick/Hoogsteen GG pairs with G residues in the syn conformation, two A residues stacked on each other in the center of the helix with inverted sugars, and two bulged-out U residues. The structure provides a benchmark for testing approaches for predicting local RNA structure and a sequence that allows the design of a unique arrangement of functional groups and/or a conformational switch into nucleic acids.

  4. A study product design of optimal solution for customer requirements

    OpenAIRE

    LIAO, Shih-Chung

    2015-01-01

    In this paper, the author uses an evaluative criteria model and their associated criteria status, product evaluative criteria software of results and product objective function of optimal values solution, along with product morphological analysis, to synthesize evaluative criteria and optimize product design values. This study focuses on how to use an evaluative criteria model’s imprecise market information by evaluative criteria design software; product mapping relationships between design p...

  5. Conformational, vibrational and DFT studies of a newly synthesized arylpiperazine-based drug and evaluation of its reactivity towards the human GABA receptor

    Science.gov (United States)

    Onawole, A. T.; Al-Ahmadi, A. F.; Mary, Y. S.; Panicker, C. Y.; Ullah, N.; Armaković, S.; Armaković, S. J.; Van Alsenoy, C.; Al-Saadi, A. A.

    2017-11-01

    This study reports a computational assessment of important biochemical properties and vibrational assignments for the synthesized 1-(4-(3-methoxy-4-nitrophenyl)piperazin-1-yl)ethanone (MNPE). MNPE is related to the commonly used arylpiperazine-based drugs that exhibit a wide range of pharmacological activities. The characterization of MNPE is based on the readily sighted 1363 cm-1 infrared band (associated with piperazine ring stretching), 1308 cm-1 Raman line (associated with the phenyl ring breathing), 1242 cm-1 Raman line and 1092 cm-1 infrared band (both associated with Csbnd N stretching) as key modes in its vibrational spectra. First principle calculations revealed that MNPE could exist in sixteen different plausible conformations, which were used as basis to understand the possible molecular docking mechanism of the molecule as an agonist in the human GABAA receptor. The best binding scenarios showed the presence of intramolecular hydrogen bonding in MNPE and was comparable with the most stable configuration. It was further evaluated for its reactivity properties by utilizing the concepts of Average Local Ionization Energies (ALIE) and Fukui functions. The autoxidation and hydrolysis degradation likelihood of MNPE estimated from the computed bond dissociation energies and radial distribution functions predicted that MNPE is to be readily biodegradable in aqueous solutions.

  6. A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules.

    Science.gov (United States)

    Forti, Flavio; Cavasotto, Claudio N; Orozco, Modesto; Barril, Xavier; Luque, F Javier

    2012-05-08

    Predicting the conformational preferences of flexible compounds is still a challenging problem with important implications in areas such as molecular recognition and drug design. In this work, we describe a multilevel strategy to explore the conformational preferences of molecules. The method relies on the predominant-state approximation, which partitions the conformational space into distinct conformational wells. Moreover, it combines low-level (LL) methods for sampling the conformational minima and high-level (HL) techniques for calibrating their relative stability. In the implementation used in this study, the LL sampling is performed with the semiempirical RM1 Hamiltonian, and solvent effects are included using the RM1 version of the MST continuum solvation model. The HL refinement of the conformational wells is performed by combining geometry optimizations of the minima at the B3LYP (gas phase) or MST-B3LYP (solution) level, followed by single point MP2 computations using Dunning's augmented basis sets. Then, the effective free energy of a conformational well is estimated by combining the MP2 energy, supplemented with the MST-B3LYP solvation free energy for a conformational search in solution, with the local curvature of the well sampled at the semiempirical level. Applications of this strategy involve the exploration of the conformational preferences of 1,2-dichloroethane and neutral histamine in both the gas phase and water solution. Finally, the multilevel strategy is used to estimate the reorganization cost required for selecting the bioactive conformation of HIV reverse transcriptase inhibitors, which is estimated to be at most 1.3 kcal/mol.

  7. Conformational study of insect adipokinetic hormones using NMR constrained molecular dynamics

    Science.gov (United States)

    Nair, Margie M.; Jackson, Graham E.; Gäde, Gerd

    2001-03-01

    Mem-CC (pGlu-Leu-Asn-Tyr-Ser-Pro-Asp-Trp-NH2), Tem-HrTH (pGlu-Leu-Asn-Phe-Ser-Pro-Asn-Trp-NH2) and Del-CC (pGlu-Leu-Asn-Phe-Ser-Pro-Asn-Trp-Gly-Asn-NH2) are adipokinetic hormones, isolated from the corpora cardiaca of different insect species. These hormones regulate energy metabolism during flight and so are intimately involved in an insect's mobility. Secondary structural elements of these peptides and the N7 analogue, [N7]-Mem-CC (pGlu-Leu-Asn-Tyr-Ser-Pro-Asn-Trp-NH2), have been determined in dimethylsulfoxide solution using NMR restrained molecular mechanic simulations. The neuropeptides were all found to have an extended structure for the first 4 residues and a β-turn between residues 4-8. For Tem-HrTH and Del-CC, asparagine (N7) which is postulated to be involved in receptor binding and/or activation, projects outward form the β-turn. Mem-CC does not have an asparagine at position 7 while, for [N7]-Mem-CC, the N7 sidechain folds inside the β-turn preventing its interaction with the receptor.

  8. Study on Growth Curves of Muscle Area, Backfat Thickness and Body Conformation for Hanwoo (Korean Native Cows

    Directory of Open Access Journals (Sweden)

    J. H. Lee

    2014-09-01

    Full Text Available The objective of this study was to estimate the parameters of Gompertz growth curves with the measurements of body conformation, real-time ultrasound longissimus dorsi muscle area (LMA and backfat thickness (BFT in Hanwoo cows. The Hanwoo cows (n = 3,373 were born in 97 Hanwoo commercial farms in the 17 cities or counties of Gyeongbuk province, Korea, between 2000 and 2007. A total of 5,504 ultrasound measurements were collected for the cows at the age of 13 to 165 months in 2007 and 2008. Wither height (HW, rump height (HR, the horizontal distance between the top of the hips (WH, and girth of chest (GC were also measured. Analysis of variance was conducted to investigate variables affecting LMA and BFT. The effect of farm nested in location was included in the statistical model, as well as the effects of HW, HR, WH, and GC as covariates. All of the effects were significant in the analysis of variance for LMA and BFT (p<0.01, except for the HR effect for LMA. The two ultrasound measures and the four body conformation traits were fitted to a Gompertz growth curve function to estimate parameters. Upper asymptotic weights were estimated as 54.0 cm2, 7.67 mm, 125.6 cm, 126.4 cm, 29.3 cm, and 184.1 cm, for LMA, BFT, HW, HR, WH, and GC, respectively. Results of ultrasound measurements showed that Hanwoo cows had smaller LMA and greater BFT than other western cattle breeds, suggesting that care must be taken to select for thick BFT rather than an increase of only beef yield. More ultrasound records per cow are needed to get accurate estimates of growth curve, which, thus, helps producers select animals with high accuracy.

  9. A split-body study evaluating the efficacy of a conformable surface cryolipolysis applicator for the treatment of male pseudogynecomastia.

    Science.gov (United States)

    Jones, Isabela T; Vanaman Wilson, Monique J; Guiha, Isabella; Wu, Douglas C; Goldman, Mitchel P

    2018-01-13

    Cryolipolysis is a non-invasive method of body shaping that has been used for male pseudogynecomastia. However, traditional vacuum suction cryolipolysis requires a minimum pinchable fat layer which may not always be present in this area. To evaluate the efficacy and safety of a conformable surface cryolipolysis applicator for the reduction of male pseudogynecomastia. Ten male subjects with pseudogynecomastia received two cycles of cryolipolysis to the breast 6 weeks apart. Ultrasound was used to measure the thickness of adipose tissue. Seven of 10 patients completed the study. Compared to baseline, the mean ± SD change in adipose tissue thickness was 8.12 ± 6.94 mm for the treated versus 1.03 ± 6.03 mm for the control breast at week 6 (p = 0.014), and 8.71 ± 7.04 mm for the treated vs. 2.66 ± 7.04 mm for the control breast at week 12 (P = 0.16). Four (4) of seven (57%) patients were at least slightly satisfied with the treated breast, and although subject satisfaction was higher in the treated breast, this did not reach significance (0.085). Adverse events were mild and transient. A conformable surface cryolipolysis applicator was effective in reducing the mean adipose tissue thickness in subjects with male pseudogynecomastia. Lasers Surg. Med. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  10. Study of the interaction of C60 fullerene with human serum albumin in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Li, Song [Vanderbilt University; Zhao, Xiongce [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Mo, Yiming [ORNL; Cummings, Peter T [ORNL; Heller, William T [ORNL

    2013-01-01

    Concern about the toxicity of engineered nanoparticles, such as the prototypical nanomaterial C60 fullerene, continues to grow. While evidence continues to mount that C60 and its derivatives may pose health hazards, the specific molecular interactions of these particles with biological macromolecules require further investigation. To better understand the interaction of C60 with proteins, the protein human serum albumin (HSA) was studied in solution with C60 at C60:HSA molar ratios ranging from 1:2 to 4:1. HSA is the major protein component of blood plasma and plays a role in a variety of functions, such as the maintenance of blood pH and pressure. The C60-HSA interaction was probed by a combination of circular dichroism (CD) spectroscopy, small-angle neutron scattering (SANS) and atomistic molecular dynamics (MD) simulations to understand C60-driven changes in the structure of HSA in solution. The CD spectroscopy demonstrates that the secondary structure of the protein decreases in -helical content in response to the presence of C60. Similarly, C60 produces subtle changes in the solution conformation of HSA, as evidenced by the SANS data and MD. The data do not indicate that C60 is causing a change in the oligomerization state of the protein. Taken together results demonstrate that C60 interacts with HSA, but it does not strongly perturb the structure of the protein by unfolding it or inducing aggregation, suggesting a mechanism for transporting C60 throughout the body to accumulate in various tissues.

  11. Wormholes in conformal gravity arXiv

    CERN Document Server

    Hohmann, Manuel; Raidal, Martti; Veermäe, Hardi

    We present a new class of solutions for static spherically symmetric wormhole spacetimes in conformal gravity and outline a detailed method for their construction. As an explicit example, we construct a class of traversable and non-traversable wormholes that are locally conformal to Schwarzschild-(anti) de Sitter spacetimes. These wormhole spacetimes are exact vacuum solutions in, but not being limited to, Weyl gravity and conformal scalar-tensor theories. Importantly, the method implies that every conformal gravity theory with local field equations will trivially contain wormholes without the need for exotic matter. Applying those results on gravitational theories that possess conformal symmetry in the ultraviolet regime, the central singularities of black holes can be replaced with wormhole throats. We speculate on possible phenomenological consequences.

  12. Synthesis and conformational study of silk model polypeptides [Ala-Gly] 12 by solid-state NMR

    Science.gov (United States)

    Kishi, Satoshi; Santos, Andres; Ishii, Osamu; Ishikawa, Kazuo; Kunieda, Shingo; Kimura, Hideaki; Shoji, Akira

    2003-04-01

    A series of well-defined model polypeptides of Bombyx mori silk fibroin, [Ala-Gly] n ( n=12 and 5-9), [Ala d4Gly] 12 and [Gly d2Ala] 12, (where Ala, Gly, Ala d4 and Gly d2 denote L-alanine, glycine, 2,3,3,3-deuterated L-alanine and 2,2-deuterated glycine residues, respectively), were successfully synthesized by an automatic solid phase peptide synthesizer. Followed by treatment with 9 M lithium bromide (LiBr) solution to convert their conformation from the silk II to the silk I form. We determined the intrinsic 1H, 13C and 15N NMR chemical shifts of Ala and Gly residues, characteristic to the silk I and silk II forms in Bombyx mori, by high-resolution and solid-state 13C CP-MAS, 1H CRAMPS, 1H- 13C HETCOR and 15N CP-MAS NMR measurements. Next, we demonstrated that it is necessary at least 12 amino acid residues ( n=6) in the [Ala-Gly] n-I series for the formation of stable silk I form by 13C CP-MAS NMR. Finally, we found that the intrinsic 1H and 13C chemical shifts of the specific deuterium labeled polypeptides, [Ala d4-Gly] 12 and [Gly d2-Ala] 12, cause a meaningful chemical shift displacement, suggesting that the deuterium interacts with proton and/or carbon atoms in the solid state. Thus, the selective deuterium labeling has a potential to useful for the structural analysis by 1H NMR in the solid state.

  13. A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

    Science.gov (United States)

    Tarnowska, Monika; Liwo, Adam; Shenderovich, Mark D.; Liepiņa, Inta; Golbraikh, Alexander A.; Grzonka, Zbigniew; Tempczyk, Anna

    1993-12-01

    within the first residue. Based on the selection of the conformations which are low in energy for both the reference and β-substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both βI/βIII and βII types of backbone structure, while the second one is allowed only for the βII type of backbone. No conformation of the βI'/βIII' type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.

  14. Small angle neutron scattering study of lysozyme solutions

    Science.gov (United States)

    Boué, F.; Lefaucheux, F.; Robert, M. C.; Rosenman, I.

    1993-10-01

    In order to investigate how macromolecular aggregation proceeds for obtaining nucleation and crystal growth, a series of hen egg white (HEW) lysozyme solutions representative of a large supersaturation range have been investigated by small angle neutron scattering (SANS). In all these solutions, the signal well corresponds to species of radii of gyration Rg below 50 Å. Moreover, the effective values Rg are compatible with a rather monodisperse distribution of species the size of which increases when the supersaturation increases; for example, saturated solutions correspond to dimer populations. The largest size which has been identified corresponds to octomers which seems a limit beyond which nucleation and growth occur. The growth units are larger than dimers and probably correspond to tetramers or octomers. SANS allows one to study kinetic aspects. We observe that when a given supersaturation is quickly established, the radius of gyration increases with time. In the light of these results, it appears that SANS affords a powerful tool to study aggregation phenomena occurring in the metastable zone.

  15. Herding, Social Preferences and (Non-) Conformity

    OpenAIRE

    Luca Corazzini; Ben Greiner

    2005-01-01

    We study the role of social preferences and conformity in explaining herding behavior in anonymous risky environments. In an experiment similar to information cascade settings, but with no private information, we find no evidence for conformity. On the contrary, we observe a significant amount of non-conforming behavior, which cannot be attributed to errors.

  16. Conformable Fractional Nikiforov—Uvarov Method

    Science.gov (United States)

    Karayer, H.; Demirhan, D.; Büyükkılıç, F.

    2016-07-01

    We introduce conformable fractional Nikiforov—Uvarov (NU) method by means of conformable fractional derivative which is the most natural definition in non-integer calculus. Since, NU method gives exact eigenstate solutions of Schrödinger equation (SE) for certain potentials in quantum mechanics, this method is carried into the domain of fractional calculus to obtain the solutions of fractional SE. In order to demonstrate the applicability of the conformable fractional NU method, we solve fractional SE for harmonic oscillator potential, Woods—Saxon potential, and Hulthen potential.

  17. Conformal geometry and quasiregular mappings

    CERN Document Server

    Vuorinen, Matti

    1988-01-01

    This book is an introduction to the theory of spatial quasiregular mappings intended for the uninitiated reader. At the same time the book also addresses specialists in classical analysis and, in particular, geometric function theory. The text leads the reader to the frontier of current research and covers some most recent developments in the subject, previously scatterd through the literature. A major role in this monograph is played by certain conformal invariants which are solutions of extremal problems related to extremal lengths of curve families. These invariants are then applied to prove sharp distortion theorems for quasiregular mappings. One of these extremal problems of conformal geometry generalizes a classical two-dimensional problem of O. Teichmüller. The novel feature of the exposition is the way in which conformal invariants are applied and the sharp results obtained should be of considerable interest even in the two-dimensional particular case. This book combines the features of a textbook an...

  18. Conformable fractional Dirac system on time scales.

    Science.gov (United States)

    Gulsen, Tuba; Yilmaz, Emrah; Goktas, Sertac

    2017-01-01

    We study the conformable fractional (CF) Dirac system with separated boundary conditions on an arbitrary time scale [Formula: see text]. Then we extend some basic spectral properties of the classical Dirac system to the CF case. Eventually, some asymptotic estimates for the eigenfunction of the CF Dirac eigenvalue problem are obtained on [Formula: see text]. So, we provide a constructive procedure for the solution of this problem. These results are important steps to consolidate the link between fractional calculus and time scale calculus in spectral theory.

  19. A Study on the Stability of Diluted Bee Venom Solution

    Directory of Open Access Journals (Sweden)

    Mi-Suk Kang

    2003-06-01

    Full Text Available Objective : The purpose of this study was to investigate the stability of bee venom according to the keeping method and period. Method : The author observed microbial contamination of bee venom in nutrient agar, broth, YPD agar and YPD media and antibacterial activity for S. aureus, E. coli manufactured 12, 6 and 3 months ago as the two type of room temperature and 4℃ cold storage. Result : 1. 1:3,000 and 1:4,000 diluted bee venom solution did not show microbial contamination both room temperature and cold storage within twelve months. 2. There was antibacterial activity of diluted bee venom for S. aureus in cold storage within twelve months and there was no antibacterial activity of diluted bee venom for S. aureus in twelve months, room temperature storage. 3. We could not observe the zone of inhibition around paper disc of all for E.coli. in 1:3,000, 1:30,000 and 1:3,000,000 diluted bee venom solution, respectively. According to results, we expect that diluted bee venom solution is stable both cold and room temperature storage within twelve months.

  20. Multiscale conformal pattern transfer

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  1. Multiscale conformal pattern transfer.

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-22

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  2. Conformity assessment of multicomponent materials or objects: Risk of false decisions due to measurement uncertainty - A case study of denatured alcohols.

    Science.gov (United States)

    Kuselman, Ilya; Pennecchi, Francesca; da Silva, Ricardo J N B; Brynn Hibbert, D

    2017-03-01

    Risk of a false decision on conformity of a multicomponent material or object due to measurement uncertainty is discussed. Even if conformity assessment for each component of a material sample is successful, the total probability of a false decision (total consumer's risk or producer's risk) concerning the sample as a whole might still be significant. A model of the total probability of such false decisions is formulated based on the law (theorem) of total probability. It is shown that the total risk can be evaluated as a combination of the particular risks of conformity assessment of sample components. For a more complicated task, i.e. for a larger number of components of a sample under control, the total risk is greater. As a case study, the total probability of false conforming (total consumer's risk) is evaluated for customs control of completely denatured alcohols, where conformity assessment is performed by comparison of chemical analytical test results with the regulatory limits. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan

    2014-10-07

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  4. Conformational changes to deamidated wheat gliadins and b-casein upon adsorption to oil-water emulsion interfaces

    DEFF Research Database (Denmark)

    Wong, Benjamin T.; Zhai, Jiali; Hoffmann, Søren Vrønning

    2012-01-01

    The conformation of deamidated gliadins and b-casein in solution and adsorbed at the interface of oil-inwater emulsions was studied using synchrotron radiation circular dichroism (SRCD) and front-facefluorescence spectroscopy. Deamidation led to partial unfolding of gliadins in solution. The a...... in the adsorbed state. Our results demonstrate that conformational re-arrangement of proteins upon adsorption to emulsion interfaces is dependent not only on the hydrophobicity of the oil phase, but more importantly on the conformational flexibility of the protein....

  5. Preliminary study of the 270 Bloom Fricke xylenol gel phantom performance for 3D conformal radiotherapy using multiple radiation fields

    Energy Technology Data Exchange (ETDEWEB)

    Cavinato, Christianne C.; Campos, Leticia L., E-mail: ccavinato@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (DIRF/IPEN/CNEN-SP), Sao Paulo, SP (Brazil). Gerencia de Metrologia das Radiacoes; Souza, Benedito H.; Carrete Junior, Henrique; Daros, Kellen A.C.; Medeiros, Regina B. [Universidade Federal de Sao Paulo (UNIFESP), SP (Brazil). Dept. de Diagnostico por Imagens; Giordani, Adelmo J. [Universidade Federal de Sao Paulo (UNIFESP), Sao Paulo, SP (Brazil). Servico de Radioterapia

    2011-07-01

    The complex cancer treatment techniques require rigorous quality control (QC). The Fricke xylenol gel (FXG) dosimeter has been studied to be applied as a three-dimensional (3D) dosimeter since it is possible to produce 3D FXG phantoms of various shapes and sizes. In this preliminary study, the performance of the FXG spherical phantom developed at IPEN, prepared using 270 Bloom gelatin from porcine skin made in Brazil, was evaluated using magnetic resonance imaging technique, aiming to use this phantom to 3D conformal radiotherapy (3DCRT) with multiple radiation fields and clinical photon beams. The obtained results indicate that for all magnetic resonance images of the FXG phantom irradiated with 6 MV clinical photon beam can be observed clearly the target volume and, in the case of coronal image, can also be observed the radiation beam projection and the overlap of different radiation fields used. The Fricke xylenol gel phantom presented satisfactory results for 3DCRT and clinical photon beams in this preliminary study. These results encourage the additional tests using complex treatment techniques and indicate the viability of applying the phantom studied to routine quality control measurements and in 3DCRT and intensity modulated radiotherapy treatment planning. (author)

  6. Studying the efficacy of escalated dose conformal radiation therapy in prostate carcinoma – Pakistan experience

    Directory of Open Access Journals (Sweden)

    Asad Zamir

    2017-11-01

    Conclusion: Our data were comparable to international studies of dose escalation using 3D and beneficial as compared to conventional radiation therapy delivered by 2D in terms of biochemical failure rate and treatment related toxicity.

  7. Conformationally Preorganized Diastereomeric Norbornane-Based Maltosides for Membrane Protein Study

    DEFF Research Database (Denmark)

    Das, Manabendra; Du, Yang; Ribeiro, Orquidea

    2017-01-01

    Detergents are essential tools for functional and structural studies of membrane proteins. However, conventional detergents are limited in their scope and utility, particularly for eukaryotic membrane proteins. Thus, there are major efforts to develop new amphipathic agents with enhanced properti...

  8. Theoretical studies on beta-lactam antibiotics. I. Conformational similarity of penicillins and cephalosporins to X-D-alanyl-D-alanine and correlation of their structure with activity.

    Science.gov (United States)

    Virudachalam, R; Rao, V S

    1977-01-01

    The substrate analogue hypothesis proposed for the mechanism of the action of penicillins and cephalosporins is examined by stereochemical criteria. These beta-lactam antibiotics assume conformation similar to X-D-alanyl-D-alanine due to the presence of the lactam ring; this disagrees with the assumption made by Tipper & Strominger that L and D amino acid residues take similar conformation. The model proposed in this study for the activity of these antibiotics differs considerably from the earlier models, mainly in phi2 rotational angle which determines the conformation of the aminoacyl group. The inactivity of C6 or C7 epimers and the effect of various substitutions at 6alpha or 7alpha and C2 positions of penicillins and cephalosporins on the biological activity are explained.

  9. The corrosion of aluminum in dilute solutions: laboratory studies

    Energy Technology Data Exchange (ETDEWEB)

    Draley, J.E.; Arendt, J.W.; English, G.C.; Story, E.F.; Wainscott, M.M.; Berger, R.W.

    1945-06-19

    After it had been decided that aluminum was to be used as a corrosion-resistant material with good heat transfer properties, it was desired to determine the operating conditions to be used in the water-cooled Handford plant in order to avoid danger of corrosion penetration of thin aluminum parts. The studies here reported were undertaken with the object of determining these conditions by investigating the effects of all the known variables which might influence the corrosion behavior of aluminum in a water-coolded plant at HEW. The addition of hydrogen peroxide to the testing solutions was the only effort made to simulate special conditions at the plant.

  10. Spectral study of Rhodamine dyes in binary solutions

    Science.gov (United States)

    Benchea, Andreea Celia; Babusca, Daniela; Morosanu, Ana Cezarina; Dimitriu, Dan Gheorghe; Dorohoi, Dana Ortansa

    2017-07-01

    Electronic absorption and fluorescence spectra of two Rhodamine dyes (Rhodamine B and Rhodamine 6G) in binary solutions are studied in this paper. The excited state dipole moments have been computed using the correlation coefficients obtained by linear solvation energy relationship (LSER) applied to electronic spectra and the values of the dipole moments in the ground state of Rhodamines computed by HyperChem 8.0.6. The nature and the contributions of each type of interactions to the spectral shifts from visible range are established based on solvatochromic analysis.

  11. Hypofractionated Dose Escalated 3D Conformal Radiotherapy for Prostate Cancer: Outcomes from a Mono-Institutional Phase II Study.

    Science.gov (United States)

    Tramacere, Francesco; Arcangeli, Stefano; Pignatelli, Antonietta; Castagna, Roberta; Portaluri, Maurizio

    2015-05-01

    Based on a radiobiological assumption of a low alpha/beta (α/β) ratio for prostate cancer, hypofractionated radiotherapy has increasingly gained traction in the clinical practice and recent guidelines have confirmed the non-inferiority of this approach. Nevertheless, the largest studies that have used hypofractionation so far, employed image-guided radiation therapy/intensity modulated radiation therapy (IGRT/IMRT) facilities that might have overcome the radiobiological advantages, which remain to be fully confirmed. The aim of this trial was to evaluate the feasibility of a hypofractionated schedule delivered with 3D-Conformal Radiotherapy to prostate and seminal vesicles in combination with hormonal therapy. The study included 97 consecutive patients with localized prostate cancer (PCa), irrespective of risk class, treated with a schedule of 62 Gy in 20 fractions over 5 weeks (4 fractions of 3.1 Gy each per week). According to National Comprehensive Cancer Network (NCCN) prognostic classification, patients were divided into a favourable group (19%), intermediate group (41%) and unfavourable group (40%). Early and late toxicities were scored using the radiation toxicity grading/European Organisation for Research and Treatment of Cancer (RTOG/EORTC) criteria. Additionally, the international prostate symptom index (IPSS) for benign prostate hypertrophy was used to evaluate obstructive urinary symptoms. Biochemical outcome was reported according to the Phoenix definition for biochemical failure. Hormonal therapy (HT) was administrated in 92% of patients. After a median follow-up of 39 months (range=25-52), maximum ≥G2 late genitourinary (GU) and gastrointestinal (GI) toxicities occurred in 8% and 11% patients, respectively. The corresponding figures for acute toxicities were 24% and 15%. Patients with higher IPSS score before enrolment had significantly worse urinary function after treatment. Only 2% of patients died from PCa. Biochemical non-evidence of disease

  12. Single molecules in soft matter : a study of biomolecular conformation, heterogeneity and plasmon enhanced fluorescence

    NARCIS (Netherlands)

    Yuan, Haifeng

    2013-01-01

    We study the dynamics of single molecules and individual gold nanorods in glycerol at variable temperatures. We demonstrate temperature-cycle microscopy on FRET-labeled polyproline and double-stranded DNA molecules to access micro-second dynamics of single molecules, and reveal the influences of

  13. Study of educational furniture conformity with students anthropometric dimensions of Isfahan university of medical sciences

    Directory of Open Access Journals (Sweden)

    mehdi Sadeghi

    2010-02-01

    Full Text Available Musculoskeletal disorders, early fatigue induced by static work and the same symptoms are caused by inappropriate designed tools, equipment, building and workplace. Inadequate educational furniture is taken to be the reason of severe posture problems such as low back pain, spinal disorders, fatigue, shoulder and neck pain, and disturbance circulation in legs. So ergonomic design of educational furniture should be carefully considered. Materials and Methods: The present research was a cross-sectional study. Samples included desks and chairs (n=150 chosen from reading rooms of dormitories and faculties of Isfahan university of medical sciences Isfahan- Iran. In the study 2 parameters from desk and 5 parameters from chairs were assessed using a tape-measure and a set-sqare. Data were analyzed by SPSS ver 10 software. Results: Comparing the results from the mean of measured values (for seating height, desk height and desk clearance indicated a significant difference between them (p<0. 00. Conclusion: Findings of the study showed that existing standard in Iran about chairs and tables for educational institutions should be reviewed. Also the most important problem with chairs and desks are seating height and desk surface height respectively. These two parameters didn’t match with anthropometric dimensions of the sudents of Isfahan university of medical sciences.

  14. Body conformation, diet, and risk of breast cancer in pet dogs: a case-control study.

    Science.gov (United States)

    Sonnenschein, E G; Glickman, L T; Goldschmidt, M H; McKee, L J

    1991-04-01

    Canine and human breast cancer share several important clinical and histologic features. A case-control study of nutritional factors and canine breast cancer was conducted at the Veterinary Hospital of the University of Pennsylvania in 1984-1987 by interviewing owners of 150 pet dogs diagnosed with breast cancer, owners of 147 cancer control dogs, and owners of 131 noncancer control dogs. The risk of breast cancer was significantly reduced in dogs spayed at or before 2.5 years of age. Neither a high-fat diet nor obesity 1 year before diagnosis increased the risk of breast cancer according to multiple logistic regression analysis. However, the risk of breast cancer among spayed dogs was significantly reduced in dogs that had been thin at 9-12 months of age (odds ratio (OR) = 0.04 (95% confidence interval (CI) 0.004-0.4) and OR = 0.04 (95% CI 0.004-0.5) for cases vs. cancer controls and cases vs. noncancer controls, respectively, after adjustment for age at spay). Among intact dogs, the risk associated with being thin at 9-12 months of age was reduced, but not significantly so (OR = 0.60 (95% CI 0.2-1.9) and OR = 0.51 (95% CI 0.2-1.4) for the two comparisons, respectively). Results of this study suggest that nutritional factors operating early in life may be of etiologic importance in canine breast cancer.

  15. Towards Al3+-Induced Manganese-Containing Superoxide Dismutase Inactivation and Conformational Changes: An Integrating Study with Docking Simulations

    Directory of Open Access Journals (Sweden)

    Jiang-Liu Yang

    2011-01-01

    Full Text Available Superoxide dismutase (SOD, EC 1.15.1.1 plays an important antioxidant defense role in skins exposed to oxygen. We studied the inhibitory effects of Al3+ on the activity and conformation of manganese-containing SOD (Mn-SOD. Mn-SOD was significantly inactivated by Al3+ in a dose-dependent manner. The kinetic studies showed that Al3+ inactivated Mn-SOD follows the first-order reaction. Al3+ increased the degree of secondary structure of Mn-SOD and also disrupted the tertiary structure of Mn-SOD, which directly resulted in enzyme inactivation. We further simulated the docking between Mn-SOD and Al3+ (binding energy for Dock 6.3: −14.07 kcal/mol and suggested that ASP152 and GLU157 residues were predicted to interact with Al3+, which are not located in the Mn-contained active site. Our results provide insight into the inactivation of Mn-SOD during unfolding in the presence of Al3+ and allow us to describe a ligand binding via inhibition kinetics combined with the computational prediction.

  16. An in silico study of the molecular basis of B-RAF activation and conformational stability

    DEFF Research Database (Denmark)

    Fratev, Filip Filipov; Jonsdottir, Svava Osk

    2009-01-01

    based on molecular dynamics (MD) simulations of B-RAFWT and the B-RAFV600E, B-RAFK601E and B-RAFD594V mutants. A strong hydrogen bond network was identified in B-RAFWT in which the interactions between Lys601 and the well known catalytic residues Lys483, Glu501 and Asp594 play an important role......B-RAF kinase plays an important role both in tumour induction and maintenance in several cancers and it is an attractive new drug target. However, the structural basis of the B-RAF activation is still not well understood. RESULTS: In this study we suggest a novel molecular basis of B-RAF activation...

  17. Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain.

    Science.gov (United States)

    Brünger, A T; Huber, R; Karplus, M

    1987-08-11

    The trypsinogen to trypsin transition has been investigated by a stochastic boundary molecular dynamics simulation that included a major portion of the trypsin molecule and the surrounding solvent. Attention focused on the "activation domain", which crystallographic studies have shown to be ordered in trypsin and disordered in its zymogen, trypsinogen. The chain segments that form the activation domain were found to exhibit large fluctuations during the simulation of trypsin. To model a difference between trypsin and trypsinogen, the N-terminal residues Ile-16 and Val-17 were removed in the former and replaced by water molecules. As a result of the perturbation, a structural drift of 1-2 A occurred that is limited to the activation domain. Glycine residues are found to act as hinges for the displaced chain segments.

  18. Substitution effect on a hydroxylated chalcone: Conformational, topological and theoretical studies

    Science.gov (United States)

    Custodio, Jean M. F.; Vaz, Wesley F.; de Andrade, Fabiano M.; Camargo, Ademir J.; Oliveira, Guilherme R.; Napolitano, Hamilton B.

    2017-05-01

    The effect of substituents on two hydroxylated chalcones was studied in this work. The first chalcone, with a dimethylamine group (HY-DAC) and the second, with three methoxy groups (HY-TRI) were synthesized and crystallized from ethanol on centrosymmetric space group P21/c. The geometric parameters and supramolecular arrangement for both structures obtained from single crystal X-ray diffraction data were analyzed. The intermolecular interactions were investigated by Hirshfeld surfaces with their respective 2D plot for quantification of each type of contact. Additionally, the observed interactions were characterized by QTAIM analysis, and DFT calculations were applied for theoretical vibrational spectra, localization and quantification of frontier orbitals and potential electrostatic map. The flatness of both structures was affected by the substituents, which led to different monoclinic crystalline packing. The calculated harmonic vibrational frequencies and homo-lumo gap confirmed the stability of the structures, while intermolecular interactions were confirmed by potential electrostatic map and QTAIM analysis.

  19. Conformational parameters of poly(N-methyl-N-vinylacetamide) molecules through the hydrodynamic characteristics studies.

    Science.gov (United States)

    Pavlov, George M; Okatova, Olga V; Mikhailova, Anastasia V; Ulyanova, Natalia N; Gavrilova, Irina I; Panarin, Evgenii F

    2010-07-07

    Water-soluble PMVA was synthesized by radical polymerization methods. A number of polymer samples were fractionated in the chloroform-diethyl ether system. Fractions were studied by molecular hydrodynamics methods (sedimentation velocity, translational isothermal diffusion and viscosity) in H(2)O and DMF. The molecular masses of fractions were determined and the Kuhn-Mark-Houwink-Sakurada relationships were obtained in the molecular mass range of 3.5 < M x 10(-3) g x mol(-1) <540. A negative temperature coefficient of the characteristic viscosity was obtained in both solvents. The Kuhn statistic segment length and the hydrodynamic diameter of the molecule were estimated for PMVA. The hydrodynamic volumes, occupied by the molecules of PMVA, poly(1-vinyl-2-pyrrolidone), poly(vinylformamide), and pullulan were compared.

  20. Resonant X-ray scattering studies of concentrated aqueous solutions

    CERN Document Server

    Ramos, S

    2001-01-01

    structure of the three cations is also presented in this thesis. This work illustrates one of the main advantages of RXD: the possibility of carrying out systematic structural studies on all elements with atomic number greater than 28 (Ni). Finally, a critical discussion on the actual stage of development of RXD is presented. The results shown offer evidence of the future prospects of the technique and justify further efforts to develop it to the level of reliability and ease of use that NDIS has reached after more than three decades of development. The microscopic structure of concentrated aqueous electrolyte solutions has been studied by resonant X-ray diffraction (RXD). This technique provides a method for the measurement of the structure around a specific atom or ion in solution. In that sense, RXD is the X-ray equivalent of neutron diffraction with isotopic substitution (NDIS). The use of RXD as an alternative to NDIS has been considered of interest for some time; it is potentially one of the best method...

  1. From Conformity to Excellence – Study on Quality of Services in Accounting Profession in Romania

    Directory of Open Access Journals (Sweden)

    Costin Daniel Avram

    2017-11-01

    Full Text Available Professional bodies that manage distinct segments of the accounting profession in Romania, respectively CECCAR, CAFR, CCF and ANEVAR are focused on the public interest and expectations of the business environment. The quality of services specific to accounting profession is primarily aimed at compliance with the ethical and professional standards, without depending only on regulatory and monitoring activities exercised by professional bodies but being determined by the mentality of professionals and their ability to meet customer expectations and assess their future needs. In our research we analysed the evolution of quality classes obtained within each professional body during 2009-2014, by ranking the performance of entities that were submitted to quality audit. Though we found an upward trend for promotion in the higher quality classes, we consider that supervision only seeks the degree of compliance with professional and ethical standards in the field. Competition requirements in the accounting profession in the digital era, together with the globalization of markets and standardization of financial communication at regional and global level, are demanding from the professional accountant far more than compliance with existing standards. To study the potential for shifting from compliance to excellence in the accounting profession we conducted an empirical study using survey as a quantitative research method. The survey results revealed that the vast majority of those surveyed are organized in private offices and do not have quality control procedures and only a small proportion of respondents considered necessary to implement a quality management system. We deepened our researches and identified a compliance of professional standards with the requirements of a quality management system based on PEVA cycle and we concluded that the decisive step from compliance to excellence can be achieved by an effect of size, brought along by the

  2. Comment on the paper: “Spectroscopic and computational study of the major oxidation products formed during the reaction of two quercetin conformers with a free radical”

    Science.gov (United States)

    Scognamiglio, Monica; Temussi, Fabio; D'Abrosca, Brigida; Fiorentino, Antonio

    2013-12-01

    The title paper reports a study on the structural elucidation by spectroscopic and computational methods of the products obtained from the reaction of two conformers of quercetin with the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH•). Many points of criticism, concerning both theoretical principles and experimental data, are highlighted in the present communication.

  3. Conformers and non-covalent interactions studied by laser spectroscopies and ab initio calculations

    CERN Document Server

    Ullrich, S

    2001-01-01

    The model peptides, formanilide and acetanilide, and their weakly bound complexes were studied in the gas-phase using resonance enhanced multi-photon ionisation (REMPI) and zero electron kinetic energy (ZEKE) photoelectron spectroscopy. Both, cis- and trans-isomers of formanilide, were observed under molecular beam conditions. Trans-formanilide displayed predominantly in-plane vibrational excitation indicative of a planar geometry with modest geometry changes upon excitation and ionisation. In cis-formanilide the side-chain is twisted compared to the phenyl plane in the S sub 0 state, but planar in the S sub 1 and D sub 0 states, revealed in characteristic side-chain torsional and out-of-plane bending excitations. Additionally, the ZEKE spectra provide evidence that excess cationic charge is delocalised from the aromatic ring to the side chain. The work on trans-formanilide was extended to its van der Waals complex with Argon with the purpose of investigating the torsional potential of the side-chain and prob...

  4. Thermodynamic Study on the Protonation Reactions of Glyphosate in Aqueous Solution: Potentiometry, Calorimetry and NMR spectroscopy.

    Science.gov (United States)

    Liu, Bijun; Dong, Lan; Yu, Qianhong; Li, Xingliang; Wu, Fengchang; Tan, Zhaoyi; Luo, Shunzhong

    2016-03-10

    Glyphosate [N-(phosphonomethyl)glycine] has been described as the ideal herbicide because of its unique properties. There is some conflicting information concerning the structures and conformations involved in the protonation process of glyphosate. Protonation may influence the chemical and physical properties of glyphosate, modifying its structure and the chemical processes in which it is involved. To better understand the species in solution associated with changes in pH, thermodynamic study (potentiometry, calorimetry and NMR spectroscopy) about the protonation pathway of glyphosate is performed. Experimental results confirmed that the order of successive protonation sites of totally deprotonated glyphosate is phosphonate oxygen, amino nitrogen, and finally carboxylate oxygen. This trend is in agreement with the most recent theoretical work in the literature on the subject (J. Phys. Chem. A 2015, 119, 5241-5249). The result is important because it confirms that the protonated site of glyphosate in pH range 7-8, is not on the amino but on the phosphonate group instead. This corrected information can improve the understanding of the glyphosate chemical and biochemical action.

  5. Maillard induced complexes of bovine serum albumin--a dilute solution study.

    Science.gov (United States)

    Easa, A M; Armstrong, H J; Mitchell, J R; Hill, S E; Harding, S E; Taylor, A J

    1996-06-01

    Association of bovine serum albumin (BSA) on heating in the presence and absence of 2% xylose has been studied using dynamic light scattering and sedimentation velocity. When 3% solutions of the protein alone are heated at 95 degrees C association products are formed with molar masses of approximately 2 x 10(6) g/mol, a value which is independent of the time of heating. These aggregates can be dissociated in solvents that disrupt non-covalent bonds. When the reducing sugar xylose is present there is a continuous change in the hydrodynamic properties with time. After 80 min a molar mass in excess of 7 x 10(6) g/mol is obtained. This increase in molar mass is attributed to additional non-disulphide linkages resulting from the Maillard reaction. Information about the gross conformation of the Maillard induced association products has been obtained from MHKS (Mark-Houwink-Kuhn-Sakarada) double logarithmic plots of D20,w and S20,w against molar mass. The values of the MHKS coefficients obtained are most consistent with a linear rod: i.e. the association is of an end-to-end type.

  6. Conformers and non-covalent interactions studied by laser spectroscopies and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Ullrich, Susanne

    2001-07-01

    The model peptides, formanilide and acetanilide, and their weakly bound complexes were studied in the gas-phase using resonance enhanced multi-photon ionisation (REMPI) and zero electron kinetic energy (ZEKE) photoelectron spectroscopy. Both, cis- and trans-isomers of formanilide, were observed under molecular beam conditions. Trans-formanilide displayed predominantly in-plane vibrational excitation indicative of a planar geometry with modest geometry changes upon excitation and ionisation. In cis-formanilide the side-chain is twisted compared to the phenyl plane in the S{sub 0} state, but planar in the S{sub 1} and D{sub 0} states, revealed in characteristic side-chain torsional and out-of-plane bending excitations. Additionally, the ZEKE spectra provide evidence that excess cationic charge is delocalised from the aromatic ring to the side chain. The work on trans-formanilide was extended to its van der Waals complex with Argon with the purpose of investigating the torsional potential of the side-chain and probing charge delocalisation. Complexation of amides with water is of considerable interest since water is not only present as a bulk solvent surrounding a peptide but also attached to specific binding sites in its interior. Evidence was found for the existence of a NH- and CO-bound isomer of trans-formanilide in the neutral, S{sub 0} and S{sub 1}, states, with the ZEKE spectrum of the cationic 'CO-bound' complex indicating a strong preference for the NH binding site. (author)

  7. Conformational and quantitative structure-activity relationship study of cytotoxic 2-arylidenebenzocycloalkanones.

    Science.gov (United States)

    Dimmock, J R; Kandepu, N M; Nazarali, A J; Kowalchuk, T P; Motaganahalli, N; Quail, J W; Mykytiuk, P A; Audette, G F; Prasad, L; Perjési, P; Allen, T M; Santos, C L; Szydlowski, J; De Clercq, E; Balzarini, J

    1999-04-22

    Various 2-arylideneindanones 1, 2-arylidenetetralones 2, and 2-arylidenebenzosuberones 3 were synthesized with the aim of determining the relative orientations of the two aryl rings which favored cytotoxicity. Molecular modeling of the unsubstituted compound in each series revealed differences in the spatial arrangements of the two aryl rings, and evaluation of these compounds against P388, L1210, Molt 4/C8, and CEM cells as well as a panel of human tumor cell lines indicated that in general the order of cytotoxicity was 3 > 2 > 1. In particular 2-(4-methoxyphenylmethylene)-1-benzosuberone (3k) had the greatest cytotoxicity, possessing 11 times the potency of the reference drug melphalan when all five screens were considered. Series 3 was considered in further detail. First, excision of the aryl ring fused to the cycloheptanone moiety in series 3 led to some 2-arylidene-1-cycloheptanones 4 which had approximately one-third of the bioactivity of the analogues 3. Second, in some screens cytotoxicity was correlated negatively with the sigma values and positively with the MR constants of the substituents in the arylidene aryl ring of 3. Third, X-ray crystallography of five representative compounds (3i,k-n) revealed differences in the locations of the aryl rings which may have contributed to the variations in cytotoxicity. Finally three members of series 3 inhibited RNA and protein syntheses and induced apoptosis in human Jurkat T cells. This study has revealed that 2-arylidene-1-benzosuberones are a group of useful cytotoxic agents, and in particular 3k serves as a prototypic molecule for subsequent structural modifications.

  8. Conformational analysis of nine-membered cyclic acetals. Stereoelectronic effect in 2,4- and 3,5-benzodioxonine derivatives.

    Science.gov (United States)

    Migda, Wojciech; Rys, Barbara

    2006-07-21

    Conformations of the title compounds were examined using DFT calculations and NBO analysis in order to find the origins of their conformational preferences. The most stable conformations were TBC and TCBtype-1 for the 2,4- and 3,5-benzodioxonine derivatives, respectively. In both of these conformations the acetal moiety adopts the g+/-g+/- geometry. The NBO analysis yielded values of the stabilization energy associated with the stereoelectronic nO --> sigmaC-O* interactions that were highest for conformations other than the global minima. Conformers displaying the strongest interactions followed different patterns of atom arrangement within the acetal moiety, namely g+g-, and those in which one or both of the torsion angles within the C-O-C-O-C segment were close to 90 degrees . Steric repulsion caused by alkyl substituents at the anomeric carbon was found to influence the strength of the nO --> sigmaC-O* stabilization through modification of bond lengths and torsion angles. The adopted ground-state conformations result from accommodation of steric repulsions and stabilizing stereoelectronic interactions. It was shown that DFT calculations of conformational preferences of acetals together with GIAO prediction of 13C chemical shifts should be a useful methodology for studies on conformation and conformational equilibria of acetals in solution.

  9. Some Progress in Conformal Geometry

    Directory of Open Access Journals (Sweden)

    Sun-Yung A. Chang

    2007-12-01

    Full Text Available This is a survey paper of our current research on the theory of partial differential equations in conformal geometry. Our intention is to describe some of our current works in a rather brief and expository fashion. We are not giving a comprehensive survey on the subject and references cited here are not intended to be complete. We introduce a bubble tree structure to study the degeneration of a class of Yamabe metrics on Bach flat manifolds satisfying some global conformal bounds on compact manifolds of dimension 4. As applications, we establish a gap theorem, a finiteness theorem for diffeomorphism type for this class, and diameter bound of the $sigma_2$-metrics in a class of conformal 4-manifolds. For conformally compact Einstein metrics we introduce an eigenfunction compactification. As a consequence we obtain some topological constraints in terms of renormalized volumes.

  10. Synthesis, structure combined with conformational analysis, biological activities and docking studies of bis benzylidene cyclohexanone derivatives

    Directory of Open Access Journals (Sweden)

    Gehad Lotfy

    2017-07-01

    Full Text Available We report the synthesis and biological evaluation of bis benzylidne cyclohexanone derivatives 2,6-di(4-fluorobenzylidenecyclohexanone 3a and (2E,6E‐2,6‐bis({[4‐(trifluoromethylphenyl]methylidene}cyclohexanone 3b. Compound 3b crystallized in the monoclinic space group P21/n with unit cell parameters a = 29.3527(12 Å, b = 8.3147(3 Å, c = 32.7452(14 Å, β = 112.437(2°, and V = 7386.8(5 Å3, Z = 16, and Rint = 0.072 at T = 100 K. The asymmetric unit contains four independent molecules, each of which has slight differences in the bond lengths and angles. One non-classical C11D–H11F⋯F3A hydrogen bond connects the molecules. Density functional theory was used to optimize the structures and calculate the natural charges, dipole moments, frontier molecular orbitals, and NMR and UV–Vis spectroscopic properties, which are discussed and compared with the experimental data. The synthetic derivatives were evaluated for α-glucosidase inhibitory activity, and we found that compound 3a (IC50 = 96.3 ± 0.51 μM is a potent α-glucosidase inhibitor, showing superior activity to the standard drug acarbose (IC50 = 841 ± 1.73 μM. Compound 3b (IC50 = 7.92 ± 1.3 μg/mL was found to be a potent antileishmanial compound, especially compared to the antileishmanial drugs pentamidine (IC50 = 5.09 ± 0.04 μM and amphotericine B (IC50 = 0.29 ± 0.05 μg/mL. In addition, 3a and 3b have cytotoxic effects against PC3 (prostate cancer, HeLa (cervical cancer, and MCF-3 (breast cancer cell lines. Docking study for compounds activity was performed with Openeye software in order to understanding their pose of interaction in the target receptors.

  11. The solid-state and solution-state reassigned structures of tagitinin A, a 3,10-epoxy-germacrolide from Tithonia diversifolia, and the interconversion of 3,10-epoxy-germacrolide conformational families via a ring-atom flip mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Glaser, Robert [Ben-Gurion University of the Negev (Israel). Dept. of Chemistry]. E-mail: rglaser@bgumail.bgu.ac.il; Garcia, Abraham; Chavez, Maria Isabel; Delgado, Guillermo [Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico). Inst. de Quimica]. E-mail: delgado@servidor.unam.mx

    2005-05-15

    Tagitinin A (2), a known 3,10-epoxy-germacrolide-6,7-trans-lactone isolated from Tithonia diversifolia, was investigated by single crystal X-ray diffraction analysis. It was found to have a 1{beta},4{alpha},6{alpha},7{beta},8{beta} relative configuration which differed at C(1) from the 1a-orientation originally reported in the literature which was determined by Horeau's Rule. Analysis of the 1H NMR spectrum of 2 shows the molecule to maintain its crystallographically observed twist-chair-boat (TCB) nine-membered ring conformation in acetone-d6 solution. The twist-chair-boat/skew-chair-boat type 3 conformations of saturated/unsaturated nine-membered rings within 3,10-epoxy-germacrolides can be interconverted to the skew-chair-chair (SCC) conformation by means of a C(9) ring atom flip mechanism. As a result of this conformational change, the orientation of the C(1) atom and the C(8)-oxycarbonyl moiety are transformed from diequatorial to diaxial. The reported stereochemistry of 3,10-epoxy-germacrolide lactone structures, and the DFT B3LYP/6-31g(d) modeling findings in this work indicate that tetrahedral C(1) atoms stabilize the TCB/SCB type 3 conformations, while their trigonal counterparts stabilize the SCC conformation. (author)

  12. Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclohexen-1-ol.

    Science.gov (United States)

    Ocola, Esther J; Laane, Jaan

    2016-01-14

    The infrared and Raman spectra of 2-cyclohexen-1-ol have been recorded and analyzed. The experimental work has been complemented by ab initio and density functional theory computations. The calculations show that in the vapor phase the conformations with the π-type hydrogen bonding are the lowest in energy, and these findings are supported by the experimental spectra, which agree well with the theoretical predictions. The six conformers predicted result from differences between the direction on the ring-twisting angle and the -OH internal rotation angle. The lowest-energy conformer has the hydrogen of the OH group pointing to the middle of the C═C double bond. The other conformers are calculated to be 72 cm(-1) (0.21 kcal/mol) to 401 cm(-1) (1.15 kcal/mol) higher in energy. In the liquid phase, only two conformers can be identified in the spectra, and these correspond to different directions of the ring-twisting.

  13. Conformational entropic maps of functional coupling domains in GPCR activation: A case study with beta2 adrenergic receptor

    Science.gov (United States)

    Liu, Fan; Abrol, Ravinder; Goddard, William, III; Dougherty, Dennis

    2014-03-01

    Entropic effect in GPCR activation is poorly understood. Based on the recent solved structures, researchers in the GPCR structural biology field have proposed several ``local activating switches'' that consisted of a few number of conserved residues, but have long ignored the collective dynamical effect (conformational entropy) of a domain comprised of an ensemble of residues. A new paradigm has been proposed recently that a GPCR can be viewed as a composition of several functional coupling domains, each of which undergoes order-to-disorder or disorder-to-order transitions upon activation. Here we identified and studied these functional coupling domains by comparing the local entropy changes of each residue between the inactive and active states of the β2 adrenergic receptor from computational simulation. We found that agonist and G-protein binding increases the heterogeneity of the entropy distribution in the receptor. This new activation paradigm and computational entropy analysis scheme provides novel ways to design functionally modified mutant and identify new allosteric sites for GPCRs. The authors thank NIH and Sanofi for funding this project.

  14. Structure and cytotoxic activity of sesquiterpene glycoside esters from Calendula officinalis L.: Studies on the conformation of viridiflorol.

    Science.gov (United States)

    D'Ambrosio, Michele; Ciocarlan, Alexandru; Colombo, Elisa; Guerriero, Antonio; Pizza, Cosimo; Sangiovanni, Enrico; Dell'Agli, Mario

    2015-09-01

    Topic applications of Calendula officinalis L. lipophilic extracts are used in phytotherapy to relieve skin inflammatory conditions whereas infusions are used as a remedy for gastric complaints. Such a different usage might be explained by some cytotoxicity of lipophilic extracts at gastric level but little is known about this. Therefore, we screened the CH2Cl2 extract from the flowers of C. officinalis by MTT and LDH assays in human epithelial gastric cells AGS. This bioassay-oriented approach led to the isolation of several sesquiterpene glycosides which were structurally characterized by spectroscopic measurements, chemical reactions and MM calculations. The conformational preferences of viridiflorol fucoside were established and a previously assigned stereochemistry was revised. The compounds 1a, 2a and 3f showed comparably high cytotoxicity in the MTT assays, whereas the effect on LDH release was lower. Our study provides new insights on the composition of C. officinalis extracts of medium polarity and identifies the main compounds that could be responsible for cytotoxic effects at gastric level. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Conformational analysis, inter-molecular interactions, electronic properties and vibrational spectroscopic studies on cis-4-hydroxy-d-proline

    Directory of Open Access Journals (Sweden)

    Ambrish Kumar Srivastava

    2016-12-01

    Full Text Available The present study deals with a non-native amino acid, cis-4-hydroxy-d-proline (CHDP using density functional theory at B3LYP/6-31+G(d,p level. The potential energy surface scan reveals the global minimum structure of CHDP along with two potential conformers. Highest occupied molecular orbital, lowest unoccupied molecular orbital, and molecular electrostatic potential surfaces are used to explain the chemical reactivity of title molecule. The atomic charge analysis has been carried out using Mulliken and natural population schemes. The equilibrium geometry of CHDP dimer has been obtained and inter-molecular interactions are explored using QTAIM and Natural bonding orbital analyses. Vibrational spectroscopic analysis has been performed on CHDP monomer and dimer at the same level of theory. Assignments to all vibrational modes up to 400 cm−1 have been offered along with their potential energy distribution to the maximum possible accuracy. The calculated frequencies are scaled by an equation, rather than by a constant factor and then compared with experimental FT-IR frequencies obtained by KBr disc and Nujol mull techniques. A number of electronic and thermodynamic parameters have also been evaluated for CHDP monomer and dimer.

  16. AWS certified solutions architect official study guide associate exam

    CERN Document Server

    Baron, Joe; Bixler, Tim; Gaut, Biff; Kelly, Kevin E; Senior, Sean; Stamper, John

    2017-01-01

    This is your opportunity to take the next step in your career by expanding and validating your skills on the AWS cloud. AWS has been the frontrunner in cloud computing products and services, and the AWS Certified Solutions Architect Official Study Guide for the Associate exam will get you fully prepared through expert content, and real-world knowledge, key exam essentials, chapter review questions, access to Sybex's interactive online learning environment, and much more. This official study guide, written by AWS experts, covers exam concepts, and provides key review on exam topics, including: * Mapping Multi-Tier Architectures to AWS Services, such as web/app servers, firewalls, caches and load balancers * Understanding managed RDBMS through AWS RDS (MySQL, Oracle, SQL Server, Postgres, Aurora) * Understanding Loose Coupling and Stateless Systems * Comparing Different Consistency Models in AWS Services * Understanding how AWS CloudFront can make your application more cost efficient, faster and secure * Implem...

  17. New terahertz dielectric spectroscopy for the study aqueous solutions

    CERN Document Server

    George, Deepu K; Vinh, N Q

    2015-01-01

    We present a development of a high precision, tunable far-infrared (terahertz) frequency-domain dielectric spectrometer for studying the dynamics of biomolecules in aqueous solutions in the gigahertz-to-terahertz frequency. As a first application we report on the measurement of the absorption and refractive index for liquid water in the frequency range from 5 GHz to 1.12 THz (0.17 to 37.36 cm-1 or 0.268 to 60 mm). The system provides a coherent radiation source with a power up to 20 mW in the gigahertz-to-terahertz region. The power signal-to-noise ratio of our instrument reaches 1015 and the system achieves a spectral resolution of less than 100 Hz. The temperature of samples can be controlled precisely with an error bars of 0.02 oC from above 0 oC to 90 oC. Given these attributes, our spectrometer provides unique capabilities for the accurate measurement of even very strongly absorbing materials such as aqueous solutions.

  18. Viscous conformal gauge theories

    DEFF Research Database (Denmark)

    Toniato, Arianna; Sannino, Francesco; Rischke, Dirk H.

    2017-01-01

    We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories.......We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories....

  19. Conformable heat equation on a radial symmetric plate

    Directory of Open Access Journals (Sweden)

    Avci Derya

    2017-01-01

    Full Text Available The conformable heat equation is defined in terms of a local and limit-based definition called conformable derivative which provides some basic properties of integer order derivative such that conventional fractional derivatives lose some of them due to their non-local structures. In this paper, we aim to find the fundamental solution of a conformable heat equation acting on a radial symmetric plate. Moreover, we give a comparison between the new conformable and the existing Grunwald-Letnikov solutions of heat equation. The computational results show that conformable formulation is quite successful to show the sub-behaviors of heat process. In addition, conformable solution can be obtained by a analytical method without the need of a numerical scheme and any restrictions on the problem formulation. This is surely a significant advantageous compared to the Grunwald-Letnikov solution.

  20. Superspace conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Quella, Thomas [Koeln Univ. (Germany). Inst. fuer Theoretische Physik; Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2013-07-15

    Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

  1. A Study of the Conformers of the (Nonafluorobutanesulfonylimide Ion by Means of Infrared Spectroscopy and Density Functional Theory (DFT Calculations

    Directory of Open Access Journals (Sweden)

    Oriele Palumbo

    2017-02-01

    Full Text Available Pyrrolidinium-based ionic liquids with anions of the per(fluoroalkylsulfonylimide family are particularly interesting for their use as electrolytes in lithium batteries. These ions have several geometric isomers and the presence of different ion conformers and their distribution affects the ILs (Ionic liquids physical and chemical properties. In the present work, we report the temperature dependence of the infrared spectra of the N-butyl-N-methyl-pyrrolidinium(trifluoromethanesulfonyl(nonafluorobutanesulfonylimide (PYR14‑IM14 ionic liquid; DFT (Density Functional Theory calculations performed with different models provides indications about the IM14 conformers and their vibrational spectra. Moreover the temperature dependence of the intensity of the lines identified as markers of different conformers provide indications about the conformers’ distribution and the difference of their enthalpy in the liquid phase.

  2. Fluorescence study on ligand induced conformational changes of glutamine synthetase from Bacillus brevis Bb G1 under sporulating conditions

    Directory of Open Access Journals (Sweden)

    SUJA ABRAHAM

    2015-04-01

    Full Text Available Glutamine synthetase, an important enzyme of nitrogen metabolism, was purified under sporulating conditions (GSala. The effect of ligands on the tryptophan fluorescence of the purified enzyme GSala was investigated. With increasing concentrations of L-glutamine in GSala, a blue shift in emission maximum with an increase in fluorescence intensity and decrease in life times were observed compared to the emission maximum, fluorescence intensity and life times of GSala. With increasing concentrations of glycine in GSala, a shift in emission maximum, change in fluorescence intensity and change in lifetimes were observed compared to the emission maximum, fluorescence intensity and life times of GSala. These observations strongly support the possibility that GSala undergoes a conformational change on binding with ligands and each ligand produced different conformational changes in GSala. Also, different concentrations of each ligand produced different protein conformations in the enzyme GSala.

  3. Conformational analysis and vibrational study of daidzein by using FT-IR and FT-Raman spectroscopies and DFT calculations.

    Science.gov (United States)

    Singh, Harshita; Singh, Swapnil; Srivastava, Anubha; Tandon, Poonam; Bharti, Purnima; Kumar, Sudhir; Maurya, Rakesh

    2014-01-01

    Daidzein (C15H10O4) is a type of isoflavone. It was isolated from Butea monosperma that belongs to the Fabaceae family. Soybeans and soy products are the abundant source of daidzein. It is the subject of investigation for many reasons, as it has got wide applications, such as anti-tumor, anti-estrogen, weak pro-estrogen and anti-cancer activities. In the present study, a complete vibrational assignment is provided for the observed IR and Raman spectra of daidzein. Electronic properties have been analyzed using TD-DFT method for both gaseous and solvent phase. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of daidzein have been determined using density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set and a good correlation was found between observed and calculated values. The double well potential energy curve of the molecule about three bonds, has been plotted, as obtained from DFT/6-31G basis. The HOMO-LUMO energy gap of possible conformers has been calculated for comparing their chemical activity. Global reactivity descriptors have been calculated for predicting the chemical reactivity and the stability of chemical systems. Electrostatic potential surface has been plotted for predicting the structure activity relationship. NBO analysis has also been performed to study the stability of the molecule. NLO study reveals the nonlinear properties of the molecule. 1H and 13C NMR spectra have also been studied. Finally, the calculated results were used to simulate infrared and Raman spectra of the title compound which showed a good agreement with the observed spectra. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3.

    Science.gov (United States)

    Nowroozi, Amin; Shahlaei, Mohsen

    2017-02-01

    In this study, a computational pipeline was therefore devised to overcome homology modeling (HM) bottlenecks. The coupling of HM with molecular dynamics (MD) simulation is useful in that it tackles the sampling deficiency of dynamics simulations by providing good-quality initial guesses for the native structure. Indeed, HM also relaxes the severe requirement of force fields to explore the huge conformational space of protein structures. In this study, the interaction between the human bombesin receptor subtype-3 and MK-5046 was investigated integrating HM, molecular docking, and MD simulations. To improve conformational sampling in typical MD simulations of GPCRs, as in other biomolecules, multiple trajectories with different initial conditions can be employed rather than a single long trajectory. Multiple MD simulations of human bombesin receptor subtype-3 with different initial atomic velocities are applied to sample conformations in the vicinity of the structure generated by HM. The backbone atom conformational space distribution of replicates is analyzed employing principal components analysis. As a result, the averages of structural and dynamic properties over the twenty-one trajectories differ significantly from those obtained from individual trajectories.

  5. Families and degenerations of conformal field theories

    Energy Technology Data Exchange (ETDEWEB)

    Roggenkamp, D.

    2004-09-01

    In this work, moduli spaces of conformal field theories are investigated. In the first part, moduli spaces corresponding to current-current deformation of conformal field theories are constructed explicitly. For WZW models, they are described in detail, and sigma model realizations of the deformed WZW models are presented. The second part is devoted to the study of boundaries of moduli spaces of conformal field theories. For this purpose a notion of convergence of families of conformal field theories is introduced, which admits certain degenerated conformal field theories to occur as limits. To such a degeneration of conformal field theories, a degeneration of metric spaces together with additional geometric structures can be associated, which give rise to a geometric interpretation. Boundaries of moduli spaces of toroidal conformal field theories, orbifolds thereof and WZW models are analyzed. Furthermore, also the limit of the discrete family of Virasoro minimal models is investigated. (orig.)

  6. Einstein equations and conformal structure: Existence of Anti-de Sitter-type space-times

    Science.gov (United States)

    Friedrich, Helmut

    1995-10-01

    We discuss Einstein's equations in the context of normal conformal Cartan connections, derive a new conformal representation of the equations, and express the equations in a conformally invariant gauge. The resulting formulation of the equations is used to show the existence of asymptotically simple solutions to Einstein's equations with a positive cosmological constant. The solutions are characterized by Cauchy data on a space-like slice and by the intrinsic conformal structure on the conformal boundary at space-like and null infinity.

  7. Electrochemical Studies of Lead Telluride Behavior in Acidic Nitrate Solutions

    Directory of Open Access Journals (Sweden)

    Rudnik E.

    2015-04-01

    Full Text Available Electrochemistry of lead telluride stationary electrode was studied in nitric acid solutions of pH 1.5-3.0. E-pH diagram for Pb-Te-H2O system was calculated. Results of cyclic voltammetry of Pb, Te and PbTe were discussed in correlation with thermodynamic predictions. Anodic dissolution of PbTe electrode at potential approx. -100÷50 mV (SCE resulted in tellurium formation, while above 300 mV TeO2 was mainly produced. The latter could dissolve to HTeO+2 under acidic electrolyte, but it was inhibited by increased pH of the bath.

  8. Multiple spectroscopic studies of the structural conformational changes of human serum albumin—Essential oil based nanoemulsions conjugates

    Energy Technology Data Exchange (ETDEWEB)

    Sekar, Gajalakshmi; Sugumar, Saranya; Mukherjee, Amitava; Chandrasekaran, Natarajan, E-mail: nchandra40@hotmail.com

    2015-05-15

    Nanoemulsions have numerous biomedical applications. For the first time, we have investigated the effects of orange and eucalyptus essential oil based nanoemulsions towards the structural aspect of human serum albumin (HSA). Quenching effect of nanoemulsion against the intrinsic fluorescence potential of tryptophan and tyrosine residues were evidenced from the fluorescence spectroscopic analysis. Static quenching mechanism was found to lead the binding of HSA–nanoemulsion systems. Synchronous and three dimensional spectroscopic studies have revealed the possible changes to the aromatic environment of HSA by the nanoemulsion. UV–Visible spectroscopic studies have confirmed the existence of the ground state complex formation between HSA and the surface of nanoemulsions by exhibiting the hyper-chromic effect in a concentration dependant manner. FTIR spectroscopy revealed the slight alteration in the Amide I, II and III bands of HSA after interaction. FT-Raman spectroscopy showed the decrease in the Raman intensity of the aromatic amino acid residues and shift in the amide bands of HSA upon binding with the nanoemulsion. Dichoric band obtained from the far UV-CD spectra at 208 and 222 nm of HSA showed the corresponding decrease in the alpha-helical contents upon interaction with nanoemulsions. Near UV-CD spectra also showed the prominent changes in the aromatic positions of the amino acid residues of HSA on binding with nanoemulsions. The above study has extrapolated the side effect analysis of the nanoemulsions in pharmaceutical applications in vitro in reference to their interaction with serum proteins. - Highlights: • Orange and eucalyptus oil based nanoemulsions were formulated and characterized. • UV–Visible spectroscopy confirmed the ground state complex formation. • Fluorescence spectroscopy confirmed the molecular conformational changes. • FTIR spectroscopy deep-rooted the alteration in the amide bands of HSA. • FT-Raman spectroscopy established

  9. Scalar perturbations of nonsingular nonrotating black holes in conformal gravity

    OpenAIRE

    Toshmatov, Bobir; Bambi, Cosimo; Ahmedov, Bobomurat; Stuchlík, Zdeněk; Schee, Jan

    2017-01-01

    We study scalar and electromagnetic perturbations of a family of nonsingular nonrotating black hole spacetimes that are solutions in a large class of conformally invariant theories of gravity. The effective potential for scalar perturbations depends on the exact form of the scaling factor. Electromagnetic perturbations do not feel the scaling factor, and the corresponding quasinormal mode spectrum is the same as in the Schwarzschild metric. We find that these black hole metrics are stable und...

  10. The ab initio study and NBO interpretation of solvent effects on the structural stability and the chemical reactivity of penicillin-V conformations

    Directory of Open Access Journals (Sweden)

    Ali Akbar Salari

    2017-05-01

    Full Text Available Quantum mechanics (QM methods were used to examine the electronic structure and the relative stability of penicillin-V (PV conformations in the gas phase and the different solvent media. The effects of solvent dielectric constant and the computational methods were analyzed on the conformational stability of β-lactam-thiazolidine bicyclic system, its geometry and its reactivity. Our findings indicated that in the PV, the axial form of thiazolidine ring is more stable than equatorial form one in all of the tested media. This is in agreement with the NMR studies performed on PV that indicate the axial conformation is the dominant form in solid state. Furthermore, the atomic charges computations and natural bond orbital Interpretation (NBO represented that by increasing the solvent dielectric constant, the charge values on the C5 and C7 atoms of the β-lactam ring decrease, while HOMO–LUMO gap and occupancy values of the contained bonds in β-lactam ring of the interested structures increase. Hence, the β-lactam ring possesses the lowest reactivity against nucleophilic attacks and the highest stability in presence of implicit waters. However, it can be concluded that the structural stability of penicillin-V conformations is controlled by solvent’s polarity and its dielectric constant, the electrophilic nature of β-lactam ring and HOMO–LUMO gap.

  11. {sup 13}CHD{sub 2}–CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins

    Energy Technology Data Exchange (ETDEWEB)

    Rennella, Enrico; Huang, Rui; Velyvis, Algirdas; Kay, Lewis E., E-mail: kay@pound.med.utoronto.ca [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2015-10-15

    An NMR experiment for quantifying slow (millisecond) time-scale exchange processes involving the interconversion between visible ground state and invisible, conformationally excited state conformers is presented. The approach exploits chemical exchange saturation transfer (CEST) and makes use of {sup 13}CHD{sub 2} methyl group probes that can be readily incorporated into otherwise highly deuterated proteins. The methodology is validated with an application to a G48A Fyn SH3 domain that exchanges between a folded conformation and a sparsely populated and transiently formed unfolded ensemble. Experiments on a number of different protein systems, including a 360 kDa half-proteasome, establish that the sensitivity of this {sup 13}CHD{sub 2}{sup 13}C–CEST technique can be upwards of a factor of 5 times higher than for a previously published {sup 13}CH{sub 3}{sup 13}C–CEST approach (Bouvignies and Kay in J Biomol NMR 53:303–310, 2012), suggesting that the methodology will be powerful for studies of conformational exchange in high molecular weight proteins.

  12. A Group Theoretical and Quantum Chemical Study of Electronic Absorption and Fluorescence, Vibrational Spectra, and Conformations of Trimethine Cyanine Dye Molecules

    Directory of Open Access Journals (Sweden)

    Vita Solomko

    2016-01-01

    Full Text Available The energetic structures and conformations of trimethine cyanine dye molecules were investigated. For research, group theoretical and quantum chemical calculation methods were used. The theoretical group analysis of electronic and vibrational structure of molecules was carried out. Also, the energetic structures and conformations of the molecule of this dye were studied. Research shows that the investigated molecule may reside in three different conformational states, one of which is highly symmetric (symmetry C2v and the other two with low symmetry. The third conformer is characterized by lowering of binding energy of the electronic system by 0.23 eV, and the long-wavelength absorption band is shifted to lower energies. Also the group theoretical analysis of the trimethine cyanine molecule had allowed systematizing the vibrational and electronic quantum transitions and identifying the bands in the absorption spectra. It is shown that the excitation of the molecule in S1-state causes trans-cis-isomerization. The presence of the barrier of ~0.1 eV allows the fluorescence process to compete with isomerization process, but isomerization causes a decrease in the fluorescence quantum yield of the dye.

  13. Conformational preferences of ethyl propionate molecule: Raman, temperature dependent FTIR spectroscopic study aided by ab initio quantum chemical and Car-Parrinello molecular dynamics simulation studies.

    Science.gov (United States)

    Dutta, Bipan; Tanaka, Takeyuki; Banerjee, Arup; Chowdhury, Joydeep

    2013-06-13

    The conformational preferences of the industrially significant ethyl propionate (EP) molecule have been investigated from the Raman and FTIR spectra, aided by ab initio and Car-Parrinello molecular dynamics (CPMD) simulation studies. The vibrational signatures of various rotameric forms of the EP molecule have been assigned for the first time from the potential energy distributions (PEDs). The critical analyses of the vibrational signatures reveal the coexistences of the Trans-Trans (TT), Trans-Antigauche (TG(-)) [Trans-Gauche (TG(+))], Antigauche-Trans (G(-)T) [Gauche-Trans (G(+)T)], Antigauche-Antigauche (G(-)G(-)) [Gauche-Gauche (G(+)G(+))], and Gauche-Antigauche (G(+)G(-)) [Antigauche-Gauche (G(-)G(+))] forms of the EP molecule at room and at high temperatures. However, at low temperature (ca. 70 °C), the TT and TG(-) forms of the EP molecule is estimated to be preponderant. The Car-Parrinello molecular dynamics simulation studies of the EP molecule estimated at high, room, and low temperatures are also in harmony with our conjecture as suggested from the vibrational analyses. The ab intio molecular dynamics simulations are observed to be a useful tool for the conformational analyses of the molecule.

  14. Struvite Precipitation and Phosphorous Removal from Urine Synthetic Solution: Reaction Kinetic Study

    Directory of Open Access Journals (Sweden)

    Marwa Saied Shalaby

    2015-03-01

    Full Text Available Phosphorus, like oil, is a non-renewable resource that must be harvested from finite resources in the earth’s crust. An essential element for life, phosphorus is becoming increasingly scarce, contaminated, and difficult to extract. Struvite or magnesium ammonium phosphate (MgNH4PO4.6H2O is a white, crystalline phosphate mineral that can be used as a bio-available fertilizer. The main objective of this research is to indicate the most important operating parameters affecting struvite precipitation by means of chemical reaction kinetics. The present study explores struvite precipitation by chemical method under different starting molar ratios, pH and SSR. It is shown that an increase of starting Mg: PO4: NH4 with respect to magnesium (1.6:1:1 strongly influences the growth rate of struvite and so the efficiency of the phosphate removal. This was attributed to the effect of magnesium on the struvite solubility product and on the reached supersaturation Super Saturation Ratio at optimum starting molar ratio and pH. It was also shown, by using chemical precipitation method that the determined Super Saturation Ratio (SSR values of struvite, at 8, 8.5, 9, 9.5 and 10 are 1.314, 4.29, 8.89, 9.87 and 14.89 respectively are close to those presented in the literature for different origins of wastewater streams. The results show that SSR , pH, and starting molar ratio strongly influences the kinetics of precipitation and so phosphorous removal to reach 93% removal percent , 5.95 mg/lit as a minimum PO4 remained in solution, and 7.9 gm precipitated struvite from feed synthetic solution of 750 ml . The product was subjected to chemical analysis by means of EDIX-FTIR, SEM and XRD showing conformity with published literature. First-order kinetics was found to be sufficient to describe the rate data. The rates increased with increasing pH and so SSR and the apparent rate constants for the reaction were determined. © 2015 BCREC UNDIP. All rights reserved

  15. Struggling with solutions : a case study of using organisation concepts

    NARCIS (Netherlands)

    Benders, Jos; Slomp, Jannes

    2009-01-01

    Engineers contribute to the constant flow of new tools and organisation concepts. These tend to be presented as solutions to existing organisational problems. These solutions may become problems themselves, however. We present a longitudinal case of how a truck manufacturer struggled with various

  16. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    Science.gov (United States)

    Yu, Rongjun; Sun, Sai

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  17. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    Directory of Open Access Journals (Sweden)

    Rongjun Yu

    Full Text Available When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN, an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  18. QENS and NMR studies of 3-picoline-water solutions

    CERN Document Server

    Almasy, L; Bokor, M; Cser, L; Tompa, K; Zanotti, J M; Jancso, G

    2002-01-01

    Quasi-elastic neutron scattering measurements were performed on aqueous solutions of 3-picoline (3-methylpyridine) at room temperature. H-D substitution on both the solute and the water was used to separate the dynamics of the two species. The analysis of the translational diffusive motion at different concentrations shows that at high picoline content the diffusion coefficient of water decreases strongly and becomes similar to that of the solute, indicating strong coupling between the motions of the solute and the solvent. Activation energies characteristic of the dynamic behavior of the methyl group were determined from sup 1 H spin-lattice relaxation rate measurements for H sub 2 O and D sub 2 O solutions of 3-picoline above 310 K. (orig.)

  19. Structures of W(2.2 Lie conformal algebra

    Directory of Open Access Journals (Sweden)

    Yuan Lamei

    2016-01-01

    . In this paper, we study conformal derivations, central extensions and conformal modules for this Lie conformal algebra. Also, we compute the cohomology of this Lie conformal algebra with coefficients in its modules. In particular, we determine its cohomology with trivial coefficients both for the basic and reduced complexes.

  20. Computational study on the conformations of CD38 and inclusion complexes of some lower-size large-ring cyclodextrins

    Science.gov (United States)

    Ivanov, Petko; Atanassov, Emanouil; Jaime, Carlos

    2014-01-01

    The conformations of CD38 were examined by conformational search with molecular dynamics simulations using the Glycam04 force field. The results were compared with previous ones for CD26, the largest cyclodextrin for which crystal data are available. Principal component analysis (PCA) was applied for post-processing of the simulation trajectories. Limited number of modes determine the overall deformations of the macroring of CD38. The longer perimeter of the macroring allowed the formation of a form not observed so far - a three-turn helix shaped as a short tube. In analogy with CD26, significant participation was monitored for conformations of CD38 with one-turn spirals at the opposite sides of the macroring linked together from the 'bottom' and from the 'top' with extended bridge spacers. Computationally were examined for the first time inclusion complexes of some lower-size LR-CDs, namely complexes of CDn (n = 13, 14, 26) with adamantane and of CD14 with 1-hydroxyadamantane. The macroring conformation of CD13 was not altered by the inclusion of the substrate molecule which acquired preferred positioning not in the middle of the cavity but rather close to the glucose residues at one of the sides. The same positioning of the small molecule in the cavity of the more flexible CD14 macroring enhanced the appearance of bent onto two conformation of this cyclodextrin. The most interesting behaviour presented the complex of CD26 with adamantane in which case the small molecule acts as a 'nucleation center' for the formation of a second helical turn about the substrate molecule.

  1. Ultrafast infrared studies of complex ligand rearrangements in solution

    Energy Technology Data Exchange (ETDEWEB)

    Payne, Christine K. [Univ. of California, Berkeley, CA (United States)

    2003-01-01

    The complete description of a chemical reaction in solution depends upon an understanding of the reactive molecule as well as its interactions with the surrounding solvent molecules. Using ultrafast infrared spectroscopy it is possible to observe both the solute-solvent interactions and the rearrangement steps which determine the overall course of a chemical reaction. The topics addressed in these studies focus on reaction mechanisms which require the rearrangement of complex ligands and the spectroscopic techniques necessary for the determination of these mechanisms. Ligand rearrangement is studied by considering two different reaction mechanisms for which the rearrangement of a complex ligand constitutes the most important step of the reaction. The first system concerns the rearrangement of a cyclopentadienyl ring as the response of an organometallic complex to a loss of electron density. This mechanism, commonly referred to as ''ring slip'', is frequently cited to explain reaction mechanisms. However, the ring slipped intermediate is too short-lived to be observed using conventional methods. Using a combination of ultrafast infrared spectroscopy and electronic structure calculations it has been shown that the intermediate exists, but does not form an eighteen-electron intermediate as suggested by traditional molecular orbital models. The second example examines the initial steps of alkyne polymerization. Group 6 (Cr, Mo, W) pentacarbonyl species are generated photolytically and used to catalyze the polymerization of unsaturated hydrocarbons through a series of coordination and rearrangement steps. Observing this reaction on the femto- to millisecond timescale indicates that the initial coordination of an alkyne solvent molecule to the metal center results in a stable intermediate that does not rearrange to form the polymer precursor. This suggests that polymerization requires the dissociation of additional carbonyl ligands before

  2. Study of galactic halo F(T,TG) wormhole solutions

    Science.gov (United States)

    Sharif, M.; Nazir, Kanwal

    In this paper, we investigate static spherically symmetric wormhole solutions with galactic halo region in the background of F(T,TG) gravity. Here, T represents torsion scalar and TG is teleparallel equivalent Gauss-Bonnet term. For this purpose, we consider a diagonal tetrad and two specific F(T,TG) models. We analyze the wormhole structure through shape function graphically for both models. We also investigate the behavior of null/weak energy conditions. Finally, we evaluate the equilibrium condition to check stability of the wormhole solutions. It is concluded that there exists physically viable wormhole solution only for the first model that turns out to be stable.

  3. Sodium tetraphenylborate solution stability: A long term study

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, M.J.

    1992-06-11

    Sodium tetraphenylborata (NaTPB) is a specialty chemical required for the In Tank Precipitation Process (ITP). It precipitates cesium, aiding in the decontamination of high level radioactive waste solutions. Long term stability of aqueous alkaline solutions of NATPB has been investigated. The focus of the investigation is on the relative stabilities of NATPB solutions exposed to varying temperatures and copper concentrations over an extended period of time. Additionally, vendor-supplied samples, incubated at 40{degree}C, were stored for more than a year without decomposing. Collected data demonstrates that in the absence of elevated copper concentrations, NATPB solutions will remain stable for periods of 1 to 2 years (at a minimum) at maximum expected operating conditions (<40{degree}C). Additionally, biuret, (H{sub 2}NCO){sub 2}NH, was tested as an additive to prevent copper-induced decomposition without success.

  4. Sodium tetraphenylborate solution stability: A long term study

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, M.J.

    1992-06-11

    Sodium tetraphenylborata (NaTPB) is a specialty chemical required for the In Tank Precipitation Process (ITP). It precipitates cesium, aiding in the decontamination of high level radioactive waste solutions. Long term stability of aqueous alkaline solutions of NATPB has been investigated. The focus of the investigation is on the relative stabilities of NATPB solutions exposed to varying temperatures and copper concentrations over an extended period of time. Additionally, vendor-supplied samples, incubated at 40[degree]C, were stored for more than a year without decomposing. Collected data demonstrates that in the absence of elevated copper concentrations, NATPB solutions will remain stable for periods of 1 to 2 years (at a minimum) at maximum expected operating conditions (<40[degree]C). Additionally, biuret, (H[sub 2]NCO)[sub 2]NH, was tested as an additive to prevent copper-induced decomposition without success.

  5. Dielectric relaxation studies of dilute solutions of amides

    Energy Technology Data Exchange (ETDEWEB)

    Malathi, M.; Sabesan, R.; Krishnan, S

    2003-11-15

    The dielectric constants and dielectric losses of formamide, acetamide, N-methyl acetamide, acetanilide and N,N-dimethyl acetamide in dilute solutions of 1,4-dioxan/benzene have been measured at 308 K using 9.37 GHz, dielectric relaxation set up. The relaxation time for the over all rotation {tau}{sub (1)} and that for the group rotation {tau}{sub (2)} of (the molecules were determined using Higasi's method. The activation energies for the processes of dielectric relaxation and viscous flow were determined by using Eyring's rate theory. From relaxation time behaviour of amides in non-polar solvent, solute-solvent and solute-solute type of molecular association is proposed.

  6. Volumetric studies of some amino acids in binary aqueous solutions ...

    Indian Academy of Sciences (India)

    Unknown

    L-alanine, and L-valine in aqueous magnesium chlo- ride solutions (0⋅1–0⋅8 mol kg–1), at 288⋅15 and. 308⋅15 K. These results are expected to highlight the role of amino acids in presence of aqueous mag- nesium chloride solutions and the influence of tem- perature on them. 2.1 Experimental. 2.1 Materials. The amino ...

  7. Stability studies on aqueous and oily ophthalmic solutions of diclofenac.

    Science.gov (United States)

    Ahuja, Munish; Dhake, Avinash Shridhar; Sharma, Surendra Kumar; Majumdar, Dipak Kanti

    2009-04-01

    Various aqueous and oily diclofenac ophthalmic formulations were subjected to accelerated and long term stability studies. Degradation of diclofenac was found to follow first-order kinetics. Among the aqueous formulations containing preservative, formulation with PMA, PMN, SA, MP/PP and SMS showed diclofenac content above 90% after 6 months of accelerated and 12 months of room temperature storage. Diclofenac 0.1%, w/v aqueous formulation (pH 7.4), with 5-10% overages, containing SMS, MP/PP or PMN look promising taking both stability and corneal permeability in view. However, for use in cataract surgery formulation without preservative appears ideal. Oily ophthalmic formulations except those in olive and mustard oil, had more than 90% drug content after 6 months of accelerated and 12 months of room temperature storage. Diclofenac (0.2%, w/v) ophthalmic solution in sesame oil with 3% overage and containing benzyl alcohol (0.5%, v/v) as preservative, appears ideal, taking both stability and corneal permeability in view.

  8. Interactive Tutoring in Blended Studies: Hindrances and Solutions

    Directory of Open Access Journals (Sweden)

    Asim Ismail Ilyas (Al-Titinchy

    2016-01-01

    Full Text Available This paper distinguishes between traditional teaching known as lecturing (the teacher centered approach; and tutoring (the contemporary technology-oriented interactive teaching/learning approach. It is based on the implementation of tutoring strategies of ‘blended studies’  at the Arab Open University. It investigates the application of modern interactive teaching/learning strategies, specifying some hindering factors in the AOU-Jordan Branch context. The factors include four variables: tutors, students, course material and assessment. The paper is based on qualitative research in terms of a real teaching/leaning context, using both observation and conversation with learners, besides the use of some quantitative data retrieved from a questionnaire in which learners’ views are sought regarding a number of relevant matters. A number of suggested solutions related to each of the hindering factors are presented, which if applied, may secure shifting the balance of the teaching/learning process to a more interactive technology-based tutoring level, which in turn will enhance learners’ opportunities for the attainment of better academic standards, and secure a higher degree of achievement of the shared educational goals of learners and the educational institution they study in.

  9. Logarithmic conformal field theory

    Science.gov (United States)

    Gainutdinov, Azat; Ridout, David; Runkel, Ingo

    2013-12-01

    Conformal field theory (CFT) has proven to be one of the richest and deepest subjects of modern theoretical and mathematical physics research, especially as regards statistical mechanics and string theory. It has also stimulated an enormous amount of activity in mathematics, shaping and building bridges between seemingly disparate fields through the study of vertex operator algebras, a (partial) axiomatisation of a chiral CFT. One can add to this that the successes of CFT, particularly when applied to statistical lattice models, have also served as an inspiration for mathematicians to develop entirely new fields: the Schramm-Loewner evolution and Smirnov's discrete complex analysis being notable examples. When the energy operator fails to be diagonalisable on the quantum state space, the CFT is said to be logarithmic. Consequently, a logarithmic CFT is one whose quantum space of states is constructed from a collection of representations which includes reducible but indecomposable ones. This qualifier arises because of the consequence that certain correlation functions will possess logarithmic singularities, something that contrasts with the familiar case of power law singularities. While such logarithmic singularities and reducible representations were noted by Rozansky and Saleur in their study of the U (1|1) Wess-Zumino-Witten model in 1992, the link between the non-diagonalisability of the energy operator and logarithmic singularities in correlators is usually ascribed to Gurarie's 1993 article (his paper also contains the first usage of the term 'logarithmic conformal field theory'). The class of CFTs that were under control at this time was quite small. In particular, an enormous amount of work from the statistical mechanics and string theory communities had produced a fairly detailed understanding of the (so-called) rational CFTs. However, physicists from both camps were well aware that applications from many diverse fields required significantly more

  10. Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study.

    Science.gov (United States)

    Flannelly, David F; Aoki, Thalia G; Aristilde, Ludmilla

    2015-09-01

    The complete degradation of cellulose to glucose is essential to carbon turnover in terrestrial ecosystems and to engineered biofuel production. A rate-limiting step in this pathway is catalyzed by beta-glucosidase (BG) enzymes, which convert cellulobiose into two glucose molecules. The activity of these enzymes has been shown to vary with solution pH. However, it is not well understood how pH influences the enzyme conformation required for catalytic action on the substrate. A structural understanding of this pH effect is important for predicting shifts in BG activity in bioreactors and environmental matrices, in addition to informing targeted protein engineering. Here we applied molecular dynamics simulations to explore conformational and substrate binding dynamics in two well-characterized BGs of bacterial (Clostridium cellulovorans) and fungal (Trichoderma reesei) origins as a function of pH. The enzymes were simulated in an explicit solvated environment, with NaCl as electrolytes, at their prominent ionization states obtained at pH 5, 6, 7, and 7.5. Our findings indicated that pH-dependent changes in the ionization states of non-catalytic residues localized outside of the immediate active site led to pH-dependent disruption of the active site conformation. This disruption interferes with favorable H-bonding interactions with catalytic residues required to initiate catalysis on the substrate. We also identified specific non-catalytic residues that are involved in stabilizing the substrate at the optimal pH for enzyme activity. The simulations further revealed the dynamics of water-bridging interactions both outside and inside the substrate binding cleft during structural changes in the enzyme-substrate complex. These findings provide new structural insights into the pH-dependent substrate binding specificity in BGs. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. A quantitative measure for protein conformational heterogeneity.

    Science.gov (United States)

    Lyle, Nicholas; Das, Rahul K; Pappu, Rohit V

    2013-09-28

    Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.

  12. Fluorescence quenching studies of apolipoprotein A-I in solution and in lipid-protein complexes: protein dynamics.

    Science.gov (United States)

    Mantulin, W W; Pownall, H J; Jameson, D M

    1986-12-02

    Fluorescence lifetime and intensity quenching studies of human plasma apolipoprotein A-I (apo A-I) in aqueous solution and in recombinant lipoprotein complexes with dimyristoylphosphatidylcholine (DMPC) indicate differences in conformational dynamics. In aqueous solution, the bimolecular quenching constants (k*) for lipid-free apo A-I fluorescence quenching by oxygen and acrylamide are 2.4 X 10(9) and 0.38 X 10(9) M-1 s-1, respectively. These values are independent of the oligomeric form of the protein. There is no correlation between the relatively small k* for apo A-I, which reflects rapid, low-amplitude protein fluctuations, and the labile conformational changes of apo A-I folding reactions, like denaturation, which occur on a slower time scale. In recombinant DMPC/apo A-I complexes (100:1 molar ratio) the protein increases in amphiphilic alpha-helical structure as it blankets the lipid matrix. The apparent k* for oxygen quenching of apo A-I fluorescence in the complex is large and increases in a temperature-dependent manner. We have introduced a two-compartment model, which discriminates the source of quencher molecules as aqueous or lipid, to describe oxygen quenching of DMPC/apo A-I fluorescence. The magnitude and temperature dependence of the apparent k* predominantly reflect the partitioning of oxygen between the two phases rather than being a probe of the lipid physical state. Calculations of the helical hydrophobic moment in apo A-I indicate that tryptophan residues 8 and 72 occur at the lipid-protein interface of amphiphilic alpha-helices, whereas the other two tryptophan residues (50, 108) lie on the nonpolar faces of amphiphilic helices.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Conformational flexibility in DNA structure as revealed by structural studies of drug intercalation and its broader implications in understanding the organization of DNA in chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Sobell, H.M.; Reddy, B.S.; Bhandary, K.K.; Jain, S.C.; Sakore, T.D.; Seshadri, T.P.

    1978-01-01

    This paper reviews evidence for conformational flexibility in DNA structure (i.e., the kink) as revealed by structural studies of drug intercalation. It then describes the implications these concepts have in understanding the organization of DNA in chromatin. It is possible that the kink has still broader meaning in understanding the nature of protein-DNA interactions that are important in RNA transcription and DNA replication.

  14. Studying the Relationship between Rate of Organizational Socialization and Rate of Employees Conformity (Group Stress, Kind of Character, Individualism Culture and Pluralism Culture) in Nehbandan Executive Systems

    OpenAIRE

    Mohammad Ziaadini; Marzieh Hashemi

    2013-01-01

    This research basically aims to study the relationship between rate of organizational socialization and rate of employees’ conformity (group stress, kind of character, individualism culture and pluralism culture) in Nehbandan executive systems. Statistical society of this research includes 70 newcomer employees in Nehbandan government offices and centers and sample size was regarded equal to statistical society. Instruments of collecting data are two questionnaires of socialization and confor...

  15. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

    Directory of Open Access Journals (Sweden)

    Qing Wang

    2016-05-01

    Full Text Available Free energy calculations of the potential of mean force (PMF based on the combination of targeted molecular dynamics (TMD simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35. The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.

  16. H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

    Science.gov (United States)

    Ikebe, Jinzen; Sakuraba, Shun; Kono, Hidetoshi

    2016-01-01

    Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker. PMID:26967163

  17. Gas-Phase Conformations and Energetics of Sodium Cationized 2^'-DEOXYGUANOSINE and Guanosine: Irmpd Action Spectroscopy and Theoretical Studies

    Science.gov (United States)

    Zhu, Yanlong; Hamlow, Lucas; He, Chenchen; Bao, Xun; Rodgers, M. T.; Gao, Juehan; Oomens, J.

    2015-06-01

    In living systems, the local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent binding interactions with cations. In order to determine the effects of Na+ cationization on the gas-phase structures of 2^'-deoxyguanosine, [dGuo+Na]+, and guanosine, [Guo+Na]+, infrared multiple photon dissociation (IRMPD) action spectra of these two sodium cationized DNA and RNA mononucleosides are measured over the range extending from ~500 to ~1850 cm-1 using the FELIX free electron laser. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses of these species are performed at the B3LYP/6-31G* level of theory, whereas single-point energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory to determine the relative stabilities of these conformations. Comparison of the measure IRMPD action spectra and computed linear IR spectra enable the conformations accessed in the experiments to be elucidated. In both cases, preferential binding of the Na+ cation to O6 and N7 positions of the nucleobase is observed. Present results for the sodium cationized nucleosides are compared to results for the analogous protonated forms of these nucleosides to elucidate the effects of multiple chelating interactions with the sodium cation to hydrogen bonding interactions in the protonated systems on the structures and stabilities of these nucleosides.

  18. Genotoxicity study of photolytically treated 2-chloropyridine aqueous solutions

    Energy Technology Data Exchange (ETDEWEB)

    Vlastos, Dimitris, E-mail: dvlastos@cc.uoi.gr [Department of Environmental and Natural Resources Management, University of Ioannina, Seferi 2, Agrinio 30100 (Greece); Skoutelis, Charalambos G.; Theodoridis, Ioannis T. [Department of Environmental and Natural Resources Management, University of Ioannina, Seferi 2, Agrinio 30100 (Greece); Stapleton, David R. [Chemical Engineering, IPSE, School of Process Environmental and Materials Engineering, University of Leeds, Leeds LS2 9JT (United Kingdom); Papadaki, Maria I. [Department of Environmental and Natural Resources Management, University of Ioannina, Seferi 2, Agrinio 30100 (Greece); Chemical Engineering, IPSE, School of Process Environmental and Materials Engineering, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2010-05-15

    2-Chloropyridine (2-CPY) has been identified as a trace organic chemical in process streams, wastewater and even drinking water. Furthermore, it appears to be formed as a secondary pollutant during the decomposition of specific insecticides. As reported in our previous work, 2-CPY was readily removed and slowly mineralised when subjected to ultraviolet (UV) irradiation at 254 nm. Moreover, 2-CPY was found to be genotoxic at 100 {mu}g ml{sup -1} but it was not genotoxic at or below 50 {mu}g ml{sup -1}. In this work 2-CPY aqueous solutions were treated by means of UV irradiation at 254 nm. 2-CPY mineralisation history under different conditions is shown. 2-CPY was found to mineralise completely upon prolonged irradiation. Identified products of 2-CPY photolytic decomposition are presented. Solution genotoxicity was tested as a function of treatment time. Aqueous solution samples, taken at different photo-treatment times were tested in cultured human lymphocytes applying the cytokinesis block micronucleus (CBMN) assay. It was found that the solution was genotoxic even when 2-CPY had been practically removed. This shows that photo-treatment of 2-CPY produces genotoxic products. Upon prolonged irradiation solution genotoxicity values approached the control value.

  19. Genotoxicity study of photolytically treated 2-chloropyridine aqueous solutions.

    Science.gov (United States)

    Vlastos, Dimitris; Skoutelis, Charalambos G; Theodoridis, Ioannis T; Stapleton, David R; Papadaki, Maria I

    2010-05-15

    2-Chloropyridine (2-CPY) has been identified as a trace organic chemical in process streams, wastewater and even drinking water. Furthermore, it appears to be formed as a secondary pollutant during the decomposition of specific insecticides. As reported in our previous work, 2-CPY was readily removed and slowly mineralised when subjected to ultraviolet (UV) irradiation at 254 nm. Moreover, 2-CPY was found to be genotoxic at 100 microg ml(-1) but it was not genotoxic at or below 50 microg ml(-1). In this work 2-CPY aqueous solutions were treated by means of UV irradiation at 254 nm. 2-CPY mineralisation history under different conditions is shown. 2-CPY was found to mineralise completely upon prolonged irradiation. Identified products of 2-CPY photolytic decomposition are presented. Solution genotoxicity was tested as a function of treatment time. Aqueous solution samples, taken at different photo-treatment times were tested in cultured human lymphocytes applying the cytokinesis block micronucleus (CBMN) assay. It was found that the solution was genotoxic even when 2-CPY had been practically removed. This shows that photo-treatment of 2-CPY produces genotoxic products. Upon prolonged irradiation solution genotoxicity values approached the control value. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  20. Study of accurate volume measurement system for plutonium nitrate solution

    Energy Technology Data Exchange (ETDEWEB)

    Hosoma, T. [Power Reactor and Nuclear Fuel Development Corp., Tokai, Ibaraki (Japan). Tokai Works

    1998-12-01

    It is important for effective safeguarding of nuclear materials to establish a technique for accurate volume measurement of plutonium nitrate solution in accountancy tank. The volume of the solution can be estimated by two differential pressures between three dip-tubes, in which the air is purged by an compressor. One of the differential pressure corresponds to the density of the solution, and another corresponds to the surface level of the solution in the tank. The measurement of the differential pressure contains many uncertain errors, such as precision of pressure transducer, fluctuation of back-pressure, generation of bubbles at the front of the dip-tubes, non-uniformity of temperature and density of the solution, pressure drop in the dip-tube, and so on. The various excess pressures at the volume measurement are discussed and corrected by a reasonable method. High precision-differential pressure measurement system is developed with a quartz oscillation type transducer which converts a differential pressure to a digital signal. The developed system is used for inspection by the government and IAEA. (M. Suetake)

  1. Spherical conformal models for compact stars

    Energy Technology Data Exchange (ETDEWEB)

    Takisa, P.M.; Maharaj, S.D.; Manjonjo, A.M.; Moopanar, S. [University of KwaZulu-Natal, Astrophysics and Cosmology Research Unit, School of Mathematics, Statistics and Computer Science, Durban (South Africa)

    2017-10-15

    We consider spherical exact models for compact stars with anisotropic pressures and a conformal symmetry. The conformal symmetry condition generates an integral relationship between the gravitational potentials. We solve this condition to find a new anisotropic solution to the Einstein field equations. We demonstrate that the exact solution produces a relativistic model of a compact star. The model generates stellar radii and masses consistent with PSR J1614-2230, Vela X1, PSR J1903+327 and Cen X-3. A detailed physical examination shows that the model is regular, well behaved and stable. The mass-radius limit and the surface red shift are consistent with observational constraints. (orig.)

  2. Esterification activity and conformation studies of Burkholderia cepacia lipase in conventional organic solvents, ionic liquids and their co-solvent mixture media.

    Science.gov (United States)

    Pan, Shaotao; Liu, Xue; Xie, Yadong; Yi, Yuyin; Li, Chong; Yan, Yunjun; Liu, Yun

    2010-12-01

    In this work, experiments were carried out to evaluate the esterification activity and conformation of lipase from Burkholderia cepacia in the selected conventional organic solvents, ionic liquids and their co-solvent mixture media. The results revealed that the activity of esterification of B. cepacia lipase was mostly highest in co-solvent mixture of ionic liquids-organic solvents, followed by conventional organic solvents and ionic liquids. Hence, co-solvent mixture was a high-effective strategy to enhance the activity of B. cepacia lipase for non-aqueous enzymology reaction. Conformational studies via circular dichroism spectroscopy indicated that the secondary structure of B. cepacia lipase was variant in the above-mentioned media, especially the content of alpha-helix, which was probably responsible for lipase activity difference. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  3. First clinical experience with polysol solution: pilot study in living kidney transplantation

    NARCIS (Netherlands)

    Schreinemachers, M.-C. J. M.; Bemelman, F. J.; Idu, M. M.; van Donselaar-van der Pant, K. A. M. I.; van de Berg, P. J. E. J.; Reitsma, J. B.; Legemate, D. A.; Florquin, S.; ten Berge, I. J. M.; Doorschodt, B. M.; van Gulik, T. M.

    2013-01-01

    In this study, we assessed the safety of the new organ preservation solution polysol solution in the clinical setting of living kidney transplantation. We conducted a prospective pilot study in nine adult donor-recipient couples using polysol solution for washout and cold storage of kidney grafts.

  4. Spectroscopic study on the stability of morin in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Bark, Ki Min [Dept. of Chemical Education and Research Institute of Life Science, Gyeongsang National University, Chinju (Korea, Republic of); Im, Seo Eun; Seo, Jung Ja; Park, Ok Hyun; Park, Hyoung Ryun [Dept. of Chemistry, Chonnam National University, Gwangju (Korea, Republic of); Park, Chul Ho [Dept. of Cosmetic Science, Nambu University, Gwangju (Korea, Republic of)

    2015-02-15

    Morin (3,2,4,5,7-pentahydroxyflavone) is a flavonol conjugated to a resorcinol moiety at the C-2 position, different from many other flavonoids. The UV–vis spectrum of morin in neat water reveals two major absorption bands with maxima at 265 and 387 nm. The substance is stable in acidic solution and neat water. However, its absorption maximum at 387 nm continuously shifts to longer wavelengths and new peaks appeared at wavelengths of 312 nm with increasing pH of the solution. The shape of the absorption spectrum of morin depends on the storage time at a given pH, indicating the occurrence of other successive chemical reactions. The fluorescence spectroscopic results also prove that new conjugated double bonds are formed in the deaerated basic solution at the initial state and decompose with time. This behavior indicates that morin is very unstable, and therefore its decomposition occurs by a sequence of multistep reactions in basic solution. Probable reaction pathways for the reaction are suggested based on the spectroscopic results.

  5. Physicochemical studies on ion-pair amphiphiles: Solution and ...

    Indian Academy of Sciences (India)

    Administrator

    cation potentials in the field of membrane mimick- ing systems, drug delivery, nanoparticle synthesis, etc. 4–10 ... The phase diagrams consist- ing of a micellar solution phase, and a liquid crystal- line phase (at higher ... madzu, Japan) using a matched pair of quartz cells of path length 1cm. The ion-pairs produced appre-.

  6. Light scattering studies on solutions containing calcium phosphates

    NARCIS (Netherlands)

    Feenstra, T.P.; Bruyn, P.L. de

    A number of light scattering experiments was performed on calcium and phosphate containing solutions at pH 8.33 and 26°C. Supplementary information was obtained by means of dynamic light scattering, scanning electron microscopy, and transmission electron microscopy. The measurements prove that

  7. Salt Effect on Osmotic Pressure of Polyelectrolyte Solutions: Simulation Study

    Directory of Open Access Journals (Sweden)

    Jan-Michael Y. Carrillo

    2014-07-01

    Full Text Available Abstract: We present results of the hybrid Monte Carlo/molecular dynamics simulations of the osmotic pressure of salt solutions of polyelectrolytes. In our simulations, we used a coarse-grained representation of polyelectrolyte chains, counterions and salt ions. During simulation runs, we alternate Monte Carlo and molecular dynamics simulation steps. Monte Carlo steps were used to perform small ion exchange between simulation box containing salt ions (salt reservoir and simulation box with polyelectrolyte chains, counterions and salt ions (polyelectrolyte solution. This allowed us to model Donnan equilibrium and partitioning of salt and counterions across membrane impermeable to polyelectrolyte chains. Our simulations have shown that the main contribution to the system osmotic pressure is due to salt ions and osmotically active counterions. The fraction of the condensed (osmotically inactive counterions first increases with decreases in the solution ionic strength then it saturates. The reduced value of the system osmotic coefficient is a universal function of the ratio of the concentration of osmotically active counterions and salt concentration in salt reservoir. Simulation results are in a very good agreement with osmotic pressure measurements in sodium polystyrene sulfonate, DNA, polyacrylic acid, sodium polyanetholesulfonic acid, polyvinylbenzoic acid, and polydiallyldimethylammonium chloride solutions.

  8. Kinetic Studies of Reactions in Solution Using Fast Mass Spectrometry

    Science.gov (United States)

    2013-08-13

    fuel source. Many hypergols are toxic, corrosive , and/or volatile such that they are difficult to handle and harmful to the environment. Dicyanamide... electrochemistry and the mass spectrometry analysis of the solutions in which an electrocatalyst is present. NN NN ee meetthyll vviioolloogeenn (93

  9. Mass decomposition of SLACS lens galaxies in Weyl conformal gravity

    CERN Document Server

    Potapov, Alexander A; Nandi, Kamal K

    2016-01-01

    We study here, using the Mannheim-Kazanas solution of Weyl conformal theory, the mass decomposition in the representative subsample of $57$ early-type elliptical lens galaxies of the SLACS on board the HST. We begin by showing that the solution need not be an exclusive solution of conformal gravity but can also be viewed as a solution of a class of $f(R)$ gravity theories coupled to non-linear electrodynamics thereby rendering the ensuing results more universal. Since lensing involves light bending, we shall first show that the solution adds to Schwarzschild light bending caused by the luminous mass ($M_{\\ast }$) a positive contribution $+\\gamma R$ contrary to the previous results in the literature, thereby resolving a long standing problem. The cause of the error is critically examined. Applying the expressions for light bending together with an input equating Einstein and Weyl angles, we develop a novel algorithm for separating the luminous component from the total lens mass (luminous+dark) within the Einst...

  10. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Trandum, Christa; Larsen, Nanna Brink

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (Tm) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal alpha-helix was of major importance to the conformational stability of calreticulin....

  11. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C.S.; Trandum, C.; Larsen, N.

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

  12. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...... procedure. Both are only partly solved problems. Here, we focus on the problem of conformational sampling. The current state of the art solution is based on fragment assembly methods, which construct plausible conformations by stringing together short fragments obtained from experimental structures. However...... efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D...

  13. NMR in natural products: understanding conformation, configuration and receptor interactions.

    Science.gov (United States)

    Carlomagno, Teresa

    2012-05-01

    Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of

  14. Accounting for conformational flexibility and torsional anharmonicity in the H + CH3CH2OH hydrogen abstraction reactions: a multi-path variational transition state theory study.

    Science.gov (United States)

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio

    2014-05-07

    This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel.

  15. Multiple receptor conformation docking, dock pose clustering and 3D QSAR studies on human poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors.

    Science.gov (United States)

    Fatima, Sabiha; Jatavath, Mohan Babu; Bathini, Raju; Sivan, Sree Kanth; Manga, Vijjulatha

    2014-10-01

    Poly(ADP-ribose) polymerase-1 (PARP-1) functions as a DNA damage sensor and signaling molecule. It plays a vital role in the repair of DNA strand breaks induced by radiation and chemotherapeutic drugs; inhibitors of this enzyme have the potential to improve cancer chemotherapy or radiotherapy. Three-dimensional quantitative structure activity relationship (3D QSAR) models were developed using comparative molecular field analysis, comparative molecular similarity indices analysis and docking studies. A set of 88 molecules were docked into the active site of six X-ray crystal structures of poly(ADP-ribose)polymerase-1 (PARP-1), by a procedure called multiple receptor conformation docking (MRCD), in order to improve the 3D QSAR models through the analysis of binding conformations. The docked poses were clustered to obtain the best receptor binding conformation. These dock poses from clustering were used for 3D QSAR analysis. Based on MRCD and QSAR information, some key features have been identified that explain the observed variance in the activity. Two receptor-based QSAR models were generated; these models showed good internal and external statistical reliability that is evident from the [Formula: see text], [Formula: see text] and [Formula: see text]. The identified key features enabled us to design new PARP-1 inhibitors.

  16. The generalized block-localized wavefunction method: A case study on the conformational preference and C-O rotational barrier of formic acid

    Science.gov (United States)

    Jia, Jian-Feng; Wu, Hai-Shun; Mo, Yirong

    2012-04-01

    A Lewis structure corresponding to the most stable electron-localized state is often used as a reference for the measure of electron delocalization effect in the valence bond (VB) theory. As the simplest variant of ab initio VB theory, the generalized block-localized wavefunction (BLW) method defines the wavefunction for an electron-localized state with block-localized orbitals without the orthogonalization constraint on different blocks. The validity of the method can be critically examined with experimental evidences. Here the BLW method has been applied to the investigation of the roles of both the π conjugation and σ hyperconjugation effects in the conformational preference of formic acid for the trans (Z) conformer over the cis (E) conformer. On one hand, our computations showed that the deactivation of the π conjugation or σ hyperconjugation has little impact on the Z-E energy gap, thus neither is decisive and instead the local dipole-dipole electrostatic interaction between the carbonyl and hydroxyl groups is the key factor determining the Z-E energy gap. On the other hand, the present study supported the conventional view that π conjugation is largely responsible for the C-O rotation barrier in formic acid, though the existence of hyperconjugative interactions in the perpendicular structure lowers the barrier considerably.

  17. Theory and applications of the transferred nuclear overhauser effect to the study of the conformations of small ligands bound to proteins

    Science.gov (United States)

    Clore, G. M.; Gronenborn, A. M.

    The principles, theory, and applications of the transferred proton-proton nuclear Overhauser effect (TRNOE) to the study of the conformations of small molecules to proteins are presented and discussed. The basis of the TRNOE involves the transfer of information concerning cross relaxation between two bound ligand nuclei from the bound to the free state by chemical exchange so that negative NOEs on the easily detectable free or observed ligand resonances may be seen following irradiation of other ligand resonances (free, bound, or observed), thus conveying information on the proximity in space of bound ligand nuclei. In the presence of protein, a negative TRNOE on either the free or observed resonance of nucleus i will be observed following irradiation of either the free, bound, or observed resonance of nucleus j, providing several conditions are met. Methods for obtaining quantitative conformational information from TRNOE measurements are discussed. The TRNOE method is applicable even when no individual proton resonances of either the protein or the bound ligand can be resolved, and is not limited by the molecular weight of the protein, extending the molecular weight range over which 1H NMR can provide useful conformational information to the very largest systems. This is illustrated by the determination of the glycosidic bond torsion angle of adenosine 5'-monophosphate bound to horse liver alcohol dehydrogenase, yeast alcohol dehydrogenase, and bovine liver glutamate dehydrogenase.

  18. A study on gender non-conforming subjects in current society : Self-perception of body and identity

    OpenAIRE

    Martínez, Ariel

    2015-01-01

    This article presents the results of a research to be included in a PhD Thesis on Gender nonconformity. Behind the results there is bibliographic research and fieldwork with 11 subjects over18 years-old from La Plata and La Plata metropolitan area. The theoretical framework doesn’t look into the specific realities of gender non-conforming subjects. I attempted to explore the subjects’ narrations on themselves and their self-perception with a quantitative view. From a diversity standing point,...

  19. The Area Between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies

    Science.gov (United States)

    Mazur, Sharlyn J.; Weber, Daniel P.

    2017-05-01

    Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, A bec , a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, A bec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding.

  20. Characterization of Skeletonema costatum Intracellular Organic Matter and Study of Nanomechanical Properties under Different Solution Conditions

    KAUST Repository

    Gutierrez, Leonardo

    2016-06-17

    In the current investigation, a rigorous characterization of the high molecular weight (HMW) compounds of Skeletonema costatum (SKC) intracellular organic matter (IOM), including nanomechanical properties, was conducted. HMW SKC-IOM was characterized as a mixture of polysaccharides, proteins, and lipids. Atomic force microscopy (AFM) provided crucial information of this isolate at a nanoscale resolution. HMW SKC-IOM showed highly responsive to solution chemistry: fully extended chains at low ionic strength, and compressing structures with increasing electrolyte concentration in solution. Interestingly, two regions of different nanomechanical properties were observed: (a) Region #1: located farther from the substrate and showing extended polymeric chains, and (b) Region #2: located <10 nm above the substrate and presenting compressed structures. The polymer length, polymer grafting density, and compressibility of these two regions were highly influenced by solution conditions. Results suggest that steric interactions originating from HMW SKC-IOM polymeric structure would be a dominant interacting mechanism with surfaces. The current investigation has successfully applied models of polymer physics to describe the complex HMW SKC-IOM structural conformation at different solution conditions. The detailed methodology presented provides a tool to characterize and understand biopolymers interactions with surfaces, including filtration membranes, and can be extended to other environmentally relevant organic compounds.

  1. Exceptional and Spinorial Conformal Windows

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Ryttov, Thomas

    2012-01-01

    We study the conformal window of gauge theories containing fermionic matter fields, where the gauge group is any of the exceptional groups with the fermions transforming according to the fundamental and adjoint representations and the orthogonal groups where the fermions transform according...

  2. On the Study of Global Solutions for a Nonlinear Equation

    Directory of Open Access Journals (Sweden)

    Haibo Yan

    2014-01-01

    Full Text Available The well-posedness of global strong solutions for a nonlinear partial differential equation including the Novikov equation is established provided that its initial value v0(x satisfies a sign condition and v0(x∈Hs(R with s>3/2. If the initial value v0(x∈Hs(R  (1≤s≤3/2 and the mean function of (1-∂x2v0(x satisfies the sign condition, it is proved that there exists at least one global weak solution to the equation in the space v(t,x∈L2([0,+∞,Hs(R in the sense of distribution and vx∈L∞([0,+∞×R.

  3. Microrheology of viscoelastic solutions studied by magnetic rotational spectroscopy

    CERN Document Server

    Berret, Jean-François

    2016-01-01

    Magnetic rotational spectroscopy is based on the use of magnetic micron-size wires for viscosity measurements. Submitted to a rotational magnetic field with increasing frequency, the wires undergo a hydrodynamic instability between a synchronous and an asynchronous regime. From a comparison between predictions and experiments, the static shear viscosity and elastic modulus of wormlike micellar solutions are here determined. The values agree with the determination by cone-and-plate rheometry.

  4. Dynamic nuclear-polarization studies of paramagnetic species in solution

    Energy Technology Data Exchange (ETDEWEB)

    Glad, W.E.

    1982-07-01

    Dynamic Nuclear Polarization (DNP) was used to measure the electron spin lattice relaxation times, T/sub 1/, of transition metal ions in aqueous solution. Saturation which is induced in the electron spin system is transferred to the solvent proton spins by dipole-dipole interactions. The change in the polarization of the proton spins is much larger than it is in the electron spins. The change in proton polarization is easily measured by proton Nuclear Magnetic Resonance (NMR). In one experimental arrangement the sample solution was continuously flowed through a microwave cavity to the NMR coil. The NMR was observed with a continuous wave NMR spectrometer. In a second arrangement the whole sample tube was moved from within the microwave cavity to the NMR coil in less than 40 ms by a blast of compressed air. The NMR was then observed with a pulse-Fourier-transform spectrometer. With the second arrangement a mean-square microwave magnetic field at the sample of more than 10 G/sup 2/ is obtainable with 14 W of microwave power. Measurements of DNP at 9 GHz were made on aqueous solutions of VO/sup 2 +/, Mn/sup 2 +/, Cr(CN)/sub 6//sup 3 -/, Cu/sup 2 +/ and Cu(ethylenediamine)/sub 2/(H/sub 2/0)/sub 2//sup 2 +/ ions from 3 to 60/sup 0/C. It was also possible to observe DNP on resolved proton resonances from mixed water-acetonitrile solutions of VO/sup 2 +/ and Cr(CN)/sub 6//sup 3 -/ ions.

  5. Viscometric study of high-cis polybutadiene in toluene solution

    OpenAIRE

    Mello,Ivana L.; Delpech,Marcia C.; Coutinho,Fernanda M. B.; Albino,Fernanda F. M.

    2006-01-01

    Viscometric measurements, in toluene solution at 30 ºC, were performed with high-cis polybutadiene synthesized by neodymium based catalyst. Six different equations were used to calculate intrinsic viscosities and viscosimetric constant values: Huggins, Kraemer, Martin and Schulz-Blaschke by graphic extrapolation, and Solomon-Ciuta, Deb-Chanterjee and again Schulz-Blaschke, through a single point determination. The molecular weight of the polymers was also determined applying Mark-Houwink-Saku...

  6. Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain.

    Directory of Open Access Journals (Sweden)

    Chao-Yie Yang

    Full Text Available Suppression of Tumorigenicity 2 (ST2, a member of the interleukin-1 receptor (IL-1R family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2ECD models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2ECD (containing D1-D3 domains in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2ECD contributes predominantly to the interaction between ST2ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2ECD and modulation sites conformed to ST2ECD conformations. Our study provides structural models and analyses of ST2ECD that could be useful for inhibitor discovery.

  7. Epigenetic dominance of prion conformers.

    Directory of Open Access Journals (Sweden)

    Eri Saijo

    2013-10-01

    Full Text Available Although they share certain biological properties with nucleic acid based infectious agents, prions, the causative agents of invariably fatal, transmissible neurodegenerative disorders such as bovine spongiform encephalopathy, sheep scrapie, and human Creutzfeldt Jakob disease, propagate by conformational templating of host encoded proteins. Once thought to be unique to these diseases, this mechanism is now recognized as a ubiquitous means of information transfer in biological systems, including other protein misfolding disorders such as those causing Alzheimer's and Parkinson's diseases. To address the poorly understood mechanism by which host prion protein (PrP primary structures interact with distinct prion conformations to influence pathogenesis, we produced transgenic (Tg mice expressing different sheep scrapie susceptibility alleles, varying only at a single amino acid at PrP residue 136. Tg mice expressing ovine PrP with alanine (A at (OvPrP-A136 infected with SSBP/1 scrapie prions propagated a relatively stable (S prion conformation, which accumulated as punctate aggregates in the brain, and produced prolonged incubation times. In contrast, Tg mice expressing OvPrP with valine (V at 136 (OvPrP-V136 infected with the same prions developed disease rapidly, and the converted prion was comprised of an unstable (U, diffusely distributed conformer. Infected Tg mice co-expressing both alleles manifested properties consistent with the U conformer, suggesting a dominant effect resulting from exclusive conversion of OvPrP-V136 but not OvPrP-A136. Surprisingly, however, studies with monoclonal antibody (mAb PRC5, which discriminates OvPrP-A136 from OvPrP-V136, revealed substantial conversion of OvPrP-A136. Moreover, the resulting OvPrP-A136 prion acquired the characteristics of the U conformer. These results, substantiated by in vitro analyses, indicated that co-expression of OvPrP-V136 altered the conversion potential of OvPrP-A136 from the S to

  8. Crises Solutions for SMEs Case Study: ERP Cloud vs Classic Solution

    OpenAIRE

    Gheorghe, Gabriela; Ioana LUPASC

    2012-01-01

    Information Technology has responded to the crisis by change and innovation. The phenomenon of cloud computing represents a huge chance for a country like Romania, as a technologically low economy has, from the start, a handicap. Cloud technologies redefine concepts such as saving time and money, flexibility, scalability and global access, transforming them into business advantages. This case study wishes to argument the software provider’s decision to change his strategy, choosing an “all in...

  9. Conformity to Peer Pressure in Preschool Children

    Science.gov (United States)

    Haun, Daniel B. M.; Tomasello, Michael

    2011-01-01

    Both adults and adolescents often conform their behavior and opinions to peer groups, even when they themselves know better. The current study investigated this phenomenon in 24 groups of 4 children between 4;2 and 4;9 years of age. Children often made their judgments conform to those of 3 peers, who had made obviously erroneous but unanimous…

  10. Studies on the Solute Solvent Interaction of Nimesulide in Aqueous Solutions of Hydrotropic Agents at Different Temperatures

    Directory of Open Access Journals (Sweden)

    Chandravir S. Solanki

    2010-01-01

    Full Text Available The present study deals with experiments so as to highlight the solute (drug nimesulide - solvent(water interactions and related modifications in case of the presence of hydrotropic agents at different temperatures T(=298.15 to 313.15K. Density and viscosity values of nimesulide have been determined in water in (0.1, 0.2, 0.4, 0.6, 0.8, 1 and 2 mol dm-3 aqueous solutions of hydrotropic agents (sodium benzoate, sodium salicylate, sodium bromide and nicotinamide at temperatures 298.15, 303.15, 308.15 and 313.15 K where as the solubility was studied at 308.15 K. From the density values, the limiting partial molar volumes and expansibilities have been calculated. The experimental viscosity values have been analyzed in terms of jones-dole equation and on the basis of transition theory for relative viscosity.

  11. Defects in conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Billò, Marco [Dipartimento di Fisica, Università di Torino, and Istituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Gonçalves, Vasco [Centro de Física do Porto,Departamento de Física e Astronomia Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); ICTP South American Institute for Fundamental Research Instituto de Física Teórica,UNESP - University Estadual Paulista,Rua Dr. Bento T. Ferraz 271, 01140-070, São Paulo, SP (Brazil); Lauria, Edoardo [Institute for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Meineri, Marco [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada); Scuola Normale Superiore, and Istituto Nazionale di Fisica Nucleare - sezione di Pisa,Piazza dei Cavalieri 7 I-56126 Pisa (Italy)

    2016-04-15

    We discuss consequences of the breaking of conformal symmetry by a flat or spherical extended operator. We adapt the embedding formalism to the study of correlation functions of symmetric traceless tensors in the presence of the defect. Two-point functions of a bulk and a defect primary are fixed by conformal invariance up to a set of OPE coefficients, and we identify the allowed tensor structures. A correlator of two bulk primaries depends on two cross-ratios, and we study its conformal block decomposition in the case of external scalars. The Casimir equation in the defect channel reduces to a hypergeometric equation, while the bulk channel blocks are recursively determined in the light-cone limit. In the special case of a defect of codimension two, we map the Casimir equation in the bulk channel to the one of a four-point function without defect. Finally, we analyze the contact terms of the stress-tensor with the extended operator, and we deduce constraints on the CFT data. In two dimensions, we relate the displacement operator, which appears among the contact terms, to the reflection coefficient of a conformal interface, and we find unitarity bounds for the latter.

  12. Black Hole Monodromy and Conformal Field Theory

    NARCIS (Netherlands)

    Castro, A.; Lapan, J.M.; Maloney, A.; Rodriguez, M.J.

    2013-01-01

    The analytic structure of solutions to the Klein-Gordon equation in a black hole background, as represented by monodromy data, is intimately related to black hole thermodynamics. It encodes the "hidden conformal symmetry" of a nonextremal black hole, and it explains why features of the inner event

  13. Attraction and Repulsion in Conformal Gravity

    CERN Document Server

    Phillips, Peter R

    2015-01-01

    We use numerical integration to solve the field equations of conformal gravity, assuming a metric that is static and spherically symmetric. Our solution is an extension of that found by Mannheim and Kazanas; it indicates, as expected, that gravitation in this model should be attractive on small scales and repulsive on large ones.

  14. Conformable Pressurized Structures : Design and Analysis

    NARCIS (Netherlands)

    Geuskens, F.J.J.M.M.

    2012-01-01

    There are many applications where volume needs to be pressurised within a geometrical space for which conventional pressure vessels do not provide suitable solutions. Applications are for example found in pressure cabins for Blended Wing Body Aircraft and conformable pressure vessels for an

  15. Ceramic Ultrafiltration of Marine Algal Solutions: A Comprehensive Study

    KAUST Repository

    Dramas, Laure

    2014-09-01

    Algal bloom can significantly impact reverse osmosis desalination process and reduce the drinking water production. In 2008, a major bloom event forced several UAE reverse osmosis plants to stop their production, and in this context, a better understanding of UF membrane fouling caused by algal organic matter (AOM) is needed, in order to adjust the filtration conditions during algal bloom events. Polymeric MF/UF membranes are already widely used for RO pretreatment, but ceramic UF membranes can also be an alternative for the filtration of marine algal solutions. The fouling potential of the Red Sea and the Arabian Sea, sampled at different seasons, along with four algal monocultures grown in laboratory, and one mesocosm experiment in the Red Sea was investigated. Algal solutions induce a stronger and more irreversible fouling than terrestrial humic solution, toward ceramic membrane. During algal bloom events, this fouling is enhanced and becomes even more problematic at the decline phase of the bloom, for a similar initial DOC. Three main mechanisms are involved: the formation of a cake layer at the membrane surface; the penetration of the algal organic matter (AOM) in the pore network of the membrane; the strong adhesion of AOM with the membrane surface. The last mechanism is species-specific and metal-oxide specific. In order to understand the stronger ceramic UF fouling at the decline phase, AOM quality was analyzed every two days. During growth, AOM is getting enriched in High Molecular Weight (HMW) structures (> 200 kDa), which are mainly composed by proteins and polysaccharides, and these compounds seem to be responsible for the stronger fouling at decline phase. In order to prevent the fouling of ceramic membrane, coagulation-flocculation (CF) using ferric chloride was implemented prior to filtration. It permits a high removal of HMW compounds and greatly reduces the fouling potential of the algal solution. During brief algal bloom events, CF should be

  16. Experimental Study of the Interaction between Vortices in Electrolytic Solutions

    Science.gov (United States)

    Izaguirre, E. W.

    1996-11-01

    The interaction between vortices and their structure are analyzed in a system of three vortices in electrolytic solutions using crosed electric and magnetic fields in a square tray. The flow pattern and the speed field are obtained using image techniques and anemometry. The experiment is repeated for different strengths of the magnetic and electric fields, and thickness of the fluid layer. Self oscillations, coupling and competition between vortices are observed. A model of the system is presented and numerical results contrasted with the experimental data.

  17. Carbon Market and Integrated Waste Solutions : a Case Study of ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Marché du carbone et solutions de gestion intégrée des déchets : étude de cas menée en Indonésie. Le Mécanisme de développement propre (MDP) prévu au Protocole de Kyoto signé en 1997 a le double objectif d'aider les pays en développement à connaître un développement durable (tel que défini.

  18. Efficient Solutions for New Homes Case Study: Savannah Gardens

    Energy Technology Data Exchange (ETDEWEB)

    None

    2016-03-15

    The Savannah Housing Department is leading sustainable and affordable housing development in Georgia. It partnered with Southface Energy Institute, a member of the U.S. Department of Energy’s Partnership for Home Innovation Building America research team, to seek cost-effective solutions for increasing the energy efficiency of the Savannah Housing Department’s standard single-family home plans in the Savannah Gardens Community. Based on engineering, cost, and constructability analyses, the combined research team chose to pilot two technologies to evaluate efficiency and comfort impacts for homeowners: a heat-pump water heater in an encapsulated attic and an insulated exterior wall sheathing.

  19. Conformal Dynamics of Precursors to Fracture

    OpenAIRE

    Barra, Felipe; Herrera, Mauricio; Procaccia, Itamar

    2002-01-01

    An exact integro-differential equation for the conformal map from the unit circle to the boundary of an evolving cavity in a stressed 2-dimensional solid is derived. This equation provides an accurate description of the dynamics of precursors to fracture when surface diffusion is important. The solution predicts the creation of sharp grooves that eventually lead to material failure via rapid fracture. Solutions of the new equation are demonstrated for the dynamics of an elliptical cavity and ...

  20. Gamma Radiolysis Studies of Aqueous Solution of Brilliant Green Dye

    Directory of Open Access Journals (Sweden)

    D. V. Parwate

    2011-01-01

    Full Text Available The effect of γ–radiation on colour intensity of aqueous solution of Brilliant Green has been investigated at two different concentrations. The degradation of Brilliant Green (BG has also been investigated in presence of suspended ZnO, by adding different amounts of ZnO. Simultaneously the conductance and pH of each solution system were measured before and after γ-irradiation. All the γ–irradiations were performed at a dose rate of 0.60 kGyhr-1 in GC-900. The maximum dose required for the complete degradation of the dye was found to be 0.39 kGy. G(-dye values were found to decrease with increase in gamma dose and were in the range 4.26 - 12.81. The conductance (7.6 - 25.3 μS and pH values increased marginally with dose for both the concentrations. The rate of decolouration was found to be high at lower doses and the efficiency of dye removal was higher at low concentration of the dye. This may be attributed to the presence of reaction by-products from the destruction of parent compound build up and compete for reaction intermediate species. The rate of reaction and rate constants were calculated and it was found that the degradation reaction follows first order kinetics. It was found that the decolouration percentage was more in dye systems in absence of ZnO.

  1. Thermodynamics of star polymer solutions: A coarse-grained study

    Science.gov (United States)

    Menichetti, Roberto; Pelissetto, Andrea; Randisi, Ferdinando

    2017-06-01

    We consider a coarse-grained (CG) model with pairwise interactions, suitable to describe low-density solutions of star-branched polymers of functionality f. Each macromolecule is represented by a CG molecule with (f + 1) interaction sites, which captures the star topology. Potentials are obtained by requiring the CG model to reproduce a set of distribution functions computed in the microscopic model in the zero-density limit. Explicit results are given for f = 6, 12, and 40. We use the CG model to compute the osmotic equation of state of the solution for concentrations c such that Φp=c /c*≲1 , where c* is the overlap concentration. We also investigate in detail the phase diagram for f = 40, identifying the boundaries of the solid intermediate phase. Finally, we investigate how the polymer size changes with c. For Φp≲0.3 , polymers become harder as f increases at fixed reduced concentration c /c*. On the other hand, for Φp≳0.3 , polymers show the opposite behavior: At fixed Φp, the larger the value of f, the larger their size reduction is.

  2. LED Street Lighting Solutions: Flagstaff, Arizona as a Case Study

    Science.gov (United States)

    Hall, Jeffrey C.

    2018-01-01

    Dark-sky protection in Flagstaff, Arizona extends back to 1958, with the first ordinance in the City banning advertising floodlights. The current ordinance, adopted in 1989, is comprehensive and has played a critical role in maintaining the quality of the night sky for astronomy, tourism, public enjoyment, and other purposes. Flagstaff, like many communities around the world, is now working on a transition from legacy bulb-based technology to LED for its outdoor lighting. The City, Lowell Observatory, the U. S. Naval Observatory, and the Flagstaff Dark Skies Coalition have been working intensively for two years to identify an LED-based street lighting solution that will preserve the City's dark skies while meeting municipal needs. We will soon be installing test fixtures for an innovative solution incorporating narrow-band amber LED and modest amounts of low-CCT white LED. In this talk, I will review the types of LEDs available for outdoor lighting and discuss the plans for Flagstaff's street lighting in the LED era, which we hope will be a model for communities worldwide.

  3. Development of non-metallic and conformal dual band meta-skin and its absorption study for microwave applications

    Science.gov (United States)

    Borah, Dipangkar; Bhattacharyya, Nidhi S.

    2017-08-01

    An efficient approach for achieving a dual, conformal and non-metallic metamaterial absorber for microwave applications is proposed in this paper. The unit cell structures are simple circular ring resonators, made up of non-metallic and conducting expanded graphite, fabricated on a linear low density polyethylene substrate. The expanded graphite is synthesized, characterized and processed to be used as a conducting layer. The materials properties of linear low density polyethylene is investigated and found to be a promising candidate for flexible microwave applications. The developed absorber showed more than 90% absorption at 7.72 GHz and 9.92 GHz. Electric and magnetic fields are also simulated at the resonating frequency to understand the absorption mechanism. The proposed expanded graphite based metamaterial absorber possesses the advantages of being ultra-thin, flexible and non-corrosive.

  4. A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Gale, J.D.; Lassen, Peter Rygaard

    2008-01-01

    In this work we present the experimental and theoretical vibrational absorption (VA) and the theoretical vibrational circular dichroism (VCD) spectra for aframodial. In addition, we present the theoretical VA and VCD spectra for the diasteriomers of aframodial. Aframodial has four chiral centers...... in the molecule, since one has two contributions; one due to the inherent chirality at the four chiral centers, and one due to the chirality of the side chain groups in specific conformers, that is, its helicity. Theoretical simulations for various levels of theory are compared to the experimental VA recorded...... of this molecule, even though the chiral part of the molecule is very rigid and has four chiral centers. In addition to VCD and Raman measurements, Raman optical activity (ROA) measurements would be very enlightening, as in many cases bands which are weak in both the VA and VCD, may be large in the Raman and...

  5. How ionic strength affects the conformational behavior of human and rat beta amyloids--a computational study.

    Directory of Open Access Journals (Sweden)

    Zdeněk Kříž

    Full Text Available Progressive cerebral deposition of amyloid beta occurs in Alzheimers disease and during the aging of certain mammals (human, monkey, dog, bear, cow, cat but not others (rat, mouse. It is possibly due to different amino acid sequences at positions 5, 10 and 13. To address this issue, we performed series of 100 ns long trajectories (each trajectory was run twice with different initial velocity distribution on amyloid beta (1-42 with the human and rat amino acid sequence in three different environments: water with only counter ions, water with NaCl at a concentration of 0.15 M as a model of intracellular Na(+ concentration at steady state, and water with NaCl at a concentration of 0.30 M as a model of intracellular Na(+ concentration under stimulated conditions. We analyzed secondary structure stability, internal hydrogen bonds, and residual fluctuation. It was observed that the change in ionic strength affects the stability of internal hydrogen bonds. Increasing the ionic strength increases atomic fluctuation in the hydrophobic core of the human amyloid, and decreases the atomic fluctuation in the case of rat amyloid. The secondary structure analyses show a stable α-helix part between residues 10 and 20. However, C-terminus of investigated amyloids is much more flexible showing no stable secondary structure elements. Increasing ionic strength of the solvent leads to decreasing stability of the secondary structural elements. The difference in conformational behavior of the three amino acids at position 5, 10 and 13 for human and rat amyloids significantly changes the conformational behavior of the whole peptide.

  6. Conformal expansions and renormalons

    CERN Document Server

    Gardi, E; Gardi, Einan; Grunberg, Georges

    2001-01-01

    The large-order behaviour of QCD is dominated by renormalons. On the other hand renormalons do not occur in conformal theories, such as the one describing the infrared fixed-point of QCD at small beta_0 (the Banks--Zaks limit). Since the fixed-point has a perturbative realization, all-order perturbative relations exist between the conformal coefficients, which are renormalon-free, and the standard perturbative coefficients, which contain renormalons. Therefore, an explicit cancellation of renormalons should occur in these relations. The absence of renormalons in the conformal limit can thus be seen as a constraint on the structure of the QCD perturbative expansion. We show that the conformal constraint is non-trivial: a generic model for the large-order behaviour violates it. We also analyse a specific example, based on a renormalon-type integral over the two-loop running-coupling, where the required cancellation does occur.

  7. First clinical experience with polysol solution: pilot study in living kidney transplantation.

    Science.gov (United States)

    Schreinemachers, M-C J M; Bemelman, F J; Idu, M M; van Donselaar-van der Pant, K A M I; van de Berg, P J E J; Reitsma, J B; Legemate, D A; Florquin, S; ten Berge, I J M; Doorschodt, B M; van Gulik, T M

    2013-01-01

    In this study, we assessed the safety of the new organ preservation solution polysol solution in the clinical setting of living kidney transplantation. We conducted a prospective pilot study in nine adult donor-recipient couples using polysol solution for washout and cold storage of kidney grafts. Adverse reactions possibly related to the use of polysol solution as well as renal function at 1, 6, and 12 months after transplantation were monitored. All living kidney transplantation performed in adults in our center within 2002 to 2008 using the University of Winconsin solution served as controls (n = 190). The use of polysol solution was associated with a higher acute rejection rate compared to University of Wisconsin solution at all time points. Also, antibody-mediated rejection occurred more frequently in the polysol group. Renal function at all time points was also comparable between the groups. This pilot study in living kidney transplantation is the first clinical study on the use of polysol solution. Although the study was not powered on the endpoint rejection, we observed a high number of acute rejection and antibody-mediated rejection episodes in recipients of polysol solution preserved grafts as compared to University of Wisconsin solution controls. As a consequence the study was terminated prematurely. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Quantum massive conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    Faria, F.F. [Universidade Estadual do Piaui, Centro de Ciencias da Natureza, Teresina, PI (Brazil)

    2016-04-15

    We first find the linear approximation of the second plus fourth order derivative massive conformal gravity action. Then we reduce the linearized action to separated second order derivative terms, which allows us to quantize the theory by using the standard first order canonical quantization method. It is shown that quantum massive conformal gravity is renormalizable but has ghost states. A possible decoupling of these ghost states at high energies is discussed. (orig.)

  9. Delineating the conformal window

    DEFF Research Database (Denmark)

    Frandsen, Mads Toudal; Pickup, Thomas; Teper, Michael

    2011-01-01

    We identify and characterise the conformal window in gauge theories relevant for beyond the standard model building, e.g. Technicolour, using the criteria of metric confinement and causal analytic couplings, which are known to be consistent with the phase diagram of supersymmetric QCD from Seiberg...... duality. Using these criteria we find perturbation theory to be consistent throughout the predicted conformal window for several of these gauge theories and we discuss recent lattice results in the light of our findings....

  10. Combined Spectroscopic and Calorimetric Studies to Reveal Absorption Mechanisms and Conformational Changes of Protein on Nanoporous Biomaterials

    Directory of Open Access Journals (Sweden)

    Saharnaz Ahmadi

    2015-07-01

    Full Text Available In this study the effect of surface modification of mesoporous silica nanoparticles (MSNs on its adsorption capacities and protein stability after immobilization of beta-lactoglobulin B (BLG-B was investigated. For this purpose, non-functionalized (KIT-6 and aminopropyl-functionalized cubic Ia3d mesoporous silica ([n-PrNH2-KIT-6] nanoparticles were used as nanoporous supports. Aminopropyl-functionalized mesoporous nanoparticles exhibited more potential candidates for BLG-B adsorption and minimum BLG leaching than non-functionalized nanoparticles. It was observed that the amount of adsorbed BLG is dependent on the initial BLG concentration for both KIT-6 and [n-PrNH2-KIT-6] mesoporous nanoparticles. Also larger amounts of BLG-B on KIT-6 was immobilized upon raising the temperature of the medium from 4 to 55 °C while such increase was undetectable in the case of immobilization of BLG-B on the [n-PrNH2-KIT-6]. At temperatures above 55 °C the amounts of adsorbed BLG on both studied nanomaterials decreased significantly. By Differential scanning calorimetry or DSC analysis the heterogeneity of the protein solution and increase in Tm may indicate that immobilization of BLG-B onto the modified KIT-6 results in higher thermal stability compared to unmodified one. The obtained results provide several crucial factors in determining the mechanism(s of protein adsorption and stability on the nanostructured solid supports and the development of engineered nano-biomaterials for controlled drug-delivery systems and biomimetic interfaces for the immobilization of living cells.

  11. LAPLACE EQUATIONS, CONFORMAL SUPERINTEGRABILITY AND BÔCHER CONTRACTIONS

    Directory of Open Access Journals (Sweden)

    Ernest G. Kalnins

    2016-06-01

    Full Text Available Quantum superintegrable systems are solvable eigenvalue problems. Their solvability is due to symmetry, but the symmetry is often ``hidden''.The symmetry generators of 2nd order superintegrable systems in 2 dimensions close under commutation to define quadratic algebras, a generalization of Lie algebras. Distinct systems and their algebras are related by geometric limits, induced by generalized Inönü-Wigner Lie algebra contractions of the symmetry algebras of the underlying spaces. These have physical/geometric implications, such as the Askey scheme for hypergeometric orthogonal polynomials. The systems can be best understood by transforming them to Laplace conformally superintegrable systems and using ideas introduced in the 1894 thesis of Bôcher to study separable solutions of the wave equation. The contractions can be subsumed into contractions of the conformal algebra  so(4,C to itself. Here we announce main findings, with detailed classifications in papers under preparation.

  12. Restricted amide rotation with steric hindrance induced multiple conformations

    Science.gov (United States)

    Krishnan, V. V.; Vazquez, Salvador; Maitra, Kalyani; Maitra, Santanu

    2017-12-01

    The Csbnd N bond character is dependent directly upon the resonance-contributor structure population driven by the delocalized nitrogen lone-pair of electrons. In the case of N, N-dibenzyl-ortho-toluamide (o-DBET), the molecule adopts subpopulations of conformers with distinct NMR spectral features, particularly at low temperatures. This conformational adaptation is unique to o-DBET, while the corresponding meta- and para- forms do not show such behavior. Variable-temperature (VT) NMR, two-dimensional exchange spectroscopy (EXSY), and qualitative molecular modeling studies are used to demonstrate how multiple competing interactions such as restricted amide rotation and steric hindrance effects can lead to versatile molecular adaptations in the solution state.

  13. Viscometric study of high-cis polybutadiene in toluene solution

    Energy Technology Data Exchange (ETDEWEB)

    Mwllo, Ivana L.; Coutinho, Fernanda M.B. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Macromoleculas Professora Eloisa Mano]. E-mail: fern@ima.ufrj.br; Delpech, Marcia C.; Albino, Fernanda F.M. [Universidade do Estado, Rio de Janeiro, RJ (Brazil). Inst. de Quimica

    2006-01-15

    Viscometric measurements, in toluene solution at 30 deg C, were performed with high-cis polybutadiene synthesized by neodymium based catalyst. Six different equations were used to calculate intrinsic viscosities and viscosimetric constant values: Huggins, Kraemer, Martin and Schulz-Blaschke by graphic extrapolation, and Solomon-Ciuta, Deb-Chanterjee and again Schulz- Blaschke, through a single point determination. The molecular weight of the polymers was also determined applying Mark-Houwink-Sakurada equation using the values of intrinsic viscosity obtained by the six equations. The values of intrinsic viscosity and viscosity-average molecular weight obtained by the two methods were compared in order to verify the validity of the single point determination for high-cis polybutadiene. (author)

  14. Viscometric study of high-cis polybutadiene in toluene solution

    Directory of Open Access Journals (Sweden)

    Mello Ivana L.

    2006-01-01

    Full Text Available Viscometric measurements, in toluene solution at 30 ºC, were performed with high-cis polybutadiene synthesized by neodymium based catalyst. Six different equations were used to calculate intrinsic viscosities and viscosimetric constant values: Huggins, Kraemer, Martin and Schulz-Blaschke by graphic extrapolation, and Solomon-Ciuta, Deb-Chanterjee and again Schulz-Blaschke, through a single point determination. The molecular weight of the polymers was also determined applying Mark-Houwink-Sakurada equation using the values of intrinsic viscosity obtained by the six equations. The values of intrinsic viscosity and viscosity-average molecular weight obtained by the two methods were compared in order to verify the validity of the single point determination for high-cis polybutadiene.

  15. Experimental study on thermophoresis of colloids in aqueous surfactant solutions

    Science.gov (United States)

    Dong, Ruo-Yu; Zhou, Yi; Yang, Chun; Cao, Bing-Yang

    2015-12-01

    Thermophoresis refers to the motion of particles under a temperature gradient and it is one of the particle manipulation techniques. Regarding the thermophoresis of particles in liquid media, however, many open questions still remain, especially the role of the interfacial effect. This work reports on a systematic experimental investigation of surfactant effects, especially the induced interfacial effect, on the thermophoresis of colloids in aqueous solutions via a microfluidic approach. Two kinds of commonly used surfactants, sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB), are selected and the results show that from relatively large concentrations, the two surfactants can greatly enhance the thermophilic mobilities. Specifically, it is found that the colloid-water interfaces modified with more polar end groups can potentially lead to a stronger thermophilic tendency. Due to the complex effects of surfactants, further theoretical model development is needed to quantitatively describe the dependence of thermophoresis on the interface characteristics.

  16. Pharmacophore Modelling and 4d-Qsar Study Of Ruthenium(Ii) Arene Complexes As Anticancer Agents (Inhibitors) By Electron Conformational-Genetic Algorithm Method.

    Science.gov (United States)

    Yavuz, Sevtap Çağlar; Sabancı, Nazmiye; Sarıpınar, Emin

    2017-05-28

    The EC-GA method was employed in this study as a 4D-QSAR method, for the identification of the pharmacophore (Pha) of ruthenium(II) arene complex derivatives and quantitative prediction of activity. The arrangement of the computed geometric and electronic parameters for atoms and bonds of each compound occurring in a matrix is known as the electron-conformational matrix of congruity (ECMC). It contains the data from HF/3-21G level calculations. Compounds were represented by a group of conformers for each compound rather than a single conformation, known as fourth dimension to generate the model. ECMCs were compared within a certain range of tolerance values by using the EMRE program and the responsible pharmacophore group for ruthenium(II) arene complex derivatives was found. For selecting the sub-parameter which had the most effect on activity in the series and the calculation of theoretical activity values, the non-linear least square method and genetic algorithm which are included in the EMRE program were used. In addition, compounds were classified as the training and test set and the accuracy of the models was tested by cross-validation statistically. The model for training and test sets attained by the optimum 10 parameters gave highly satisfactory results with R2training= 0.817, q 2=0.718 and SEtraining=0.066, q2ext1 = 0.867, q2ext2 = 0.849, q2ext3 =0.895, ccctr = 0.895, ccctest = 0.930 and cccall = 0.905. Since there is no 4D-QSAR research on metal based organic complexes in the literature, this study is original and supply a powerful tool to the design of novel and selective ruthenium(II) arene complexes. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. The research of conformal optical design

    Science.gov (United States)

    Li, Lin; Li, Yan; Huang, Yi-fan; Du, Bao-lin

    2009-07-01

    Conformal optical domes are characterized as having external more elongated optical surfaces that are optimized to minimize drag, increased missile velocity and extended operational range. The outer surface of the conformal domes typically deviate greatly from spherical surface descriptions, so the inherent asymmetry of conformal surfaces leads to variations in the aberration content presented to the optical sensor as it is gimbaled across the field of regard, which degrades the sensor's ability to properly image targets of interest and then undermine the overall system performance. Consequently, the aerodynamic advantages of conformal domes cannot be realized in practical systems unless the dynamic aberration correction techniques are developed to restore adequate optical imaging capabilities. Up to now, many optical correction solutions have been researched in conformal optical design, including static aberrations corrections and dynamic aberrations corrections. There are three parts in this paper. Firstly, the combination of static and dynamic aberration correction is introduced. A system for correcting optical aberration created by a conformal dome has an outer surface and an inner surface. The optimization of the inner surface is regard as the static aberration correction; moreover, a deformable mirror is placed at the position of the secondary mirror in the two-mirror all reflective imaging system, which is the dynamic aberration correction. Secondly, the using of appropriate surface types is very important in conformal dome design. Better performing optical systems can result from surface types with adequate degrees of freedom to describe the proper corrector shape. Two surface types and the methods of using them are described, including Zernike polynomial surfaces used in correct elements and user-defined surfaces used in deformable mirror (DM). Finally, the Adaptive optics (AO) correction is presented. In order to correct the dynamical residual aberration

  18. Conformational Changes in Small Ligands Upon Tetanus Toxin Binding

    National Research Council Canada - National Science Library

    Henderson, Terry J; Gitti, Rossitza K

    2008-01-01

    ... A upon binding to tetanus toxin. C13 T1 measurements suggested that to a first approximation, the conformational behavior of doxorubicin in solution appears to be a composite of a rigid aromatic ring system, ring librations...

  19. A Genome-Wide Association Study Reveals That Genes with Functions for Bone Development Are Associated with Body Conformation in Catfish.

    Science.gov (United States)

    Geng, Xin; Liu, Shikai; Yuan, Zihao; Jiang, Yanliang; Zhi, Degui; Liu, Zhanjiang

    2017-12-01

    Body conformation is of great scientific and commercial interest for aquaculture fish species because it affects biological adaptation of the organism to environments, and is of economic importance to the aquaculture industry considering its direct effect on fillet yield. Catfish is the primary aquaculture species in the USA. Two major species used in the aquaculture industry, channel catfish and blue catfish, differ in body shape and therefore the backcross progenies serve as a good model for quantitative trait locus (QTL) analysis. Here, a genome-wide association study (GWAS) with hybrid catfish was conducted to identify the QTL for body conformation, including deheaded body length (DBL), body length (BL), body depth (BD), and body breadth (BB), which were all standardized by cubic root of body weight. Overall, the results indicate that the traits are polygenic. For DBL, linkage group (LG) 2 and LG 24 contain significant QTL, and LG 13 and LG 26 contain suggestively associated QTL (-log10(P value) > 4.5). Compared with DBL, additional SNPs were identified to be associated with body length on LG 2, LG 7, and LG 18. Although no significant QTL for body depth was found, three suggestively associated QTLs were identified on LG 5, LG 13, and LG 14. No SNP for body breadth reached the threshold for suggestive association. Genes close to the associated SNPs were determined, many of which are known to be involved in bone development. This work therefore provides the basis for future identification of causal genes for the control of body conformation.

  20. DFT/PCM, QTAIM, 1H NMR conformational studies and QSAR modeling of thirty-two anti-Leishmania amazonensis Morita-Baylis-Hillman Adducts

    Science.gov (United States)

    Filho, Edilson B. A.; Moraes, Ingrid A.; Weber, Karen C.; Rocha, Gerd B.; Vasconcellos, Mário L. A. A.

    2012-08-01

    Morita-Baylis-Hillman Adducts (MBHA) has been recently synthesized and bio-evaluated by our research group against Leishmania amazonensis, parasite that causes cutaneous and mucocutaneous leishmaniasis. We present here a theoretical conformational study of thirty-two leismanicidal MBHA by B3LYP/6-31+g(d) calculations with Polarized Continuum Model (PCM) to simulate water influence. Intramolecular Hydrogen Bonds (IHBs) indicated to control the most conformational preferences of MBHA. Quantum Theory Atoms in Molecules (QTAIM) calculations were able to characterize these interactions at Bond Critical Point level. Compounds presenting an unusual seven member IHB between NO2 group and hydroxyl moiety, supported by experimental spectroscopic data, showed a considerable improvement of biological activity (lower IC50 values). These results are in accordance to redox NO2 mechanism of action. Based on structural observations, some molecular descriptors were calculated and submitted to Quantitative Structure-Activity Relationship (QSAR) studies through the PLS Regression Method. These studies provided a model with good validation parameters values (R2 = 0.71, Q2 = 0.61 and Qext2 = 0.92).

  1. Effects of hesperidin, a flavanone glycoside interaction on the conformation, stability, and aggregation of lysozyme: multispectroscopic and molecular dynamic simulation studies?

    Science.gov (United States)

    Ratnaparkhi, Aditi; Muthu, Shivani A; Shiriskar, Sonali M; Pissurlenkar, Raghuvir R S; Choudhary, Sinjan; Ahmad, Basir

    2015-09-01

    Hesperidin (HESP), a flavanone glycoside, shows high antioxidant properties and possess ability to go through the blood-brain barrier. Therefore, it could be a potential drug molecule against aggregation based diseases such as Alzheimer's, Parkinson's, and systemic amyloidoses. In this work, we investigated the potential of HESP to interact with hen egg-white lysozyme (HEWL) monomer and prevent its aggregation. The HESP-HEWL binding studies were performed using a fluorescence quenching technique, molecular docking and molecular dynamics simulations. We found a strong interaction of HESP with the lysozyme monomer (Ka, ~ 5 × 10(4) M(-1)) mainly through hydrogen bonding, water bridges, and hydrophobic interactions. We showed that HESP molecule spanned the highly aggregation prone region (amino acid residues 48-101) of HEWL and prevented its fibrillar aggregation. Further, we found that HESP binding completely inhibited amorphous aggregation of the protein induced by disulfide-reducing agent tries-(2-carboxyethyl) phosphine. Conformational and stability studies as followed by various tertiary and secondary structure probes revealed that HESP binding only marginally affected the lysozyme monomer conformation and increased both stability and reversibility of the protein against thermal denaturation. Future studies should investigate detail effects of HESP on solvent dynamics, structure, and toxicity of various aggregates. The answers to these questions will not only target the basic sciences, but also have application in biomedical and biotechnological sciences.

  2. Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition.

    Directory of Open Access Journals (Sweden)

    Yonatan Savir

    Full Text Available To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.

  3. Study of the conformal symmetry breaking in field theories in gravitational background using path integrals; Estudo da quebra de simetria conforme em teorias de campo em fundo gravitacional com uso de integrais de caminho

    Energy Technology Data Exchange (ETDEWEB)

    Souza Alves, Marcelo de

    1990-03-01

    Some general aspects on field theories in curved space-time and a introduction to conformal symmetry are presented.The behavior of the physical systems under Weyl transformations is discussed. The quantization of such systems are performed through the functional integration method. The regularization in curved space-time is also discussed. An application of this analysis in String theories is made. 42 refs.

  4. Conformational changes of protein adsorbed on tailored flat substrates with different chemistries.

    Science.gov (United States)

    Huang, He; Xie, Jing; Liu, Xiaoli; Yuan, Lin; Wang, Shasha; Guo, Songxi; Yu, Haoran; Chen, Hong; Zhang, Yanliang; Wu, Xiaohu

    2011-12-23

    Changes in the bioactivity of a protein after being adsorbed on a material surface may result from conformational changes of the protein. Unfortunately, however, direct evidence of such conformational changes of proteins adsorbed on a flat material surface is sparse so far. This is because probing the conformation of an adsorbed protein on material surfaces, especially flat ones, remains a challenge due to considerable experimental difficulties. In this study, the surface-enhanced Raman scattering (SERS) technique is used to characterize the conformational changes of a protein (lysozyme) adsorbed on tailored flat gold substrates with different chemistries. Two such substrates are formed by self-assembly of octadecanethiol and thiolated PEG on gold chips (Au-C18 and Au-PEG). Preliminary results reveal that, compared to the hydrophobic Au-C18 surface, the hydrophilic Au-PEG surface has much smaller effect on the conformation of lysozyme in aqueous solution, which thereby keeps its high bioactivity. The conformational changes of lysozyme adsorbed on material surfaces with different chemistries are well correlated with changes in its bioactivity. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Planar-nonplanar conformational equilibrium in metal derivates of octaethylporphyrin and meso-nitrooctaethylporhyrin

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, K.K.; Shelnutt, J.A. (Sandia National Lab., Albuquerque, NM (United States)); Hobbs, J.D. (Sandia National Lab., Albuquerque, NM (United States)); Luo, L.; Stanley, K.D.; Quirke, J.M.E. (Florida International Univ., Miami, FL (United States))

    1993-12-29

    The planar and nonplanar conformers of metal derivatives of 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP) and 5-nitro-2,3,7,8,12,13,17,18-octaethylporphyrin (NO[sub 2]-OEP) are investigated using resonance Raman spectroscopy. The structural heterogeneity is assessed by analysis of the line shapes of the structure-sensitive Raman lines. First, heterogeneity in the conformation of the macrocycle has been detected in solutions of the nickel and cobalt derivatives of OEP, that is, both planar and nonplanar conformers are found to coexist at room temperature for these metal porphyrins but not for the Cu and Zn derivatives. The latter metals expand the porphyrin core, shifting the equilibrium entirely to the planar conformer. Second, we find that substitution with a single NO[sub 2] group at one of the methine-bridge carbons shifts this planar-nonplanar equilibrium substantially toward the nonplanar conformer. Thus, both crowding of the peripheral substituents and contracting of the porphyrin core (Ni(II) < Co(II) < Cu(II) < Zn(II)) displace the equilibrium toward the nonplanar conformer. Finally, the frequencies of several Raman lines correlate with structural parameters such as core size (obtained either from molecular mechanics calculations or from X-ray crystallographic studies). 30 refs., 6 figs., 3 tabs.

  6. In vivo effects of metal ions on conformation and mechanical performance of silkworm silks.

    Science.gov (United States)

    Wang, Xin; Li, Yi; Liu, Qingsong; Chen, Quanmei; Xia, Qingyou; Zhao, Ping

    2017-03-01

    The mechanism of silk fiber formation is of particular interest. Although in vitro evidence has shown that metal ions affect conformational transitions of silks, the in vivo effects of metal ions on silk conformations and mechanical performance are still unclear. This study explored the effects of metal ions on silk conformations and mechanical properties of silk fibers by adding K+ and Cu2+ into the silk fibroin solutions or injecting them into the silkworms. Aimed by CD analysis, FTIR analysis, and mechanical testing, the conformational and mechanical changes of the silks were estimated. By using BION Web Server, the interactions of K+ and N-terminal of silk fibroin were also simulated. We presented that K+ and Cu2+ induced the conformational transitions of silk fibroin by forming β-sheet structures. Moreover, the mechanical parameters of silk fibers, such as strength, toughness and Young's modulus, were also improved after K+ or Cu2+ injection. Using BION Web Server, we found that potassium ions may have strong electrostatic interactions with the negatively charged residues. We suggest that K+ and Cu2+ play crucial roles in the conformation and mechanical performances of silks and they are involved in the silk fiber formation in vivo. Our results are helpful for clarifying the mechanism of silk fiber formation, and provide insights for modifying the mechanical properties of silk fibers. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Mechanistic and conformational studies on the interaction of food dye amaranth with human serum albumin by multispectroscopic methods.

    Science.gov (United States)

    Zhang, Guowen; Ma, Yadi

    2013-01-15

    The mechanism of interaction between food dye amaranth and human serum albumin (HSA) in physiological buffer (pH 7.4) was investigated by fluorescence, UV-vis absorption, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy. Results obtained from analysis of fluorescence spectra indicated that amaranth had a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The negative value of enthalpy change and positive value of entropy change elucidated that the binding of amaranth to HSA was driven mainly by hydrophobic and hydrogen bonding interactions. The surface hydrophobicity of HSA increased after binding with amaranth. The binding distance between HSA and amaranth was estimated to be 3.03 nm and subdomain IIA (Sudlow site I) was the primary binding site for amaranth on HSA. The results of CD and FT-IR spectra showed that binding of amaranth to HSA induced conformational changes of HSA. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Satisfaction and Healthcare Utilization of Transgender and Gender Non-Conforming Individuals in NYC: A Community-Based Participatory Study.

    Science.gov (United States)

    Radix, Anita E; Lelutiu-Weinberger, Corina; Gamarel, Kristi E

    2014-12-01

    Transgender and gender non-conforming (TGNC) individuals face high levels of discrimination and mistreatment, including within social and medical service settings, which may lead to negative health and psychosocial sequelae. Given the many barriers to competent care, we sought to determine points of intervention by assessing the current needs, satisfaction, and health care utilization of TGNC individuals in New York City as reported by TGNC individuals. In January 2013, fifty TGNC individuals were recruited via flyers and direct referrals from healthcare professionals within community spaces and pertinent venues. We administered a brief survey and conducted four focus groups exploring participants' health care utilization and perceived barriers to care, routine care, hormone and silicone use, and recommendations for improving transgender services. Participants were 18- to 64-years-old, racially/ethnically diverse, and the majority were medically insured, underwent routine health care in the last year, and received an HIV test in their lifetime. A significant proportion reported taking hormones prescribed by a medical provider and were in the care of knowledgeable providers. Participants perceived four areas where barriers persisted: utilization of preventive services, access to transition-related procedures, access to legal assistance, and inclusion of TGNC individuals in public health education and campaigns. Structural interventions are needed, such as comprehensive provider training programs for all level staff to better serve the needs of TGNC individuals, increase service utilization and improve wellbeing, while effecting lasting institutional change. Service provision establishments should hire more TGNC staff and integrate transgender care into existing practices.

  9. Production Data Acquisition and Analysis Management System: An Example Based on a Study of Automotive Supplier Solution

    Directory of Open Access Journals (Sweden)

    Lubomir Lengyel

    2013-12-01

    Full Text Available Quality of data coming from manual entry of information is a key element in efficiency of decision making process for all support functions and as well management allowing them to quickly react on changing circumstances of working environment. Principle finding of analysis performed within an automotive production companies shows a need to cover such requirement and develop a robust solution with efficient data collection, business intelligence capabilities and analysis support required for fast decision making process speeding up reaction in case of non-conformity. Purpose of KONIS system is providing a highly efficient solution for manual data entry, statistical analysis and decision making support for modern production company.

  10. Fluoride removal from aqueous solution by pumice: case study on ...

    African Journals Online (AJOL)

    The fluoride removal from synthetic water by pumice was studied at batch experiments in this study. The effect of pH, contact time, fluoride concentration and adsorbent dose on the fluoride sequestration was investigated. The optimum conditions were studied on Kuhbonan water as a case study. The results showed that ...

  11. Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment.

    Science.gov (United States)

    Ba, Yong; Mao, Yougang; Galdino, Luiz; Günsen, Zorigoo

    2013-01-01

    The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR microimaging experiment. The solutes studied include sodium chloride and glucose and the amino acids alanine, threonine, arginine, and aspartic acid. We found that the AFP is able to induce the bulk melting of the frozen AFP solutions at temperatures lower than 0 °C and can also keep the ice melted at higher temperatures in the AFP+solute solutions than those in the corresponding solute solutions. The latter shows that the ice phases were in super-heated states in the frozen AFP+solute solutions. We have tried to understand the first experimental phenomenon via the recent theoretical prediction that type I AFP can induce the local melting of ice upon adsorption to ice surfaces. The latter experimental phenomenon was explained with the hypothesis that the adsorption of AFP to ice surfaces introduces a less hydrophilic water-AFP-ice interfacial region, which repels the ionic/hydrophilic solutes. Thus, this interfacial region formed an intermediate chemical potential layer between the water phase and the ice phase, which prevented the transfer of water from the ice phase to the water phase. We have also attempted to understand the significance of the observed melting phenomena to the survival of organisms that express AFPs over cold winters.

  12. Conformal invariance of curvature perturbation

    CERN Document Server

    Gong, Jinn-Ouk; Park, Wan Il; Sasaki, Misao; Song, Yong-Seon

    2011-01-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the delta N formalism, and show its conformal invariance.

  13. Conformal invariance of curvature perturbation

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Jinn-Ouk [Theory Division, CERN, CH-1211 Genève 23 (Switzerland); Hwang, Jai-chan [Department of Astronomy and Atmospheric Sciences, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Park, Wan Il; Sasaki, Misao; Song, Yong-Seon, E-mail: jinn-ouk.gong@cern.ch, E-mail: jchan@knu.ac.kr, E-mail: wipark@kias.re.kr, E-mail: misao@yukawa.kyoto-u.ac.jp, E-mail: ysong@kias.re.kr [Korea Institute for Advanced Study, Seoul 130-722 (Korea, Republic of)

    2011-09-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the δN formalism, and show its conformal invariance.

  14. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

    Science.gov (United States)

    Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

    2017-08-01

    We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

  15. Printable Ultrathin Metal Oxide Semiconductor-Based Conformal Biosensors.

    Science.gov (United States)

    Rim, You Seung; Bae, Sang-Hoon; Chen, Huajun; Yang, Jonathan L; Kim, Jaemyung; Andrews, Anne M; Weiss, Paul S; Yang, Yang; Tseng, Hsian-Rong

    2015-12-22

    Conformal bioelectronics enable wearable, noninvasive, and health-monitoring platforms. We demonstrate a simple and straightforward method for producing thin, sensitive In2O3-based conformal biosensors based on field-effect transistors using facile solution-based processing. One-step coating via aqueous In2O3 solution resulted in ultrathin (3.5 nm), high-density, uniform films over large areas. Conformal In2O3-based biosensors on ultrathin polyimide films displayed good device performance, low mechanical stress, and highly conformal contact determined using polydimethylsiloxane artificial skin having complex curvilinear surfaces or an artificial eye. Immobilized In2O3 field-effect transistors with self-assembled monolayers of NH2-terminated silanes functioned as pH sensors. Functionalization with glucose oxidase enabled d-glucose detection at physiologically relevant levels. The conformal ultrathin field-effect transistor biosensors developed here offer new opportunities for future wearable human technologies.

  16. Transect study on solute transport in a macroporous soil

    Science.gov (United States)

    Mallants, D.; Vanclooster, M.; Feyen, J.

    1996-01-01

    Solute transport experiments using a non-reactive tracer were conducted on short, undisturbed, saturated columns of a sandy loam soil. All columns, 20 cm in diameter and 20 cm long, were collected along a transect of 35 m. Most of the soil columns had pre-existing macropores. The columns were leached at a steady flow-rate under ponding conditions. The resulting breakthrough curves (BTCs) showed a large heterogeneity. Several of the BTCs displayed early breakthrough and long tailing. All the data were interpreted in terms of dimensional time moments, the classical convection-dispersion equation (CDE) and the mobile-immobile transport model (MIM). Experimental time moments were found to vary significantly among the different BTCs. Analysis of the time moments also revealed that the variance of the field-scale BTC was several times larger than the average of the local-scale variance. The pore water velocity v and dispersion coefficient D were obtained by fitting the CDE to the local-scale BTCs, resulting in an average dispersivity of 7·4 cm. Frequency distributions for the CDE parameters v and D were equally well described by a normal or log-normal probability density function (pdf). When a log-normal pdf for D is considered, the variance of the loge transformed D values (ln D2) was found to be 2·1. For the MIM model, two additional parameters were fitted: the fraction of mobile water, m/, and the first-order mass transfer coefficient, . The MIM was more successful in describing the data than the CDE transport model. For the MIM model, the average dispersivity was about 2 cm. The MIM parameters v, D and pdf rather than a normal pdf. Only the parameter was better described by a normal pdf. Mobile water fractions, pdf). When the CDE and MIM were applied to the data, the fitted pore water velocities,

  17. Orientation, conformation and phase transitions of thin polymer films and self-assembled monolayers studied by SFG spectroscopy

    OpenAIRE

    Kurz, Volker Luiz Siegmar

    2010-01-01

    The aim of this dissertation was the characterization of thin polymeric lms on metal substrates. Of special interest were lms of poly-N-isopropylacrylamide (pNIPAM). Their lower critical solution temperature (LCST) at 32°C makes this polymer attractive for many applications. The changes in the molecular structure and the dynamic of these changes at the LCST are related to macroscopic properties. Using inherently interface speci c sum-frequency generation spectroscopy, gave insights into the...

  18. Anion complexation with cyanobenzoyl substituted first and second generation tripodal amide receptors: crystal structure and solution studies.

    Science.gov (United States)

    Hoque, Md Najbul; Gogoi, Abhijit; Das, Gopal

    2015-09-14

    Anion complexation properties of two new tripodal amide receptors have been extensively studied here. Two tripodal receptors have been synthesized from the reaction of cyanobenzoyl acid chloride with two tri-amine building blocks such as (i) tris(2-aminoethyl)amine and (ii) tris(2-(4-aminophenoxy)ethyl)amine, which resulted in the first (L1) and second (L2) generation tripodal amides respectively. A detailed comparison of their coordination behavior with anions is also described by crystallographic and solution state experiments. The crystal structure demonstrates various types of spatial orientations of tripodal arms in two receptors and concomitantly interacts with anions distinctively. Intramolecular H-bonding between amide N–H and CO prevents opening of the receptor cavity in the crystal, which leads to a locked conformation of L1 having C(3v) symmetry and makes amide hydrogen unavailable for the anion which results in side cleft anion binding. However, in L2 we conveniently shift the anion binding sites to a distant position which increases cavity size as well as rules out any intramolecular H-bonding between amide N–H and CO. The crystal structure shows a different orientation of the arms in L2; it adopts a quasi-planar arrangement with C(2v) symmetry. In the crystal structure two arms are pointed in the same direction and while extending the contact the third arm is H-bonded with the apical N-atom through a –CN group, making a pseudo capsular cavity where the anion interacts. Most importantly spatial reorientation of the receptor L2 from a C(2v) symmetry to a folded conformation with a C(3v) symmetry was observed only in the presence of an octahedral SiF6(2-) anion and forms a sandwich type complex. Receptors L1 and L2 are explored for their solution state anion binding abilities. The substantial changes in chemical shifts were observed for the amide (-NH) and aromatic hydrogen (-CH) (especially for F(-)), indicating the role of these hydrogens in

  19. Exploring the conformational space of cysteine by matrix isolation spectroscopy combined with near-infrared laser induced conformational change.

    Science.gov (United States)

    Najbauer, Eszter E; Bazsó, Gábor; Góbi, Sándor; Magyarfalvi, Gábor; Tarczay, György

    2014-02-27

    Six conformers of α-cysteine were identified by matrix isolation IR spectroscopy combined with NIR laser irradiation. Five of these conformers are identical with the five out of six conformers that have recently been identified by microwave spectroscopy. The sixth conformer observed in the present study is a short-lived conformer, which decays by H-atom tunneling; its half-life in a 12 K N2 matrix is (1.1 ± 0.5) × 10(3) s. This study proves that matrix isolation IR spectroscopy combined with NIR laser irradiation is a suitable method to identify conformers of a complex system for which computations predict several dozens of conformers, and that the reliability of this method for conformational assignment is comparable to that of microwave spectroscopy.

  20. Conformation of single block copolymer chain in two-dimensional microphase-separated structure studied by scanning near-field optical microscopy.

    Science.gov (United States)

    Sekine, Ryojun; Aoki, Hiroyuki; Ito, Shinzaburo

    2009-05-21

    The localization and orientation of the symmetric diblock copolymer chain in a quasi-two-dimensional microphase-separated structure were studied by scanning near-field optical microscopy (SNOM). In the monolayer of poly(isobutyl methacrylate)-block-poly(octadecyl methacrylate) (PiBMA-b-PODMA), the individual PiBMA subchains were directly observed by SNOM, and the center of mass (CM) and orientational angle relative to the phase interface were examined at the single chain level. It was found that the position of the CM and the orientation of the PiBMA subchain in the lamellar structure were dependent on the curvature of the PiBMA/PODMA interface. As the interface was bent toward the objective chain, the block chain preferred the CM position closer to the domain center, and the conformation was strongly oriented perpendicularly to the domain interface. With increase of the curvature, the steric hindrance among the block chain increases, resulting in the stretched conformation.