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Sample records for solution conformation studies

  1. New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

    Science.gov (United States)

    Thach, Trung Thanh; Shin, Donghyuk; Han, Seungsu; Lee, Sangho

    2016-04-01

    The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

  2. 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.

  3. NMR studies of the solution conformation and dynamics of the tyrocidine peptide antibiotics

    International Nuclear Information System (INIS)

    Zhou, N.

    1985-01-01

    The tyrocidine B and tyrocidine C 1 H NMR spectra in DMSO-d 6 were assigned by using 2D 1 H- 1 H correlation spectroscopy and 1D double resonance experiments. Based on the proton chemical shifts, 3 J/sub NH-Nα/ coupling constants, the chemical shift temperature dependence, and 1D and 2D 1 H- 1 H NOE values, a backbone conformation consisting of an anti-parallel β-pleated sheet, a type I β-turn and a type II' β-turn was suggested for both tyrocidines B and C. Seven out of ten side chains were determined to exist predominantly in one classical Chi 1 rotamer; while the residues Val 1 and Leu 3 had two Chi 1 rotamers which were significantly populated. Chi 2 angles were determined for residues Phe 4 , Trp 6 , DPhe 7 (D Trp 7 ) and Asn 8 . The natural abundance 13 C spectra of tyrocidine B and tyrocidine C were assigned by using 1 H- 13 C correlation spectroscopy. A study of the effect of soluble paramagnetic nitroxide compounds on tyrocidine A proton T 1 values were performed which confirmed the proposed tyrocidine A conformation. It also proved that these nitroxide compounds are very useful in studying proton solvent exposure, and therefore in delineating hydrogen bonding. A proton NMR study of the opioid peptide dynorphin-(1-13) in aqueous solution was reported which was consistent with a non-ordered molecule in the solution

  4. Studies on solution conformations and mechanism of action of amrinone and milrinone

    International Nuclear Information System (INIS)

    Beedle, E.E.; Elzey, T.K.; Kauffman, R.F.; Hayes, J.S.; Robertson, D.W.

    1986-01-01

    There are two structural differences between the positive inotropes amrinone (A) and milrinone (M): (1) M has a pyridone 2-methyl substituent and; (2) the pyridone 5-amino substituent of A is replaced with a nitrile in M. SAR studies confirmed that the 2-methyl substituent is responsible for the dramatically increased potency of M relative to A (canine i.v. ED 50 's=37 and 1891 μg/kg, respectively). Both M and A inhibited canine heart PDEase III (IC 50 's=12 and 150μM, respectively). Moreover, in a series of M/A congeners, the correlation between in vitro PDEase III IC 50 's and in vivo inotropic ED 50 's was highly significant (r = 0.98, p 13 C- and 1 H-NMR spectra of A and M and have used the chemical shifts of the pyridone C-4 protons as conformational reporters. These studies revealed that the C-4 protons of methyl containing congeners (M-like) experience a 0.38-0.53 ppm upfield shift relative to the corresponding proton resonance in unmethylated congeners (A-like). These data suggest there are marked, methyl-induced differences in the solution conformations of A and M

  5. Spectral analysis and quantum chemical studies of chair and twist-boat conformers of cycloheximide in gas and solution phases

    Science.gov (United States)

    Tokatli, A.; Ucun, F.; Sütçü, K.; Osmanoğlu, Y. E.; Osmanoğlu, Ş.

    2018-02-01

    In this study the conformational behavior of cycloheximide in the gas and solution (CHCl3) phases has theoretically been investigated by spectroscopic and quantum chemical properties using density functional theory (wB97X-D) method with 6-31++G(d,p) basis set, for the first time. The calculated IR results reveal that in the ground state the molecule exits as a mixture of the chair and twist-boat conformers in the gas phase, while the calculated NMR results reveal that it only exits as the chair conformer in the solution phase. In order to obtain the contributions coming from intramolecular interactions to the stability of the conformers in the gas and solution phases, the quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI) method, and natural bond orbital analysis (NBO) have been employed. The QTAIM and NCI methods indicated that by intramolecular interactions with bond critical point (BCP) the twist-boat conformer is more stabilized than the chair conformer, while by steric interactions it is more destabilized. Considering that these interactions balance each other, the stabilities of the conformers are understood to be dictated by the van der Waals interactions. The NBO analyses show that the hyperconjugative and steric effects play an important role in the stabilization in the gas and solution phases. Furthermore, to get a better understanding of the chemical behavior of this important antibiotic drug we have evaluated and, commented the global and local reactivity descriptors of the both conformers. Finally, the EPR analysis of γ-irradiated cycloheximide has been done. The comparison of the experimental and calculated data have showed the inducement of a radical structure of (CH2)2ĊCH2 in the molecule. The experimental EPR spectrum has also confirmed that the molecule simultaneously exists in the chair and twist-boat conformers in the solid phase.

  6. Studies on solution conformations and mechanism of action of amrinone and milrinone

    Energy Technology Data Exchange (ETDEWEB)

    Beedle, E.E.; Elzey, T.K.; Kauffman, R.F.; Hayes, J.S.; Robertson, D.W.

    1986-03-05

    There are two structural differences between the positive inotropes amrinone (A) and milrinone (M): (1) M has a pyridone 2-methyl substituent and; (2) the pyridone 5-amino substituent of A is replaced with a nitrile in M. SAR studies confirmed that the 2-methyl substituent is responsible for the dramatically increased potency of M relative to A (canine i.v. ED/sub 50/'s=37 and 1891 ..mu..g/kg, respectively). Both M and A inhibited canine heart PDEase III (IC/sub 50/'s=12 and 150..mu..M, respectively). Moreover, in a series of M/A congeners, the correlation between in vitro PDEase III IC/sub 50/'s and in vivo inotropic ED/sub 50/'s was highly significant (r = 0.98, p < 0.01). In the crystal-state, the methyl substituent of M induces a marked alteration in its 3-dimensional topology relative to A. They have now completely assigned the /sup 13/C- and /sup 1/H-NMR spectra of A and M and have used the chemical shifts of the pyridone C-4 protons as conformational reporters. These studies revealed that the C-4 protons of methyl containing congeners (M-like) experience a 0.38-0.53 ppm upfield shift relative to the corresponding proton resonance in unmethylated congeners (A-like). These data suggest there are marked, methyl-induced differences in the solution conformations of A and M.

  7. Virtual and solution conformations of oligosaccharides

    International Nuclear Information System (INIS)

    Cumming, D.A.; Carver, J.P.

    1987-01-01

    The possibility that observed nuclear Overhauser enhancements and bulk longitudinal relaxation times, parameters measured by 1 H NMR and often employed in determining the preferred solution conformation of biologically important molecules, are the result of averaging over many conformational states is quantitatively evaluated. Of particular interest was to ascertain whether certain 1 H NMR determined conformations are virtual in nature; i.e., the fraction of the population of molecules actually found at any time within the subset of conformational space defined as the solution conformation is vanishingly small. A statistical mechanics approach was utilized to calculate an ensemble average relaxation matrix from which (NOE)'s and (T 1 )'s are calculated. Model glycosidic linkages in four oligosaccharides were studied. The nature of the resultant population distributions is such that 50% of the molecular population is found within 1% of available microstates, while 99% of the molecular population occupies about 10% of the ensemble microstates, a number roughly equal to that sterically allowed. From this analysis the authors conclude that in many cases quantitative interpretation of NMR relaxation data, which attempts to define a single set of allowable torsion angle values consistent with the observed data, will lead to solution conformations that are either virtual or reflect torsion angle values possessed by a minority of the molecular population. Observed values of NMR relaxation data are the result of the complex interdependence of the population distribution and NOE (or T 1 ) surfaces in conformational space. In conformational analyses, NMR data can therefore be used to test different population distributions calculated from empirical potential energy functions

  8. Photo-stability study of a solution-processed small molecule solar cell system: correlation between molecular conformation and degradation.

    Science.gov (United States)

    Newman, Michael J; Speller, Emily M; Barbé, Jérémy; Luke, Joel; Li, Meng; Li, Zhe; Wang, Zhao-Kui; Jain, Sagar M; Kim, Ji-Seon; Lee, Harrison Ka Hin; Tsoi, Wing Chung

    2018-01-01

    Solution-processed organic small molecule solar cells (SMSCs) have achieved efficiency over 11%. However, very few studies have focused on their stability under illumination and the origin of the degradation during the so-called burn-in period. Here, we studied the burn-in period of a solution-processed SMSC using benzodithiophene terthiophene rhodamine:[6,6]-phenyl C 71 butyric acid methyl ester (BTR:PC 71 BM) with increasing solvent vapour annealing time applied to the active layer, controlling the crystallisation of the BTR phase. We find that the burn-in behaviour is strongly correlated to the crystallinity of BTR. To look at the possible degradation mechanisms, we studied the fresh and photo-aged blend films with grazing incidence X-ray diffraction, UV-vis absorbance, Raman spectroscopy and photoluminescence (PL) spectroscopy. Although the crystallinity of BTR affects the performance drop during the burn-in period, the degradation is found not to originate from the crystallinity changes of the BTR phase, but correlates with changes in molecular conformation - rotation of the thiophene side chains, as resolved by Raman spectroscopy which could be correlated to slight photobleaching and changes in PL spectra.

  9. 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

  10. 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

    S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR...... and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes...... with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

  11. Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

    Science.gov (United States)

    Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

    2018-04-03

    The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrilenucleation difficulty is a function of the strength of solvent-solute interaction, with emphasis on the interaction with specific H-bonding polar sites of importance in the crystal structure. A clear exception from this rule is the most difficult nucleation in toluene despite the weakest solvent-solute interactions. However molecular dynamics modelling predicts that tolbutamide assumes an intramolecularly H-bonded conformation in toluene, substantially different from and more stable than the conformation in the crystal structure, and thus presenting an additional barrier to nucleation. This explains why nucleation in toluene is the most difficult and why the relatively higher propensity for aggregation of tolbutamide molecules in toluene solution, as observed with FTIR spectroscopy, does not translate into easier nucleation. Thus, our combined experimental and molecular modelling study suggests that the solvent can influence on the nucleation not only via differences in the desolvation but also through the influence on molecular conformation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Study of local conformation and molecular movements of homo-polypeptides in aqueous solutions by using magnetic resonance and relaxation

    International Nuclear Information System (INIS)

    Perly, Bruno

    1980-01-01

    The objective of this research thesis is to study local conformations and mobilities of some typical homo-polypeptides by using techniques of magnetic resonance. By using these techniques, it is possible to make highly local observations of molecular elements which allows very efficient analysis of structural and dynamic properties of several biologically important compounds to be performed, and the study of their interactions. After a presentation of the general properties of the studied polypeptides, of magnetic resonance and of magnetic relaxation, the author presents some elements of macromolecular dynamics and movement models. Then, he reports the study of local conformations and structural transitions, applications of spin marking to the dynamic study of polypeptides, a dynamic study of the polypeptide skeleton under the form of statistic balls, the study of local movements of side chains by using nuclear relaxation, the study of the coupling of movements of main and side chains, and of the nuclear relaxation induced by a radical spin marker

  13. 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.

  14. NMR and rotational angles in solution conformation of polypeptides

    Science.gov (United States)

    Bystrov, V. F.

    1985-01-01

    Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin "bracelet", gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

  15. 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.

  16. Small Angle Neutron Scattering Studies of the Counterion Effects on the Molecular Conformation and Structure of Charged G4 PAMAM Dendrimers in Aqueous Solutions

    International Nuclear Information System (INIS)

    Chen, Wei-Ren

    2007-01-01

    The structural properties of generation 4 (G4) poly(amidoamine) starburst dendrimers (PAMAM) with an ethylenediamine ne (EDA) central core in D O 2 solutions have been studied by small angle neutron scattering. Upon the addition of DCl , SANS patterns show a pronounced inter-particle 2 correlation peaks due to the strong repulsion introduced by the protonation of the amino groups of the dendrimers. By solving the Ornstein-Zernike integral equation (OZ) with hypernetted chain closure (HNC), the dendrimer-dendrimer er structure factor S(Q) is determined and used to fit the experimental data. Quantitative information such as the effective charge per dendrimer and its conformational change at different conditions can be obtained. The results obtained show clear evidence that significant counterion association occurs, strongly mediating the inter-dendrimer interaction. The influence of interplay between counterions and molecular protonation of dendrimers has strong effect on the dendrimer conformation and effective interaction.

  17. A magnetic resonance study of the segmental motion and local conformations of poly-(L-glutamic acid) in aqueous solutions

    International Nuclear Information System (INIS)

    Tsutsumi, Akihiro; Perly, Bruno; Forchioni, Alain; Chachaty, Claude.

    1978-01-01

    A study was made on: ESR of spin labeled poly (L-glutamic acid) (PLGA); proton chemical shifts and vicinal coupling constants; pH dependences of proton and deuteron relaxations; proton relaxation enhancement in spin labeled PLGA; proton and carbon 13 relaxations in neutral solutions

  18. Mimicking the membrane-mediated conformation of dynorphin A-(1-13)-peptide: Circular dichroism and nuclear magnetic resonance studies in methanolic solution

    International Nuclear Information System (INIS)

    Lancaster, C.R.D.; Hughes, D.W.; Epand, R.M.; Mishra, P.K.; Bothner-By, A.A.; St Pierre, S.A.

    1991-01-01

    The structural requirements for the binding of dynorphin to the κ-opioid receptor are of profound clinical interest in the search for a powerful nonaddictive analgesic. These requirements are thought to be met by the membrane-mediated conformation of the opioid peptide dynorphin A-(1-13)-peptide, Tyr 1 -Gly 2 -Gly 3 -Phe 4 -Leu 5 -Arg 6 -Arg 7 -Ile 8 -Arg 9 -Pro 10 -Lys 11 -Leu 12 -Lys 13 . Schwyzer has proposed an essentially α-helical membrane-mediated conformation of the 13 amino acid peptide. In the present study, circular dichroism (CD) studies on dynorphin A-(1-13)-peptide bound to an anionic phospholipid signified negligible helical content of the peptide. CD studies also demonstrated that the aqueous-membraneous interphase may be mimicked by methanol. The 500- and 620-MHz 1 H nuclear magnetic resonance (NMR) spectra of dynorphin A-(1-13)-peptide in methanolic solution were sequence-specifically assigned with the aid of correlated spectroscopy (COSY), double-quantum filtered phase-sensitive COSY (DQF-COSY), relayed COSY (RELAY), and nuclear Overhauser enhancement spectroscopy (NOESY). 2-D CAMELSPIN/ROESY experiments indicated that at least the part of the molecule from Arg 7 to Arg 9 was in an extended or β-strand conformation, which agreed with deuterium-exchange and temperature-dependence studies of the amide protons and analysis of the vicinal spin-spin coupling constants 3 J HNα . The results clearly demonstrated the absence of extensive α-helix formation. χ 1 rotamer analysis of the 3 J αβ demonstrated no preferred side-chain conformations

  19. Study on the conformal variations of bovine and human serum albumin in solution using small angle X-ray scattering

    International Nuclear Information System (INIS)

    Olivieri, Johnny Rizzieri.

    1992-01-01

    It is reported a Small Angle X-Ray Scattering (SAXS) study of BSA (Bovine Serum Albumin) and HSA (Human Serum Albumin) on pH between 2.5 and 7.0. The measured scattering intensities, normalized in relation to incident beam, exposition time and scattering due to solvent and capillary, and corrected due to concentration and beam shape effects, have shown a strong dependence of the protein shape with pH for both albumins. It was found that the radius of gyration varies between 26.7 and 35 A, and the analyses of the distance distribution function. P(r), indicated that these proteins undergoes conformational changes with pH. Different theoretical shapes have been proposed and analysed comparing the computed P(r) function generated from the models with the experimental P(r). A large variety of shapes were found in both proteins, indicating that BSA and HSA are very flexibility macromolecules. (author). 60 refs., 49 figs., 7 tabs

  20. 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.

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

    International Nuclear Information System (INIS)

    Azreg-Aïnou, Mustapha

    2014-01-01

    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.

  2. The solutions of affine and conformal affine Toda field theory

    International Nuclear Information System (INIS)

    Papadopoulos, G.; Spence, B.

    1994-02-01

    We give new formulations of the solutions of the field equations of the affine Toda and conformal affine Toda theories on a cylinder and two-dimensional Minkowski space-time. These solutions are parameterised in terms of initial data and the resulting covariant phase spaces are diffeomorphic to the Hamiltonian ones. We derive the fundamental Poisson brackets of the parameters of the solutions and give the general static solutions for the affine theory. (authors). 10 refs

  3. Homothetic and conformal symmetries of solutions to Einstein's equations

    International Nuclear Information System (INIS)

    Eardley, D.; Isenberg, J.; Marsden, J.; Moncrief, V.; Yale Univ., New Haven, CT

    1986-01-01

    We present several results about the nonexistence of solutions of Einstein's equations with homoethetic or conformal symmetry. We show that the only spatially compact, globally hyperbolic spacetimes admitting a hypersurface of constant mean extrinsic curvature, and also admitting an infinitesimal proper homothetic symmetry, are everywhere locally flat; this assumes that the matter fields either obey certain energy conditions, or are the Yang-Mills or massless Klein-Gordon fields. We find that the only vacuum solutions admitting an infinitesimal proper conformal symmetry are everywhere locally flat spacetimes and certain plane wave solutions. We show that if the dominant energy condition is assumed, then Minkowski spacetime is the only asymptotically flat solution which has an infinitesimal conformal symmetry that is asymptotic to a dilation. In other words, with the exceptions cited, homothetic or conformal Killing fields are in fact Killing in spatially compact or asymptotically flat spacetimes. In the conformal procedure for solving the initial value problem, we show that data with infinitesimal conformal symmetry evolves to a spacetime with full isometry. (orig.)

  4. Thermal analysis studies of doping effects on the conformational motions of polymer chains in solid solutions with lasing molecules

    Science.gov (United States)

    Kalogeras, Ioannis M.; Pallikari, Fotini; Vassilikou-Dova, Aglaia; Neagu, Eugen R.

    2007-05-01

    The advancement of the solid-state dye laser performance largely depends on the systematic study of the dye-matrix interactions at the nanoscopic scale. The current work deals with blends of a comparatively inert dye host, poly(methyl methacrylate) (PMMA), with nonionic/apolar (substituted perylenes) and ionic/polar (rhodamine 6G, pyrromethene 567) dyes at ≈10-4 mol L-1 loading. Differential scanning calorimetry (DSC) and thermally stimulated currents (TSC) were used to explore the relative strength of inter- and intramolecular guest-host interactions by monitoring blending-induced modifications of the high-temperature signals: the segmental relaxation, the space-charge relaxation, and the liquid-liquid transition. Both techniques revealed the antiplasticizing role of the oligomeric organics on the relaxation dynamics of polymer segments, evidenced by clear glass-transition temperature upshifts. It becomes apparent that this effect is independent of the size, polarity, and ionicity of the dopant, signifying a common mechanism underway. It is suggested that, at least for the dyes under investigation, the chromophores simply fill the voids within the matrix, imposing strong steric hindrances on the rearrangement of the long-range structure. A comparison between the present results and earlier low-temperature dielectric data reveals that the large-scale relaxation dynamics show stronger perturbations due to blending, in comparison to the localized rotational motion of the pendant groups. DSC provided estimates for the unconverted monomer percentages in the solid blends. These were also determined more accurately by nuclear magnetic resonance (NMR), which additionally confirmed that the tacticity of the chains is not affected by the presence of the dye.

  5. 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.

  6. Conformally flat spaces and solutions to Yang-Mills equations

    International Nuclear Information System (INIS)

    Chaohao, G.

    1980-01-01

    Using the conformal invariance of Yang-Mills equations in four-dimensional manifolds, it is proved that in a simply connected space of negative constant curvature Yang-Mills equations admit solutions with any real number as their Pontryagin number. It is also shown that the space S 3 x S 1 which is the regular counterpart of the meron solution is one example of a class of solutions to Yang-Mills equations on compact manifolds that are neither self-dual nor anti-self-dual

  7. Conformation of Single Pentablock Ionomer Chains in Dilute Solutions

    Energy Technology Data Exchange (ETDEWEB)

    Aryal, Dipak [Clemson Univ., SC (United States); Perahia, Dvora [Clemson Univ., SC (United States); Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-04-01

    The conformation of single chain pentablock ionomers (A-B-C-B-A) containing randomly sulfonated polystyrene in the center block, tethered to poly-ethylene-r-propylene end-capped by poly-t-butyl styrene is studied in dilute solutions by molecular dynamics simulations. Multi-block copolymers offer a means to tailor several properties into one molecule, taking advantage of their rich phase diagram together with unique properties of specific blocks. For this pentablock the ionic block facilitates transport while the A and B components are incorporated for mechanical stability. The present study investigates the confirmation of a single chain of pentablock ionomer of molecular weight Mw ~ 50,000 g/mol and sulfonated polystyrene of the same molecular weight as that of the center block for six sulfonation fractions f from f=0.0-0.55. For the sulfonated systems Na+ counterions are included. Results for the equilibrium conformation of the chains and the three blocks in water and 1:1 mixture of cyclohexane and n-heptane are compared to simulations in implicit poor solvents with dielectric constants ε =1.0 and 77.73. In water, the pentablock is collapsed with sulfonated groups on the outer surface. As the sulfonation fraction f increases, the ionic, center block is increasingly segregated from the hydrophobic regions. In the 1:1 mixture of cyclohexane and heptane both the flexible and end blocks are swollen while the center ionic block is collasped for f>0, while for f=0 all blocks are swollen. In both implicit poor solvents the pentablock is collapsed into a nearly spherical shape for all f. The sodium counterions are dispersed widely throughout the simulation cell for both water and ε =77.73 whereas for ε =1.0 the counterions are largely condensed on the collapsed pentablock.

  8. 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...

  9. 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...

  10. Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

    International Nuclear Information System (INIS)

    Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora; Grest, Gary S.

    2015-01-01

    The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality is studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro-optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro-optical properties which are critical in their current and potential uses. The current study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonyl PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent whereas in water and implicit poor solvent, the nonyl side chains are collapsed towards the PPE backbone. Thus, rotation around the aromatic ring is fast and no long range correlations are seen within the backbone

  11. 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.

  12. 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.

  13. Supercharging Protein Complexes from Aqueous Solution Disrupts their Native Conformations

    Science.gov (United States)

    Sterling, Harry J.; Kintzer, Alexander F.; Feld, Geoffrey K.; Cassou, Catherine A.; Krantz, Bryan A.; Williams, Evan R.

    2012-02-01

    The effects of aqueous solution supercharging on the solution- and gas-phase structures of two protein complexes were investigated using traveling-wave ion mobility-mass spectrometry (TWIMS-MS). Low initial concentrations of m-nitrobenzyl alcohol ( m-NBA) in the electrospray ionization (ESI) solution can effectively increase the charge of concanavalin A dimers and tetramers, but at higher m-NBA concentrations, the increases in charge are accompanied by solution-phase dissociation of the dimers and up to a ~22% increase in the collision cross section (CCS) of the tetramers. With just 0.8% m-NBA added to the ESI solution of a ~630 kDa anthrax toxin octamer complex, the average charge is increased by only ~4% compared with the "native" complex, but it is sufficiently destabilized so that extensive gas-phase fragmentation occurs in the relatively high pressure regions of the TWIMS device. Anthrax toxin complexes exist in either a prechannel or a transmembrane channel state. With m-NBA, the prechannel state of the complex has the same CCS/charge ratio in the gas phase as the transmembrane channel state of the same complex formed without m-NBA, yet undergoes extensive dissociation, indicating that destabilization from supercharging occurs in the ESI droplet prior to ion formation and is not a result of Coulombic destabilization in the gas phase as a result of higher charging. These results demonstrate that the supercharging of large protein complexes is the result of conformational changes induced by the reagents in the ESI droplets, where enrichment of the supercharging reagent during droplet evaporation occurs.

  14. Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method.

    Science.gov (United States)

    Lu, Chao; Li, Xubin; Wu, Dongsheng; Zheng, Lianqing; Yang, Wei

    2016-01-12

    In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment

  15. Pyrimidine homoribonucleosides: synthesis, solution conformation, and some biological properties.

    Science.gov (United States)

    Lassota, P; Kuśmierek, J T; Stolarski, R; Shugar, D

    1987-05-01

    Conversion of uridine and cytidine to their 5'-O-tosyl derivatives, followed by cyanation with tetraethylammonium cyanide, reduction and deamination, led to isolation of the hitherto unknown homouridine (1-(5'-deoxy-beta-D-allofuranosyl)uracil) and homocytidine (1-(5'-deoxy-beta-D-allofuranosyl)cytosine), analogues of uridine and cytidine in which the exocyclic 5'-CH2OH chain is extended by one carbon to CH2CH2OH. Homocytidine was also phosphorylated to its 6'-phosphate and 6'-pyrophosphate analogues. In addition, it was converted, via its 2,2'-anhydro derivative, to arahomocytidine, an analogue of the chemotherapeutically active araC. The structures of all the foregoing were established by various criteria, including 1H and 13C NMR spectroscopy, both of which were also applied to analyses of the solution conformations of the various compounds, particularly as regards the conformations of the exocyclic chains. The behaviour of the homo analogues was examined in several enzymatic systems. Homocytidine was a feeble substrate, without inhibitory properties, of E. coli cytidine deaminase. Homocytidine was an excellent substrate for wheat shoot nucleoside phosphotransferase; while homouridine was a good substrate for E. coli uridine phosphorylase. Although homoCMP was neither a substrate, nor an inhibitor, of snake venom 5'-nucleotidase, homoCDP was a potent inhibitor of this enzyme (Ki approximately 6 microM). HomoCDP was not a substrate for M. luteus polynucleotide phosphorylase. None of the compounds exhibited significant activity vs herpes simplex virus type 1, or cytotoxic activity in several mammalian cell lines.

  16. 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.

  17. Abundant closed form solutions of the conformable time fractional Sawada-Kotera-Ito equation using (G‧ / G) -expansion method

    Science.gov (United States)

    Al-Shawba, Altaf Abdulkarem; Gepreel, K. A.; Abdullah, F. A.; Azmi, A.

    2018-06-01

    In current study, we use the (G‧ / G) -expansion method to construct the closed form solutions of the seventh order time fractional Sawada-Kotera-Ito (TFSKI) equation based on conformable fractional derivative. As a result, trigonometric, hyperbolic and rational functions solutions with arbitrary constants are obtained. When the arbitrary constants are taken some special values, the periodic and soliton solutions are obtained from the travelling wave solutions. The obtained solutions are new and not found elsewhere. The effect of the fractional order on some of these solutions are represented graphically to illustrate the behavior of the exact solutions when the parameter take some special choose.

  18. Globular conformation of some ribosomal proteins in solution

    International Nuclear Information System (INIS)

    Serdyuk, I.N.; Spirin, A.S.

    1978-01-01

    The possibility that such RNA-binding proteins of the 30 S subparticle as S4, S7, S8 and S16 exist in the form of compact globules in solution has been explored experimentally. These proteins have been studied in D 2 O solution by neutron scattering to measure their radii of gyration. This type of radiation using D 2 O as a solvent provides the maximum 'contrast', that is the maximum difference between the scattering of the protein and the solvent. It allowed measurements to be made using protein at <= 1.5 mg/ml. The radii of gyration for the ribosomal proteins S4, S7, S8 and S16 were found to be relatively small corresponding to the radii of gyration of compact globular proteins of the same molecular weights. (Auth.)

  19. Study of the Conformational State of Non-Cross-Linked and Cross-Linked Poly(alkylmethyldiallylammonium chlorides) in Aqueous Solution by Fluorescence Probing

    NARCIS (Netherlands)

    Wang, Guang-Jia; Engberts, Jan B.F.N.

    The aggregation behaviour of novel non-cross-linked and cross-linked poly(alkylmethyldiallylammonium chlorides) in aqueous solutions has been investigated by fluorescence spectroscopy using pyrene as a probe. These copolymers were found to exhibit similar aggregate properties as the corresponding

  20. Conformations and solution properties of star-branched polyelectrolytes

    NARCIS (Netherlands)

    Borisov, O.V.; Zhulina, E.B.; Leermakers, F.A.M.; Ballauff, M.; Muller, A.H.E.

    2011-01-01

    Aqueous solutions of star-like polyelectrolytes (PEs) exhibit distinctive features that originate from the topological complexity of branched macromolecules. In a salt-free solution of branched PEs, mobile counterions preferentially localize in the intramolecular volume of branched macroions.

  1. THE NEW SOLUTION OF TIME FRACTIONAL WAVE EQUATION WITH CONFORMABLE FRACTIONAL DERIVATIVE DEFINITION

    OpenAIRE

    Çenesiz, Yücel; Kurt, Ali

    2015-01-01

    – In this paper, we used new fractional derivative definition, the conformable fractional derivative, for solving two and three dimensional time fractional wave equation. This definition is simple and very effective in the solution procedures of the fractional differential equations that have complicated solutions with classical fractional derivative definitions like Caputo, Riemann-Liouville and etc. The results show that conformable fractional derivative definition is usable and convenient ...

  2. Exact vacuum solution to conformal Weyl gravity and galactic rotation curves

    International Nuclear Information System (INIS)

    Mannheim, P.D.; Kazanas, D.

    1989-01-01

    The complete, exact exterior solution for a static, spherically symmetric source in locally conformal invariant Weyl gravity is presented. The solution includes the familiar exterior Schwarzschild solution as a special case and contains an extra gravitational potential term which grows linearly with distance. The obtained solution provides a potential explanation for observed galactic rotation curves without the need for dark matter. The solution also has some interesting implications for cosmology. 9 refs

  3. 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.

  4. 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....

  5. Conformation evolution of oil contaminants onto aluminum oxide surface in aqueous solution: The effect of surface coverage

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Wenkun; Liu, Haitao, E-mail: xwk584523412@126.com; Sun, Yazhou; Fu, Hongya; Liang, Yingchun

    2017-01-15

    Highlights: • The dynamic conformational change of oil contaminations, at various surface coverages onto perfect α-Al{sub 2}O{sub 3}(0001) surface in aqueous solution is given. • The effect of surface coverage of oil molecules on the driving forces for the conformational change of oil contaminations is described. • The effect of interfacial water on the conformational change and even detachment of oil contaminations is considered. - Abstract: The microscopic conformational change process of oil contaminants adhered onto perfect α-Al{sub 2}O{sub 3} (0001) surface in aqueous solution was investigated by using all-atom classic molecular dynamics simulations. The change in removal mechanism of oil contaminants induced by surface coverage (surface area per molecule) was emphatically explored. Our simulation results strongly reveal that the increase in oil surface coverage induces an evident difference in microscopic detachment processes of oil contaminants. At a low surface coverage, oil contaminants can be thoroughly detached from solid surface. The whole detachment process could be divided into multi stages, including conformational change of oil contaminants on solid surface, dynamic motion of those in bulk solution and rapid migration of those from bulk solution to air/water interface. With surface coverage increasing, water diffusion becomes the key to induce conformational change and promote the detachment of oil contaminants. When oil surface coverage exceeds a threshold value, oil contaminants also undertake an evident conformational change process exhibiting typical characteristics but an incomplete detachment process occurs. All findings of the present study are helpful for the interpretation of the removal mechanism of oil contaminants on solid surface.

  6. Synthesis of specifically 15N- and 13C-labeled antitumor (2-Haloethyl)nitrosoureas. The study of their conformations in solution by nitrogen-15 and carbon-13 nuclear magnetic resonance and evidence for stereoelectronic control in their aqueous decomposition

    International Nuclear Information System (INIS)

    Lown, J.W.; Chauhan, S.M.S.

    1981-01-01

    The synthesis of certain specifically 15 N, 13 C, and 2 H isotope labeled 1-(2-chloroethyl)-3-alkyl-1-nitrosoureas (CENUs) is described. Spectroscopic examination of CENUs and their isotope-labeled counterparts by 1 H, 15 N, and 13 C NMR and infrared spectra indicates that they adopt preferred conformations in nonpolar aprotic solvents in which the NO group is aligned toward the 2-chloroethyl group. The result is in accord with the conformation of MeCCNU in the crystalline state derived from X-ray diffraction. The chemical shifts and coupling constants in the CENUs change with both solvent polarity and basicity. In aqueous phosphate buffer there is evidence for the formation of a tetrahedral intermediate, the conformation of which alters according to the reaction conditions and ultimately controls the formation of the aqueous decomposition products of CENUs. This is revealed most clearly by 13 C NMR of carbonyl- 13 C- and nitroso- 15 N-labeled BCNU and CCNU where two distinct 15 N-coupled 13 C doublets with different chemical shifts are observed. The rate of conformational change is comparable with the rate of decomposition of CENUs (via the second conformer) and may therefore represent the critical initial step of the latter process in vivo. The intermediacy of the postulated tetrahedral intermediates for CENUs is supported by observed 18 O exchange into the carbonyl group in 18 O-enriched water. Consideration of the conformations of the intermediates and of the alignment of the heteroatom lone pairs provides a satisfactory interpretation of the reactions of CENUs in aqueous solution as well as their pH dependence in terms of strict steroelectronic control and accounts for the formation of the observed products

  7. 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

    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...

  8. Solution of the stationary vacuum equations of relativity for conformally flat 3-spaces

    International Nuclear Information System (INIS)

    Perjes, Z.; Lukacs, B.; Sebestyen, A.; Valentini, A.; Sparling, G.A.J.

    1983-08-01

    The solution of Einstein's vacuum gravitational equations for stationary space-times with a conformally flat 3-space is presented. There is no other solution of this problem than the Ehlers-rotation generalizations of the three conformastat space-times including the Schwarzschild metric. (author)

  9. Fermionization of strings, and their conformal invariant solutions

    International Nuclear Information System (INIS)

    Abdalla, E.; Abdalla, M.C.B.

    1987-01-01

    The fermionic description of bosonic string theory, which turns out to be a Thirring model, is given. The relation of continuous spin to compactification is discussed, and regular solutions with finitely many fields can be found if the spin is a rational number. The relation between W.Z.W. theory and SU (n) Thirring model is also treated. (Author) [pt

  10. A theoretical and spectroscopic study of conformational structures of piroxicam

    Science.gov (United States)

    Souza, Kely Ferreira de; Martins, José A.; Pessine, Francisco B. T.; Custodio, Rogério

    2010-02-01

    Piroxicam (PRX) has been widely studied in an attempt to elucidate the causes and mechanisms of its side effects, mainly the photo-toxicity. In this paper fluorescence spectra in non-protic solvents and different polarities were carried out along with theoretical calculations. Preliminary potential surfaces of the keto and enol forms were obtained at AM1 level of theory providing the most stable conformers, which had their structure re-optimized through the B3LYP/CEP-31G(d,p) method. From the optimized structures, the electronic spectra were calculated using the TD-DFT method in vacuum and including the solvent effect through the PCM method and a single water molecule near PRX. A new potential surface was constructed to the enol tautomer at DFT level and the most stable conformers were submitted to the QST2 calculations. The experimental data showed that in apolar media, the solution fluorescence is raised. Based on conformational analysis for the two tautomers, keto and enol, the results indicated that the PRX-enol is the main tautomer related to the drug fluorescence, which is reinforced by the spectra results, as well as the interconvertion barrier obtained from the QST2 calculations. The results suggest that the PRX one of the enol conformers presents great possibility of involvement in the photo-toxicity mechanisms.

  11. Conformational change of oil contaminants adhered onto crystalline alpha-alumina surface in aqueous solution

    International Nuclear Information System (INIS)

    Xie, Wenkun; Sun, Yazhou; Liu, Haitao; Fu, Hongya; Liang, Yingchun

    2016-01-01

    Graphical abstract: - Highlights: • Dynamic conformational change process of oil contaminations adhered onto Al-terminated α-Al_2O_3 surface in aqueous solution is given. • Effect of water penetration on the conformational change and even detachment of oil contaminants is considered. • Change of driving forces leading to the conformational change of oil contaminants is described. - Abstract: Microscopic conformational change of oil contaminants adhered onto perfect α-Al_2O_3 (0001) surface in the aqueous solution was simulated by means of detailed fully atomistic molecular dynamics simulations. The main driving forces of the conformation change process of the oil contaminants were explored. The simulation results indicate that with submerging of the contaminated α-Al_2O_3 (0001) surface into the aqueous solution, the oil contaminants undertake an evident conformational change process. The dynamic process can be divided into several stages, including early penetration of water molecules, formation and widening of water channel, and generation of molecularly adsorbed hydration layers. Moreover, the oil contaminants on the α-Al_2O_3 surface are not fully removed from solid surface after a 10 ns relaxation, while a relatively stable oil/water/solid three-phase interface is gradually formed. Further, the residual oil contaminants are finally divided into several new ordered molecular adsorption layers. In addition, by systemically analyzing the driving forces for the conformational change of the oil contaminants, the penetration of water molecules is found to be the most important driving force. With penetrating of the water molecules, the dominating interactions controlling the conformational change of the oil contaminants have been changing over the whole simulation.

  12. 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.

  13. The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution.

    Science.gov (United States)

    Hammel, Michal; Nemecek, Daniel; Keightley, J Andrew; Thomas, George J; Geisbrecht, Brian V

    2007-12-01

    The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein-protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data revealed that a four-domain isoform of Eap is a monomer in solution. In vitro proteolysis and solution small angle X-ray scattering studies both indicate that Eap adopts an extended conformation in solution, where the linkers connecting sequential EAP modules are solvent exposed. Construction of a low-resolution model of full-length Eap using a combination of ab initio deconvolution of the SAXS data and rigid body modeling of the EAP domain crystal structure suggests that full-length Eap may present several unique concave surfaces capable of participating in ligand binding. These results also raise the possibility that such surfaces may be held together by additional interactions between adjacent EAP modules. This hypothesis is supported by a comparative Raman spectroscopic analysis of full-length Eap and a stoichiometric solution of the individual EAP modules, which indicates the presence of additional secondary structure and a greater extent of hydrogen/deuterium exchange protection in full-length Eap. Our results provide the first insight into the solution structure of full-length Eap and an experimental basis for interpreting the EAP domain crystal structures within the context of the full-length molecule. They also lay a foundation for future studies into the structural and molecular bases of Eap-mediated protein-protein interactions with its many ligands.

  14. Conformational dynamics of Escherichia coli flavodoxins in apo- and holo-states by solution NMR spectroscopy.

    Directory of Open Access Journals (Sweden)

    Qian Ye

    Full Text Available Flavodoxins are a family of small FMN-binding proteins that commonly exist in prokaryotes. They utilize a non-covalently bound FMN molecule to act as the redox center during the electron transfer processes in various important biological pathways. Although extensive investigations were performed, detailed molecular mechanisms of cofactor binding and electron transfer remain elusive. Herein we report the solution NMR studies on Escherichia coli flavodoxins FldA and YqcA, belonging to the long-chain and short-chain flavodoxin subfamilies respectively. Our structural studies demonstrate that both proteins show the typical flavodoxin fold, with extensive conformational exchanges observed near the FMN binding pocket in their apo-forms. Cofactor binding significantly stabilizes both proteins as revealed by the extension of secondary structures in the holo-forms, and the overall rigidity shown by the backbone dynamics data. However, the 50 s loops of both proteins in the holo-form still show conformational exchanges on the µs-ms timescales, which appears to be a common feature in the flavodoxin family, and might play an important role in structural fine-tuning during the electron transfer reactions.

  15. Molecular dynamics studies of the conformation of sorbitol

    Science.gov (United States)

    Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

    2009-01-01

    Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

  16. Engineering polyelectrolyte multilayer structure at the nanometer length scale by tuning polymer solution conformation.

    Science.gov (United States)

    Boddohi, Soheil; Killingsworth, Christopher; Kipper, Matt

    2008-03-01

    Chitosan (a weak polycation) and heparin (a strong polyanion) are used to make polyelectrolyte multilayers (PEM). PEM thickness and composition are determined as a function of solution pH (4.6 to 5.8) and ionic strength (0.1 to 0.5 M). Over this range, increasing pH increases the PEM thickness; however, the sensitivity to changes in pH is a strong function of ionic strength. The PEM thickness data are correlated to the polymer conformation in solution. Polyelectrolyte conformation in solution is characterized by gel permeation chromatography (GPC). The highest sensitivity of PEM structure to pH is obtained at intermediate ionic strength. Different interactions govern the conformation and adsorption phenomena at low and high ionic strength, leading to reduced sensitivity to solution pH at extreme ionic strengths. The correspondence between PEM thickness and polymer solution conformation offers opportunities to tune polymer thin film structure at the nanometer length scale by controlling simple, reproducible processing conditions.

  17. DNA oligonucleotide conformations: high resolution NMR studies

    International Nuclear Information System (INIS)

    Mellema, J.-R.

    1984-01-01

    The present work describes a DNA double-helix model, which is well comparable with the models derived from fibre-diffraction studies. The model has a mononucleotide repeat with torsion angles in accordance with average geometries as derived from 1 H NMR studies. Special attention was paid to reduce the number of short H-H nonbonding contacts, which are abundantly present in the 'classical' fibre-diffraction models. Chapter 3 describes the first complete assignment of a 1 H NMR spectrum of a DNA tetramer, d(TAAT). Preliminary conformational data derived from the spectral parameters recorded at 27 0 C are given. A more detailed analysis employing temperature-dependence studies is given in Chapter 4. (Auth.)

  18. Detergent-associated solution conformations of helical and beta-barrel membrane proteins.

    Science.gov (United States)

    Mo, Yiming; Lee, Byung-Kwon; Ankner, John F; Becker, Jeffrey M; Heller, William T

    2008-10-23

    Membrane proteins present major challenges for structural biology. In particular, the production of suitable crystals for high-resolution structural determination continues to be a significant roadblock for developing an atomic-level understanding of these vital cellular systems. The use of detergents for extracting membrane proteins from the native membrane for either crystallization or reconstitution into model lipid membranes for further study is assumed to leave the protein with the proper fold with a belt of detergent encompassing the membrane-spanning segments of the structure. Small-angle X-ray scattering was used to probe the detergent-associated solution conformations of three membrane proteins, namely bacteriorhodopsin (BR), the Ste2p G-protein coupled receptor from Saccharomyces cerevisiae, and the Escherichia coli porin OmpF. The results demonstrate that, contrary to the traditional model of a detergent-associated membrane protein, the helical proteins BR and Ste2p are not in the expected, compact conformation and associated with detergent micelles, while the beta-barrel OmpF is indeed embedded in a disk-like micelle in a properly folded state. The comparison provided by the BR and Ste2p, both members of the 7TM family of helical membrane proteins, further suggests that the interhelical interactions between the transmembrane helices of the two proteins differ, such that BR, like other rhodopsins, can properly refold to crystallize, while Ste2p continues to prove resistant to crystallization from an initially detergent-associated state.

  19. 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.

  20. X-ray structure of the pestivirus NS3 helicase and its conformation in solution.

    Science.gov (United States)

    Tortorici, M Alejandra; Duquerroy, Stéphane; Kwok, Jane; Vonrhein, Clemens; Perez, Javier; Lamp, Benjamin; Bricogne, Gerard; Rümenapf, Till; Vachette, Patrice; Rey, Félix A

    2015-04-01

    Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the

  1. Multi-centered AdS{sub 3} solutions from Virasoro conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Hulík, Ondřej [Institute of Physics of the ASCR,Na Slovance 2, 182 21 Prague 8 (Czech Republic); Institute of Particle Physics and Nuclear Physics,Faculty of Mathematics and Physics, Charles University,V Holešovičkách 2, 180 00 Prague 8 (Czech Republic); Procházka, Tomáš [Arnold Sommerfeld Center for Theoretical Physics,Ludwig Maximilian University of Munich,Theresienstr. 37, D-80333 München (Germany); Raeymaekers, Joris [Institute of Physics of the ASCR,Na Slovance 2, 182 21 Prague 8 (Czech Republic)

    2017-03-24

    We revisit the construction of multi-centered solutions in three-dimensional anti-de Sitter gravity in the light of the recently discovered connection between particle worldlines and classical Virasoro conformal blocks. We focus on multi-centered solutions which represent the backreaction of point masses moving on helical geodesics in global AdS{sub 3}, and argue that their construction reduces to a problem in Liouville theory on the disk with Zamolodchikov-Zamolodchikov boundary condition. In order to construct the solution one needs to solve a certain monodromy problem which we argue is solved by a vacuum classical conformal block on the sphere in a particular channel. In this way we construct multi-centered gravity solutions by using conformal blocks special functions. We show that our solutions represent left-right asymmetric configurations of operator insertions in the dual CFT. We also provide a check of our arguments in an example and comment on other types of solutions.

  2. 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.

  3. Homothetic and conformal motions in spacelike slices of solutions of Einstein's equations

    International Nuclear Information System (INIS)

    Berger, B.K.

    1976-01-01

    Components of Killing's equation are used to obtain constraints satisfied in a spacelike hypersurface by the intrinsic metric and extrinsic curvature in the presence of a spacetime conformal motion for a solution of Einstein's equations. If the conformal motion is either a homothetic motion or a motion, it is shown that these Killing constraints are preserved by the Einstein evolution equations. It is then shown that the generator of the homothetic motion (homothetic Killing vector) can be constructed if the Killing constraints are satisfied by a set of initial data. It is shown that a homothetic motion in the intrinsic metric is a spacetime homothetic motion if the extrinsic curvature is transformed correctly under the spatial homothetic motion. Further restrictions on a proper conformal motion due to the fact that it is not identically a curvature collineation are obtained. Restrictions on the matter--stress--energy tensor are discussed. Examples are presented

  4. On solutions of Einstein and Einstein-Yang-Mills equations with (maximal) conformal subsymmetries

    International Nuclear Information System (INIS)

    Sinzinkayo, S.; Demaret, J.

    1985-01-01

    The maximal subgroups of the conformal group (which have in common as a subgroup the group of pure spatial rotations) are considered as isometry groups of conformally flat space-times. The corresponding cosmological solutions of Einstein's field equations are identified. For each of them, the possibility is investigated that it could be generated by an SU(2) Yang-Mills field built, via the Corrigan-Fairlie-'t Hooft-Wilczek ansatz, from a scalar field identical with the square root of the conformal factor defining the space-time metric tensor. In particular, the Einstein cosmological model can be generated in this manner, but in the framework of strong gravity only, a micro-Einstein universe being then viewed as a possible model for a hadron. (author)

  5. Solutions of q-deformed equations with quantum conformal symmetry and nonzero spin

    International Nuclear Information System (INIS)

    Dobrev, V.K.; Gushterski, R.I.; Petrov, S.T.

    1998-09-01

    We consider the construction of explicit solutions of a hierarchy of q-deformed equations which are (conditionally) quantum conformal invariant. We give two types of solutions - polynomial solutions and solutions in terms of q-deformations of the plane wave. We use two q-deformations of the plane wave as a formal power series in the noncommutative coordinates of q-Minkowski space-time and four-momenta. One q-plane wave was proposed earlier by the first named author and B.S. Kostadinov, the other is new. The difference between the two is that they are written in conjugated bases. These q-plane waves are used here for the construction of solutions of the massless Dirac equation - one is used for the neutrino, the other for the antineutrino. It is also interesting that the neutrino solutions are deformed only through the q-pane wave, while the prefactor is classical. Thus, we can speak of a definite left-right asymmetry of the quantum conformal deformation of the neutrino-antineutrino system. (author)

  6. The Mannheim-Kazanas solution, the conformal geometrodynamics and the dark matter

    OpenAIRE

    Gorbatenko, M. V.; Sedov, S. Yu.

    2017-01-01

    Within the framework of the Einstein's standard equations of the general theory of relativity, flat galactic rotational curves of galaxies cannot be explained without hypothesis attracting the dark matter, the particles of which had not yet been identified. The vacuum central-symmetric solution of the equations of conformal gravitation is well known as metrics of Mannheim-Kazanas, on the basis of which these curves receive purely geometrical explanation. We show in our work that the metrics o...

  7. 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.

  8. On the Solutions of Two-Extended Principal Conformal Toda Theory

    Science.gov (United States)

    Chao, L.; Hou, B. Y.

    1994-02-01

    The solutions of the two-extended principal conformal Toda theory (2-EPCT theory, also called bosonic superconformal Toda theory) are constructed in two different ways: (1) Leznov-Saveliev algebraic analysis and (2) the associated chiral embedding surface. The first approach gives rise to the general solution in terms of appropriate matrix elements in different fundamental representations of the underlying Lie algebra, whilst the second one leads to a special solution in the form of Wronski determinants and their co-minors, and it gives an explicit geometrical interpretation of the WZNW → 2-EPCT reduction. The key points of both approaches are the chiral vectors derived recently by the authors, which constitute a closed exchange algebra of the theory.

  9. Solutions of deformed d'Alembert equation with quantum conformal symmetry

    International Nuclear Information System (INIS)

    Dobrev, V.K.; Kostadinov, B.S.

    1997-10-01

    We construct explicit solutions of a conditionally quantum conformal invariant q-d'Alembert equation proposed earlier by one of us. We give two types of solutions - polynomial solutions and a q-deformation of the plane wave. The latter is a formal power series in the noncommutative coordinates of q-Minkowski space-time and four-momenta. This q-plane wave has analogous properties to the classical one, in particular, it has the properties of q-Lorentz covariance, and it satisfies the q-d'Alembert equation on the q-Lorentz covariant momentum cone. On the other hand, our q-plane wave is not an exponent or q-exponent. Thus, it differs conceptually from the classical plane wave and may serve as a regularization. (author)

  10. Influence of multiple well defined conformations on small-angle scattering of proteins in solution.

    Science.gov (United States)

    Heller, William T

    2005-01-01

    A common structural motif for many proteins comprises rigid domains connected by a flexible hinge or linker. The flexibility afforded by these domains is important for proper function and such proteins may be able to adopt more than one conformation in solution under equilibrium conditions. Small-angle scattering of proteins in solution samples all conformations that exist in the sampled volume during the time of the measurement, providing an ensemble-averaged intensity. In this paper, the influence of sampling an ensemble of well defined protein structures on the small-angle solution scattering intensity profile is examined through common analysis methods. Two tests were performed using simulated data: one with the extended and collapsed states of the bilobal calcium-binding protein calmodulin and the second with the catalytic subunit of protein kinase A, which has two globular domains connected by a glycine hinge. In addition to analyzing the simulated data for the radii of gyration Rg, distance distribution function P(r) and particle volume, shape restoration was applied to the simulated data. Rg and P(r) of the ensemble profiles could be easily mistaken for a single intermediate state. The particle volumes and models of the ensemble intensity profiles show that some indication of multiple conformations exists in the case of calmodulin, which manifests an enlarged volume and shapes that are clear superpositions of the conformations used. The effect on the structural parameters and models is much more subtle in the case of the catalytic subunit of protein kinase A. Examples of how noise influences the data and analyses are also presented. These examples demonstrate the loss of the indications of multiple conformations in cases where even broad distributions of structures exist. While the tests using calmodulin show that the ensemble states remain discernible from the other ensembles tested or a single partially collapsed state, the tests performed using the

  11. Quantum-chemical study on the bioactive conformation of epothilones.

    Science.gov (United States)

    Jiménez, Verónica A

    2010-12-27

    Herein, I report a DFT study on the bioactive conformation of epothilone A based on the analysis of 92 stable conformations of free and bound epothilone to a reduced model of tubulin receptor. The equilibrium structures and relative energies were studied using B3LYP and X3LYP functionals and the 6-31G(d) standard basis set, which was considered appropriate for the size of the systems under study. Calculated relative energies of free and bound epothilones led me to propose a new model for the bioactive conformation of epothilone A, which accounts for several structure-activity data.

  12. Decontamination solution development studies

    International Nuclear Information System (INIS)

    Allen, R.P.; Fetrow, L.K.; Kjarmo, H.E.; Pool, K.H.

    1993-09-01

    This study was conducted for the Westinghouse Hanford Company (WHC) by Pacific Northwest Laboratory (PNL) as part of the Hanford Grout Technology Program (HGTP). The objective of this study was to identify decontamination solutions capable of removing radioactive contaminants and grout from the Grout Treatment Facility (GTF) process equipment and to determine the impact of these solutions on equipment components and disposal options. The reference grout used in this study was prepared with simulated double-shell slurry feed (DSSF) and a dry blend consisting of 40 wt % limestone flour, 28 wt % blast furnace slag, 28 wt % fly ash, and 4 wt % type I/II Portland cement

  13. Conformal Infinity.

    Science.gov (United States)

    Frauendiener, Jörg

    2004-01-01

    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.

  14. 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.

  15. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution

    DEFF Research Database (Denmark)

    Eriksen, Janus J.; Olsen, Jógvan Magnus H.; Aidas, Kestutis

    2011-01-01

    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......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...

  16. Conformations of polyelectrolyte macromolecules with different charge density in solutions of different ionic strengths

    International Nuclear Information System (INIS)

    Dommes, O A; Okatova, O V; Pavlov, G M

    2016-01-01

    Studies of charged polymer chains are interesting in both fundamental and applied aspects. Especially, polyelectrolytes attract huge attention of researchers due to their ability to form interpolymer complexes with synthetic and biopolymers. The study was carried out on the fractions of hydrophilic copolymers of N-methyl-N-vinyl acetamide and N-methyl-N-vinyl amine hydrochloride of different degrees of polymerization and of different charge density using methods of molecular hydrodynamics. Hydrodynamic and conformational characteristics as well as molar masses of isolated molecules were estimated. In addition, the intrinsic viscosity of fractions was studied at the extreme ionic strengths - in distilled water (∼10 -6 M) and in 6M NaCl. Scaling relations for intrinsic viscosity, sedimentation and translational diffusion coefficients with molar mass were obtained. Conformational behavior of macromolecules with different linear charge density was compared. (paper)

  17. Hartree-Fock and density functional theory study of alpha-cyclodextrin conformers.

    Science.gov (United States)

    Jiménez, Verónica; Alderete, Joel B

    2008-01-31

    Herein, we report the geometry optimization of four conformers of alpha-cyclodextrin (alpha-CD) by means of PM3, HF/STO-3G, HF/3-21G, HF/6-31G(d), B3LYP/6-31G(d), and X3LYP/6-31G(d) calculations. The analysis of several geometrical parameters indicates that all conformers possess bond lengths, angles, and dihedrals that agree fairly well with the crystalline structure of alpha-CD. However, only three of them (1-3) resemble the polar character of CDs and show intramolecular hydrogen-bonding patterns that agree with experimental NMR data. Among them, conformer 3 appears to be the most stable species both in the gas phase and in solution; therefore, it is expected to be the most suitable representative structure for alpha-CD conformation. The purpose of selecting such a species is to identify an appropriate structure to be employed as a starting point for reliable computational studies on complexation phenomena. Our results indicate that the choice of a particular alpha-CD conformer should affect the results of ab initio computational studies on the inclusion complexation with this cyclodextrin since both the direction and the magnitude of the dipole moment depend strongly on the conformation of alpha-CD.

  18. 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.

  19. NMR and computer modelling conformational study of N-benzyl, N-n-propyl (2-methyl-3-nitrophenyl)acetamide

    International Nuclear Information System (INIS)

    Nicolle, E.; Benoit-Guyod, M.; Namil, A.; Cussac, M.; Leclerc, G.; Maldivi, P.

    1995-01-01

    The conformation of N-benzyl-N-n-propyl (2-methyl-3-nitrophenyl) acetamide 1 in dimethyl sulfoxide (DMSO-d 6 ) or chloroform (CDCL 3 ) solution was studied using 1 H and 13 CNMR analysis. In solution, 1 existed as two distinct Z and E isomers, which could not be separated at laboratory temperature. Both conformations were in equivalent proportions in chloroform whereas in a polar solvent (DMSO), the conformation Z was more usual with the aromatic rings in a transposition. Major and minor rotation isomers were assigned form the '1H and 13 C NMR chemical shifts determined at 293 K. Separate treatment of signals displayed by two different methylene groups gave comparable activation parameters (ΔG ∼ 16 kcal/mol). Conformational analysis and measurement of the rotational barrier between the E and Z conformers by molecular modeling (Sybyl program) were performed. (authors). 14 refs., 8 figs

  20. Contribution to the study of conformal theories and integrable models

    International Nuclear Information System (INIS)

    Sochen, N.

    1992-05-01

    The purpose of this thesis is the 2-D physics study. The main tool is the conformal field theory with Kac-Moody and W algebra. This theory describes the 2-D models that have translation, rotation and dilatation symmetries, at their critical point. The expanded conformal theories describe models that have a larger symmetry than conformal symmetry. After a review of conformal theory methods, the author effects a detailed study of singular vector form in sl(2) affine algebra. With this important form, correlation functions can be calculated. The classical W algebra is studied and the relations between classical W algebra and quantum W algebra are specified. Bosonization method is presented and sl(2)/sl(2) topological model, studied. Partition function bosonization of different models is described. A program of rational theory classification is described linking rational conformal theories and spin integrable models, and interesting relations between Boltzmann weights of different models have been found. With these relations, the integrability of models by a direct calculation of their Boltzmann weights is proved

  1. Novel solution conformation of DNA observed in d(GAATTCGAATTC) by two-dimensional NMR spectroscopy

    International Nuclear Information System (INIS)

    Chary, K.V.R.; Hosur, R.V.; Govil, G.; Zu-kun, T.; Miles, H.T.

    1987-01-01

    Resonance assignments of nonexchangeable base and sugar protons of the self-complementary dodecanucleotide d(GAATTCGAATTC) have been obtained by using the two-dimensional Fourier transform NMR methods correlated spectroscopy and nuclear Overhauser effect spectroscopy. Conformational details about the sugar pucker, the glycosidic dihedral angle, and the overall secondary structure of the molecule has been derived from the relative intensities of cross peaks in the two-dimensional NMR spectra in aqueous solution. It is observed that d(GAATTCGAATTC) assumes a novel double-helical structure. The solution conformations of the two complementary strands are identical, unlike those observed in a related sequence in the solid state. Most of the five-membered sugar rings adopt an unusual O1'-endo geometry. All the glycosidic dihedral angles are in the anti domain. The AATT segments A2-T5 and A8-T11 show better stacking compared to the rest of the molecule. These features fit into a right-handed DNA model for the above two segments, with the sugar geometries different from the conventional ones. There are important structural variations in the central TCG portion, which is known to show preferences for DNase I activity, and between G1-A2 and G7-A8, which are cleavage points in the EcoRI recognition sequence. The sugar puckers for G1 and G7 are significantly different from the rest of the molecule. Further, in the three segments mentioned above, the sugar phosphate geometry is such that the distances between protons on adjacent nucleotides are much larger than those expected for a right-handed DNA. The authors suggest that such crevices in the DNA structure may act as hot points in initiation of protein recognition

  2. Study of conformally flat polytropes with tilted congruence

    Science.gov (United States)

    Sharif, M.; Sadiq, Sobia

    This paper is aimed to study the modeling of spherically symmetric spacetime in the presence of anisotropic dissipative fluid configuration. This is accomplished for an observer moving relative to matter content using two cases of polytropic equation-of-state under conformally flat condition. We formulate the corresponding generalized Tolman-Oppenheimer-Volkoff equation, mass equation, as well as energy conditions for both cases. The conformally flat condition is imposed to find an expression for anisotropy which helps to study spherically symmetric polytropes. Finally, Tolman mass is used to analyze stability of the resulting models.

  3. 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 ...

  4. 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.

  5. UV Resonance Raman Elucidation of the Terminal and Internal Peptide Bond Conformations of Crystalline and Solution Oligoglycines.

    Science.gov (United States)

    Bykov, Sergei V; Asher, Sanford A

    2010-11-30

    Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy independent contributions of molecular fragments require both a local mode-like behavior and the uncoupled electronic transitions. Here we show that the deep UV resonance Raman spectra of aqueous solution phase oligoglycines show independent peptide bond molecular fragment contributions indicating that peptide bonds electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution the oligoglycine terminal residues populate conformations similar to those found in crystals (3(1)-helices and β-strands), but with a broader distribution, while the internal peptide bond conformations are centered around the 3(1)-helix Ramachandran angles.

  6. 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.

  7. Conformal cryogenic tank trade study for reusable launch vehicles

    Science.gov (United States)

    Rivers, H. Kevin

    1999-01-01

    Future reusable launch vehicles may be lifting bodies with non-circular cross section like the proposed Lockheed-Martin VentureStar™. Current designs for the cryogenic tanks of these vehicles are dual-lobed and quad-lobed tanks which are packaged more efficiently than circular tanks, but still have low packaging efficiencies with large gaps existing between the vehicle outer mold line and the outer surfaces of the tanks. In this study, tanks that conform to the outer mold line of a non-circular vehicle were investigated. Four structural concepts for conformal cryogenic tanks and a quad-lobed tank concept were optimized for minimum weight designs. The conformal tank concepts included a sandwich tank stiffened with axial tension webs, a sandwich tank stiffened with transverse tension webs, a sandwich tank stiffened with rings and tension ties, and a sandwich tank stiffened with orthogrid stiffeners and tension ties. For each concept, geometric parameters (such as ring frame spacing, the number and spacing of tension ties or webs, and tank corner radius) and internal pressure loads were varied and the structure was optimized using a finite-element-based optimization procedure. Theoretical volumetric weights were calculated by dividing the weight of the barrel section of the tank concept and its associated frames, webs and tension ties by the volume it circumscribes. This paper describes the four conformal tank concepts and the design assumptions utilized in their optimization. The conformal tank optimization results included theoretical weights, trends and comparisons between the concepts, are also presented, along with results from the optimization of a quad-lobed tank. Also, the effects of minimum gauge values and non-optimum weights on the weight of the optimized structure are described in this paper.

  8. Structure, conformation in aqueous solution and antimicrobial activity of ulvan extracted from green seaweed Ulva reticulata.

    Science.gov (United States)

    Tran, Thi Thanh Van; Truong, Hai Bang; Tran, Nguyen Ha Vy; Quach, Thi Minh Thu; Nguyen, Thi Nu; Bui, Minh Ly; Yuguchi, Yoshiaki; Thanh, Thi Thu Thuy

    2017-12-04

    The aim of this study is to elucidate the structure and investigate the antimicrobial activity of an ulvan obtained by water extraction from green seaweed Ulva reticulata collected at Nha Trang sea of Vietnam by using IR, NMR, SEC-MALLS and SAXS methods. The ulvan is composed of rhamnose, galactose, xylose, manose and glucose (mole ratio Rha: Gal: Xyl: Man: Glu = 1:0.12:0.1:0.06:0.03), uronic acid (22.5%) and sulphate groups (17.6%). Chemically structural determination showed that the ulvan mainly composed of disaccharide [→4)β-D-GlcA(1→4)α-L-Rha3S-(1→]. The results from SAXS indicated that ulvan under study has a rod-like bulky chain conformation. Ulvan from U. reticulata showed high antimicrobial activity, with inhibition zone diameter of 20 mm against Enterobacter cloace and 18 mm against Escherichia coli.

  9. 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.

  10. Conformational study of melectin and antapin antimicrobial peptides in model membrane environments

    Science.gov (United States)

    Kocourková, Lucie; Novotná, Pavlína; Čujová, Sabína; Čeřovský, Václav; Urbanová, Marie; Setnička, Vladimír

    2017-01-01

    Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity.

  11. 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.

  12. Counterion Association and Structural Conformation Change of Charged PAMAM Dendrimer in Aqueous Solutions Revealed by Small Angle Neutron Scattering

    International Nuclear Information System (INIS)

    Chen, Wei-Ren

    2009-01-01

    Our previous study of the structure change of poly(amidoamine) starburst dendrimers (PAMAM) dendrimer of generation 5 (G5) have demonstrated that although the overall molecular size is practically unaffected by increasing DCl concentration, a configurational transformation, from a diffusive density profile to a more uniform density distribution, is clearly observed. In the current paper, the focus is placed on understanding the effect of counterion identity on the inter-molecular structure and the conformational properties by studying the effect due to DBr using small angle neutron scattering (SANS) and integral equation theory. While the overall molecular size is found to be essentially unaffected by the change in the pD of solutions, it is surprising that the intra-molecular configurational transformation is not observed when DBr is used. The overall effective charge of a dendrimer is nearly the same for 1, the effect of counterion identity becomes significant, the effective charge carried by a charged G5 PAPAM protonated by DBr becomes smaller than that of solutions with DCl. As a consequence, a counterion identity dependence of counterion association is revealed: Under the same level of molecular protonation, the specific counterion association, which is defined as the ratio of bound chloride anions to positively charged amines per molecule, is larger for the G5 PAMAM dendrimer charged by DBr than the one by DCl.

  13. 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

    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-linkedimmunosorbentassay(EIA...... 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 unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...

  14. Neutron scattering studies of molecular conformations in liquid crystal polymers

    Science.gov (United States)

    Noirez, L.; Moussa, F.; Cotton, J. P.; Keller, P.; Pépy, G.

    1991-03-01

    A comblike liquid crystal polymer (LPC) is a polymer on which mesogenic molecules have been grafted. It exhibits a succession of liquid crystal phases. Usually the equilibrium conformation of an ordinary polymeric chain corresponds to a maximum entropy, i.e., to an isotropic spherical coil. How does the backbone of a LCP behave in the nematic and smectic field? Small-angle neutron scattering may answer this question. Such measurements are presented here on four different polymers as a function of temperature. An anisotropy of the backbone conformation is found in all these studied compounds, much more pronounced in the smectic phase than in the nematic phase: the backbone spreads more or less perpendicularly to its hanging cores. A comparison with existing theories and a discussion of these results is outlined.

  15. Correspondence between the contracted BTZ solution of cosmological topological massive gravity and two-dimensional Galilean conformal algebra

    International Nuclear Information System (INIS)

    Setare, M R; Kamali, V

    2011-01-01

    We show that a BTZ black hole solution of cosmological topological massive gravity has a hidden conformal symmetry. In this regard, we consider the wave equation of a massless scalar field propagating in BTZ spacetime and find that the wave equation could be written in terms of the SL(2, R) quadratic Casimir. From the conformal coordinates, the temperatures of the dual conformal field theories (CFTs) could be read directly. Moreover, we compute the microscopic entropy of the dual CFT by the Cardy formula and find a perfect match to the Bekenstein-Hawking entropy of a BTZ black hole. Then, we consider Galilean conformal algebras (GCA), which arises as a contraction of relativistic conformal algebras (x → εx, t → t, ε → 0). We show that there is a correspondence between GCA 2 on the boundary and contracted BTZ in the bulk. For this purpose we obtain the central charges and temperatures of GCA 2 . Then, we compute the microscopic entropy of the GCA 2 by the Cardy formula and find a perfect match to the Bekenstein-Hawking entropy of a BTZ black hole in a non-relativistic limit. The absorption cross section of a near-region scalar field also matches the microscopic absorption cross section of the dual GCA 2 . So we find further evidence that shows correspondence between a contracted BTZ black hole and two-dimensional GCA.

  16. Solution conformation of the antitumor antibiotic chromomycin A3 determined by two-dimensional NMR spectroscopy

    International Nuclear Information System (INIS)

    Kam, M.; Shafer, R.H.; Berman, E.

    1988-01-01

    A conformational analysis and a complete assignment of the nonexchangeable proton resonances of chromomycin A 3 , dechromose-A chromomycin A 3 , and deacetylchromose-B chromomycin A 3 were carried out in organic solvents. The resulting conformation in methanol has the three side chains of chromomycin A 3 fully extended, away from one another and from the aglycon. In dichloromethane on the other hand, the drug was shown to adopt a highly compact conformation in which most of the 26 oxygen atoms in the molecule point out toward the solvent. The two carbohydrate side chains extend parallel to each other on the same side of the aglycon. Two intramolecular nuclear Overhauser enhancement contacts have been observed between different sugar units on these side chains, indicating close proximity for these moieties. In addition, the aliphatic side chain is folded toward the aglycon, parallel to the two oligosaccharide side chains. The overall conformation has a wedge-like shape with the two phenoxy groups exposed at the pointed edge. The presence of some exchange cross-peaks in the NOESY spectra suggests the presence of intramolecular hydrogen bonds that probably help to maintain the compact information. The derivatives of chromomycin A 3 have qualitatively similar conformations, though their respective conformations are not as compact as the parent drug. The significance of these results is discussed in terms of a model of chromomycin A 3 binding to DNA in the major groove

  17. Conforming discretizations of boundary element solutions to the electroencephalography forward problem

    Science.gov (United States)

    Rahmouni, Lyes; Adrian, Simon B.; Cools, Kristof; Andriulli, Francesco P.

    2018-01-01

    In this paper, we present a new discretization strategy for the boundary element formulation of the Electroencephalography (EEG) forward problem. Boundary integral formulations, classically solved with the Boundary Element Method (BEM), are widely used in high resolution EEG imaging because of their recognized advantages, in several real case scenarios, in terms of numerical stability and effectiveness when compared with other differential equation based techniques. Unfortunately, however, it is widely reported in literature that the accuracy of standard BEM schemes for the forward EEG problem is often limited, especially when the current source density is dipolar and its location approaches one of the brain boundary surfaces. This is a particularly limiting problem given that during an high-resolution EEG imaging procedure, several EEG forward problem solutions are required, for which the source currents are near or on top of a boundary surface. This work will first present an analysis of standardly and classically discretized EEG forward problem operators, reporting on a theoretical issue of some of the formulations that have been used so far in the community. We report on the fact that several standardly used discretizations of these formulations are consistent only with an L2-framework, requiring the expansion term to be a square integrable function (i.e., in a Petrov-Galerkin scheme with expansion and testing functions). Instead, those techniques are not consistent when a more appropriate mapping in terms of fractional-order Sobolev spaces is considered. Such a mapping allows the expansion function term to be a less regular function, thus sensibly reducing the need for mesh refinements and low-precisions handling strategies that are currently required. These more favorable mappings, however, require a different and conforming discretization, which must be suitably adapted to them. In order to appropriately fulfill this requirement, we adopt a mixed

  18. Conformations and molecular interactions of poly-γ-glutamic acid as a soluble microbial product in aqueous solutions

    OpenAIRE

    Wang, Ling-Ling; Chen, Jian-Tao; Wang, Long-Fei; Wu, Sha; Zhang, Guang-zhao; Yu, Han-Qing; Ye, Xiao-dong; Shi, Qing-Shan

    2017-01-01

    Soluble microbial products (SMPs) are of significant concern in the natural environment and in engineered systems. In this work, poly-γ-glutamic acid (γ-PGA), which is predominantly produced by Bacillus sp., was investigated in terms of pH-induced conformational changes and molecular interactions in aqueous solutions; accordingly, its sedimentation coefficient distribution and viscosity were also elucidated. Experimental results indicate that pH has a significant impact on the structure and m...

  19. Solution conformation of 2-aminopurine dinucleotide determined by ultraviolet two-dimensional fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Widom, Julia R; Marcus, Andrew H; Johnson, Neil P; Von Hippel, Peter H

    2013-01-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analogue of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS)—a fluorescence-detected variation of 2D electronic spectroscopy—to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point–dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R 12 = 3.5 ± 0.5 Å , twist angle θ 12 = 5° ± 5° ), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV–2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein–nucleic acid complexes. (paper)

  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.

    2011-12-01

    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 Etg 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 (Etg 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 Etg 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. However

  1. Conformational studies of peptides representing a segment of TM7 from Vo-H+-V-ATPase in SDS micelles

    NARCIS (Netherlands)

    Duarte, A.M.; Jong, de E.R.; Koehorst, R.B.M.; Hemminga, M.A.

    2010-01-01

    The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence

  2. Set of programs for the conformational study by NMR of flexible molecules

    International Nuclear Information System (INIS)

    Chachaty, C.; Langlet, G.

    1984-09-01

    A series of programs of common modular structure have been written in APL for the interpretation of nuclear magnetic resonance and relaxation data in isotropic or anisotropic solutions (liquid crystals). After giving an outline of the computation methods, several examples are reported of the applications of these programs to conformational studies by means of the nuclear relaxation and of the diamagnetic of paramagnetic shifts of resonance lines. These programs are also convenient for studies of dipolar and quadrupolar splittings or chemical shift anisotropy in liquid crystals [fr

  3. Natural abundant solid state NMR studies in designed tripeptides for differentiation of multiple conformers.

    Science.gov (United States)

    Jayanthi, S; Chatterjee, Bhaswati; Raghothama, S

    2009-10-01

    Solid state NMR (SSNMR) experiments on heteronuclei in natural abundance are described for three synthetically designed tripeptides Piv-(L)Pro-(L)Pro-(L)Phe-OMe (1), Piv-(D)Pro-(L)Pro-(L)Phe-OMe (2), and Piv-(D)Pro-(L)Pro-(L)Phe-NHMe (3). These peptides exist in different conformation as shown by solution state NMR and single crystal X-ray analysis (Chatterjee et al., Chem Eur J 2008, 14, 6192). In this study, SSNMR has been used to probe the conformations of these peptides in their powder form. The (13)C spectrum of peptide (1) showed doubling of resonances corresponding to cis/cis form, unlike in solution where the similar doubling is attributed to cis/trans form. This has been confirmed by the chemical shift differences of C(beta) and C(gamma) carbon of Proline in peptide (1) both in solution and SSNMR. Peptide (2) and (3) provided single set of resonances which represented all trans form across the di-Proline segment. The results are in agreement with the X-ray analysis. Solid state (15)N resonances, especially from Proline residues provided additional information, which is normally not observable in solution state NMR. (1)H chemical shifts are also obtained from a two-dimensional heteronuclear correlation experiment between (1)H--(13)C. The results confirm the utility of NMR as a useful tool for identifying different conformers in peptides in the solid state. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 851-860, 2009.

  4. 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.

  5. Complete conformal field theory solution of a chiral six-point correlation function

    International Nuclear Information System (INIS)

    Simmons, Jacob J H; Kleban, Peter

    2011-01-01

    Using conformal field theory, we perform a complete analysis of the chiral six-point correlation function C(z)= 1,2 φ 1,2 Φ 1/2,0 (z, z-bar )φ 1,2 φ 1,2 >, with the four φ 1,2 operators at the corners of an arbitrary rectangle, and the point z = x + iy in the interior. We calculate this for arbitrary central charge (equivalently, SLE parameter κ > 0). C is of physical interest because for percolation (κ = 6) and many other two-dimensional critical points, it specifies the density at z of critical clusters conditioned to touch either or both vertical ends of the rectangle, with these ends 'wired', i.e. constrained to be in a single cluster, and the horizontal ends free. The correlation function may be written as the product of an algebraic prefactor f and a conformal block G, where f = f(x, y, m), with m a cross-ratio specified by the corners (m determines the aspect ratio of the rectangle). By appropriate choice of f and using coordinates that respect the symmetry of the problem, the conformal block G is found to be independent of either y or x, and given by an Appell function.

  6. Atropisomerism about Aryl-C(sp(3)) Bonds: Conformational Behavior of Substituted Phenylcyclohexanes in Solution.

    Science.gov (United States)

    Flos, Manon; Lameiras, Pedro; Denhez, Clément; Mirand, Catherine; Berber, Hatice

    2016-03-18

    A catalytic hydrogenation of cannabidiol derivatives known as phenylcyclohexenes was used to prepare epimeric (1R,1S) and/or rotameric (M,P) phenylcyclohexanes. The reaction is diastereoselective, in favor of the 1S epimer, when large groups are attached to the phenyl ring. For each epimer, variable-temperature NMR experiments, including EXSY spectroscopy and DFT calculations, were used to determine the activation energies of the conformational exchange arising from the restricted rotation about the aryl-C(sp(3)) bond that led to two unequally populated rotamers. The conformational preference arises essentially from steric interactions between substituents vicinal to the pivot bond. The conformers of epimers (1S)-2e,f show high rotational barriers of up to 92 kJ mol(-1), unlike those of (1R)-2e,f and with much lower barriers of ∼72 kJ mol(-1). The height of the barriers not only depends on the substituents at the axis of chirality but also is influenced by the position of a methyl group on the monoterpene ring. The feature most favorable to high rotational barriers is when the methyl at C1 lies equatorially. This additional substituent effect, highlighted for the first time, seems fundamental to allowing atropisomerism in hindered ortho-substituted phenylcyclohexanes.

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

    Indian Academy of Sciences (India)

    six solutions so obtained, three are in implicit form while the remaining three could be expressed explicitly. Each solution describes an .... function F whose solutions can be obtained in the following manners: Case (I). On inserting the value of ...

  8. Conformational analysis of lignin models

    International Nuclear Information System (INIS)

    Santos, Helio F. dos

    2001-01-01

    The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level. (author)

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

    African Journals Online (AJOL)

    in second-line treatment of non-small cell lung cancer ... receptor-tyrosine kinase inhibitor (EGFR-TKI) in the second-line treatment of non-small cell ... were divided into two groups: 106 patients were treated with conformal ... Conformal radiotherapy, Targeted therapy, Survival rate .... regression model was used for survival.

  10. The Asch Conformity Effect: A Study in Kuwait.

    Science.gov (United States)

    Amir, Taha

    1984-01-01

    Investigated whether conformity in the experimental setting suggested by Asch was related to American culture and less likely to be replicable elsewhere. Kuwaiti subjects (N=200) were used in replicating the original experiment. Obtained an 'Asch effect' of a comparable magnitude to that of Asch. Individual differences in conformity were evident.…

  11. On the analytical solutions of the system of conformable time-fractional Robertson equations with 1-D diffusion

    International Nuclear Information System (INIS)

    Iyiola, O.S.; Tasbozan, O.; Kurt, A.; Çenesiz, Y.

    2017-01-01

    In this paper, we consider the system of conformable time-fractional Robertson equations with one-dimensional diffusion having widely varying diffusion coefficients. Due to the mismatched nature of the initial and boundary conditions associated with Robertson equation, there are spurious oscillations appearing in many computational algorithms. Our goal is to obtain an approximate solutions of this system of equations using the q-homotopy analysis method (q-HAM) and examine the widely varying diffusion coefficients and the fractional order of the derivative.

  12. NMR studies of DNA structures in solution

    International Nuclear Information System (INIS)

    Rinkel, L.J.

    1987-01-01

    This thesis describes the conformational analysis of some polynucleotides in aqueous solution. A new graphical method is presented as an aid in the pseudorotational analysis of the sugar rings in DNA by means of sums of proton-proton coupling constants. (Auth.)

  13. Structural and conformational study of polysaccharides by nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Bossennec, Veronique

    1989-01-01

    As some natural polysaccharides are involved in important biological processes, the use of nuclear magnetic resonance appears to be an adapted mean to determine their structure-activity relationship and is therefore the object of this research thesis. By using bi-dimensional proton-based NMR techniques, it is possible to identify minority saccharide units, to determine their conformation, and to identify units which they are bound to. The author reports the application of these methods to swine mucosa heparin, and to heparins displaying a high and low anticoagulant activity. The dermatan sulphate has also been studied, and the NMR analysis allowed some polymer structure irregularities to be identified. A molecular modelling of dermatan sulphate has been performed [fr

  14. Time-resolved infrared studies of protein conformational dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Woodruff, W.H.; Causgrove, T.P.; Dyer, R.B. [Los Alamos National Laboratory, NM (United States); Callender, R.H. [Univ. of New York, NY (United States)

    1994-12-01

    We have demonstrated that TRIR in the amide I region gives structural information regarding protein conformational changes in realtime, both on processes involved in the development of the functional structure (protein folding) and on protein structural changes that accompany the functional dynamics of the native structure. Assignment of many of the amide I peaks to specific amide or sidechain structures will require much additional effort. Specifically, the congestion and complexity of the protein vibrational spectra dictate that isotope studies are an absolute requirement for more than a qualitative notion of the structural interpretation of these measurements. It is clear, however, that enormous potential exists for elucidating structural relaxation dynamics and energetics with a high degree of structural specificity using this approach.

  15. Conformational, vibrational, NMR and DFT studies of N-methylacetanilide.

    Science.gov (United States)

    Arjunan, V; Santhanam, R; Rani, T; Rosi, H; Mohan, S

    2013-03-01

    A detailed conformational, vibrational, NMR and DFT studies of N-methylacetanilide have been carried out. In DFT, B3LYP method have been used with 6-31G(**), 6-311++G(**) and cc-pVTZ basis sets. The vibrational frequencies were calculated resulting in IR and Raman frequencies together with intensities and Raman depolarisation ratios. The dipole moment derivatives were computed analytically. Owing to the complexity of the molecule, the potential energy distributions of the vibrational modes of the compound are also calculated. Isoelectronic molecular electrostatic potential surface (MEP) and electron density surface were examined. (1)H and (13)C NMR isotropic chemical shifts were calculated and the assignments made are compared with the experimental values. The energies of important MO's of the compound were also determined from TD-DFT method. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. 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.

  17. Conformational analysis of a Chlamydia-specific disaccharide α-Kdo-(2→8)-α-Kdo-(2→O)-allyl in aqueous solution and bound to a monoclonal antibody: Observation of intermolecular transfer NOEs

    International Nuclear Information System (INIS)

    Sokolowski, Tobias; Haselhorst, Thomas; Scheffler, Karoline; Weisemann, Ruediger; Kosma, Paul; Brade, Helmut; Brade, Lore; Peters, Thomas

    1998-01-01

    The disaccharide α-Kdo-(2 → 8)-α-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 α-Kdo-(2 → 8)-α-Kdo-(2 → 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 1 H NMR signals of α-Kdo-(2 → 8)-α-Kdo-(2 → 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 α-Kdo-(2 → 8)-α-Kdo-(2 → 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 α-Kdo-(2 → 8)-α-Kdo-(2 → 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

  18. Multi-centered AdS.sub.3./sub. solutions from Virasoro conformal blocks

    Czech Academy of Sciences Publication Activity Database

    Hulík, Ondřej; Procházka, Tomáš; Raeymaekers, Joris

    2017-01-01

    Roč. 2017, č. 3 (2017), s. 1-35, č. článku 129. ISSN 1029-8479 R&D Projects: GA ČR(CZ) GA14-31689S Institutional support: RVO:68378271 Keywords : AdS-CFT correspondence * classical theories of gravity * conformal and W symmetry Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 6.063, year: 2016

  19. Studies on the optical absorption of copper-dopped myoglobin: conformational changes

    International Nuclear Information System (INIS)

    Lamy, M.T.M.

    1976-03-01

    Optical absorption changes in the visible and near U.V. spectrum of myoglobin molecules are observed when copper ions are added to the macromolecule. The heme optical transitions are investigated through a theoretical simulation of the optical absorption spectrum. A study of the absorption band in the region of 700 nm associated with the copper - myoglobin complexes indicated the existence of two kinds of metal-protein complexes: one associated with the six or eitht first added copper ions and the other related with the higher concentrations. Conformational changes caused by thermal treatment are studied in myoglobin water solutions and solutions containing copper ions. The phenomenon named pre-denaturation is observed through the optical absorption at 245 nm. It is shown that interactions between myoglobin molecules occur in the pre-denaturation phenomenon. (Author) [pt

  20. Conformational analysis of quinine and its pseudo enantiomer quinidine: a combined jet-cooled spectroscopy and vibrational circular dichroism study.

    Science.gov (United States)

    Sen, Ananya; Bouchet, Aude; Lepère, Valeria; Le Barbu-Debus, Katia; Scuderi, D; Piuzzi, F; Zehnacker-Rentien, A

    2012-08-16

    Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.

  1. General solution of an exact correlation function factorization in conformal field theory

    International Nuclear Information System (INIS)

    Simmons, Jacob J H; Kleban, Peter

    2009-01-01

    The correlation function factorization with K a boundary operator product expansion coefficient, is known to hold for certain scaling operators at the two-dimensional percolation point and in a few other cases. Here the correlation functions are evaluated in the upper half-plane (or any conformally equivalent region) with x 1 and x 2 arbitrary points on the real axis, and z an arbitrary point in the interior. This type of result is of interest because it is both exact and universal, relates higher-order correlation functions to lower-order ones and has a simple interpretation in terms of cluster or loop probabilities in several statistical models. This motivated us to use the techniques of conformal field theory to determine the general conditions for its validity. Here, we discover that either (see display) factorizes in this way for any central charge c, generalizing previous results. In particular, the factorization holds for either FK (Fortuin–Kasteleyn) or spin clusters in the Q-state Potts models; it also applies to either the dense or dilute phases of the O(n) loop models. Further, only one other non-trivial set of highest-weight operators (in an irreducible Verma module) factorizes in this way. In this case the operators have negative dimension (for c<1) and do not seem to have a physical realization

  2. Differential Mobility Spectrometry-Hydrogen Deuterium Exchange (DMS-HDX) as a Probe of Protein Conformation in Solution.

    Science.gov (United States)

    Zhu, Shaolong; Campbell, J Larry; Chernushevich, Igor; Le Blanc, J C Yves; Wilson, Derek J

    2016-06-01

    Differential mobility spectrometry (DMS) is an ion mobility technique that has been adopted chiefly as a pre-filter for small- to medium-sized analytes (DMS-field asymmetric waveform ion mobility spectroscopy (FAIMS)-the application of DMS to intact biomacromolecules remains largely unexplored. In this work, we employ DMS combined with gas-phase hydrogen deuterium exchange (DMS-HDX) to probe the gas-phase conformations generated from proteins that were initially folded, partially-folded, and unfolded in solution. Our findings indicate that proteins with distinct structural features in solution exhibit unique deuterium uptake profiles as function of their optimal transmission through the DMS. Ultimately we propose that DMS-HDX can, if properly implemented, provide rapid measurements of liquid-phase protein structural stability that could be of use in biopharmaceuticals development. Graphical Abstract ᅟ.

  3. SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.

    Science.gov (United States)

    Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C; Joyce, Kevin P; Kovalenko, Andriy

    2016-11-01

    Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.

  4. SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling

    Science.gov (United States)

    Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C.; Joyce, Kevin P.; Kovalenko, Andriy

    2016-11-01

    Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing (R=0.98 for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining R=0.73 compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to R=0.93. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple pK_{ {a}} correction improved agreement with experiment from R=0.54 to R=0.66, despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.

  5. Small angle X-ray scattering study of calreticulin reveals conformational plasticity

    DEFF Research Database (Denmark)

    Toft, Katrine Nørgaard; Larsen, Nanna; Jørgensen, Flemming Steen

    2008-01-01

    . The data from the calreticulin monomer reveal the shape of calreticulin in solution: The previously structurally un-described C-terminal is seen as a globular domain, and the P-domain beta-hairpin extends from the N-domain in a spiral like conformation. In the calreticulin solution dimer, the N-, C-, and P......-domains are easily identified, and the P-domain is in an extended conformation connecting to the second calreticulin molecule. The SAXS solution data enables the construction of a medium-resolution model of calreticulin. In the light of the unresolved chaperone mechanism of calreticulin and calnexin, we discuss...

  6. Conformational Study of Taurine in the Gas Phase

    Science.gov (United States)

    Cortijo, Vanessa; Sanz, M. Eugenia; López, Juan C.; Alonso, José L.

    2009-08-01

    The conformational preferences of the amino sulfonic acid taurine (NH2-CH2-CH2-SO3H) have been investigated in the gas phase by laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) in the 6-14 GHz frequency range. One conformer has been observed, and its rotational, centrifugal distortion, and hyperfine quadrupole coupling constants have been determined from the analysis of its rotational spectrum. Comparison of the experimental constants with those calculated theoretically identifies the detected conformer unambiguously. The observed conformer of taurine is stabilized by an intramolecular hydrogen bond O-H···N between the hydrogen of the sulfonic acid group and the nitrogen atom of the amino group.

  7. Desulfurization of 2-thiouracil nucleosides: conformational studies of 4-pyrimidinone nucleosides.

    Science.gov (United States)

    Kraszewska, Karina; Kaczyńska, Iwona; Jankowski, Stefan; Karolak-Wojciechowska, Janina; Sochacka, Elzbieta

    2011-04-01

    4-Pyrimidinone ribofuranoside (H(2)o(4)U) and 4-pyrimidinone 2'-deoxyribofuranoside (dH(2)o(4)U) were synthesized by the oxidative desulfurization of parent 2-thiouracil nucleosides with m-chloroperbenzoic acid. The crystal structures of H(2)o(4)U and dH(2)o(4)U and their conformations in solution were determined and compared with corresponding 2-thiouracil and uracil nucleosides. The absence of a large 2-thiocarbonyl/2-carbonyl group in the nucleobase moiety results in C2'-endo puckering of the ribofuranose ring (S conformer) in the crystal structure of H(2)o(4)U, which is not typical of RNA nucleosides. Interestingly, the hydrogen bonding network in the crystals of dH(2)o(4)U stabilizes the sugar moiety conformation in the C3'-endo form (N conformer), rarely found in DNA nucleosides. In aqueous solution, dH(2)o(4)U reveals a similar population of the C2'-endo conformation (65%) to that of 2'-deoxy-2-thiouridine (62%), while the 62% population of the S conformer for H(2)o(4)U is significantly different from that of the parent 2-thiouridine, for which the N conformer is dominant (71%). Such a difference may be of biological importance, as the desulfurization process of natural tRNA 2-thiouridines may occur under conditions of oxidative stress in the cell and may influence the decoding process. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Study of liquids and solutions

    International Nuclear Information System (INIS)

    Bellissent-Funel, M.C.

    1994-01-01

    A critical review of what has been achieved on the structure of liquids and solutions and the capabilities and developments of neutron scattering in this domain, are presented. A great variety of simple to complex systems has been investigated with the aim of obtaining a full microscopic description of the structure. Selected examples demonstrate the neutron scattering determination of interaction potentials, intermolecular structures and partial structure factors of complex systems. The isotopic substitution method is illustrated by the application to the study of the solvation of ions in aqueous and non aqueous solutions. (author). 9 figs., 32 refs

  9. Theoretical study of γ-aminobutyric acid conformers: Intramolecular interactions and ionization energies

    Science.gov (United States)

    Wang, Ke-Dong; Wang, Mei-Ting; Meng, Ju

    2014-10-01

    Allowing for all combinations of internal single-bond rotamers, 1,296 unique trial structures of γ-Aminobutyric acid (GABA) are obtained. All of these structures are optimized at the M06-2X level of theory and a total of 68 local minimal conformers are found. The nine low-lying conformers are used for further studies. According to the calculated relative Gibbs free energies at M06-2X level of theory, we find that the dispersion is important for the relative energy of GABA. The intramolecular hydrogen bonds and hyperconjugative interaction and their effects on the conformational stability are studied. The results show that both of them have great influence on the conformers. The vertical ionization energies (VIE) are calculated and match the experimental data well. The results show that the neutral GABA in the gas phase is a multi-conformer system and at least four conformations exist.

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

    OpenAIRE

    Kumar, Ajay

    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...

  11. Beam shaping for conformal fractionated stereotactic radiotherapy: a modeling study

    International Nuclear Information System (INIS)

    Hacker, Fred L.; Kooy, Hanne M.; Bellerive, Marc R.; Killoran, Joseph H.; Leber, Zachary H.; Shrieve, Dennis C.; Tarbell, Nancy J.; Loeffler, Jay S.

    1997-01-01

    Purpose: The patient population treated with fractionated stereotactic radiotherapy (SRT) is significantly different than that treated with stereotactic radiosurgery (SRS). Generally, lesions treated with SRT are larger, less spherical, and located within critical regions of the central nervous system; hence, they offer new challenges to the treatment planner. Here a simple, cost effective, beam shaping system has been evaluated relative to both circular collimators and an ideal dynamically conforming system for effectiveness in providing conformal therapy for these lesions. Methods and Materials: We have modeled a simple system for conformal arc therapy using four independent jaws. The jaw positions and collimator angle are changed between arcs but held fixed for the duration of each arc. Eleven previously treated SRT cases have been replanned using this system. The rectangular jaw plans were then compared to the original treatment plans which used circular collimators. The plans were evaluated with respect to tissue sparing at 100%, 80%, 50%, and 20% of the prescription dose. A plan was also done for each tumor in which the beam aperture was continuously conformed to the beams eye view projection of the tumor. This was used as an ideal standard for conformal therapy in the absence of fluence modulation. Results: For tumors with a maximum extent of over 3.5 cm the rectangular jaw plans reduced the mean volume of healthy tissue involved at the prescription dose by 57% relative to the circular collimator plans. The ideal conformal plans offered no significant further improvement at the prescription dose. The relative advantage of the rectangular jaw plans decreased at lower isodoses so that at 20% of the prescription dose tissue involvement for the rectangular jaw plans was equivalent to that for the circular collimator plans. At these isodoses the ideal conformal plans gave substantially better tissue sparing. Conclusion: A simple and economical field shaping

  12. 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.

  13. The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution

    OpenAIRE

    Hammel, Michal; Němeček, Daniel; Keightley, J. Andrew; Thomas, George J.; Geisbrecht, Brian V.

    2007-01-01

    The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein–protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data r...

  14. Conformational composition of neutral leucine. Matrix isolation infrared and ab initio study

    International Nuclear Information System (INIS)

    Stepanian, Stepan G.; Ivanov, Alexander Yu.; Adamowicz, Ludwik

    2013-01-01

    Highlights: • FTIR spectra of leucine isolated in argon, neon and xenon matrices are obtained. • UV irradiation is used to separate bands of the leucine conformers. • Populations of the leucine conformers is determined. - Abstract: Low-temperature matrix-isolation FTIR spectroscopy and ab initio calculations are employed to determine conformational composition of neutral leucine. The presence of three leucine conformers in the matrices is revealed. This is in agreement with the results of a detailed study of the potential energy surface of leucine which demonstrates that only five out of 105 possible conformers should have populations in the matrices larger than 2% and only three conformers, which are the ones detected in the experiment, should have populations larger than 10%. UV irradiation of the matrix samples are used to separate bands of the different conformers. We also show that the populations of the leucine conformers in the gas phase at 440 K are significantly different from the ones in matrices. The population of the lowest energy conformer in the gas phase being approximately 23% in the gas phase increases to over 64% in matrices

  15. 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…

  16. Theoretical and NMR conformational studies of β-proline oligopeptides with alternating chirality of pyrrolidine units

    Science.gov (United States)

    Mantsyzov, Alexey B.; Savelyev, Oleg Y.; Ivantcova, Polina M.; Bräse, Stefan; Kudryavtsev, Konstantin V.; Polshakov, Vladimir I.

    2018-03-01

    Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

  17. Theoretical and NMR Conformational Studies of β-Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units

    Directory of Open Access Journals (Sweden)

    Alexey B. Mantsyzov

    2018-03-01

    Full Text Available Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

  18. 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.

  19. Complete conformal classification of the Friedmann–Lemaître–Robertson–Walker solutions with a linear equation of state

    Science.gov (United States)

    Harada, Tomohiro; Carr, B. J.; Igata, Takahisa

    2018-05-01

    We completely classify Friedmann–Lemaître–Robertson–Walker solutions with spatial curvature and equation of state , according to their conformal structure, singularities and trapping horizons. We do not assume any energy conditions and allow , thereby going beyond the usual well-known solutions. For each spatial curvature, there is an initial spacelike big-bang singularity for w  >  ‑1/3 and , while there is no big-bang singularity for w  big-bang singularity. For each spatial curvature, there is a final spacelike future big-rip singularity for w  big-rip singularity, then bounces and blows up at a final spacelike future big-rip singularity. For w    ‑1/3, the universe contracts from infinity, then bounces and expands to infinity; for  ‑1  big-bang singularity and contracts to a big-crunch singularity; for w  <  ‑1, it expands from a regular null hypersurface and contracts to another regular null hypersurface.

  20. Conformational study of glyoxal bis(amidinohydrazone) by ab initio methods

    Science.gov (United States)

    Mannfors, B.; Koskinen, J. T.; Pietilä, L.-O.

    1997-08-01

    We report the first ab initio molecular orbital study on the ground state of the endiamine tautomer of glyoxal bis(amidinohydrazone) (or glyoxal bis(guanylhydrazone), GBG) free base. The calculations were performed at the following levels of theory: Hartree-Fock, second-order Møller-Plesset perturbation theory and density functional theory (B-LYP and B3-LYP) as implemented in the Gaussian 94 software. The standard basis set 6-31G(d) was found to be sufficient. The default fine grid of Gaussian 94 was used in the density functional calculations. Molecular properties, such as optimized structures, total energies and the electrostatic potential derived (CHELPG) atomic charges, were studied as functions of C-C and N-N conformations. The lowest energy conformation was found to be all- trans, in agreement with the experimental solid-state structure. The second conformer with respect to rotation around the central C-C bond was found to be the cis conformer with an MP2//HF energy of 4.67 kcal mol -1. For rotation around the N-N bond the energy increased monotonically from the trans conformation to the cis conformation, the cis energy being very high, 22.01 kcal mol -1 (MP2//HF). The atomic charges were shown to be conformation dependent, and the bond charge increments and especially the conformational changes of the bond charge increments were found to be easily transferable between structurally related systems.

  1. Study of the flow development of polymer solutions through capillaries

    International Nuclear Information System (INIS)

    Perez-Gonzalez, J.; De Vargas, L.; Tejero, M.

    1991-01-01

    Flow experiments through capillaries with semirigid and rigid polymers in aqueous solutions were carried out in order to study the dependence of the flow development on the molecular conformation and the length to diameter ratio (L/D), of the capillary at relatively low shear rates. It was found that the apparent viscosity has a strong dependence upon the ratio L/D for a given shear rate, although an asymptotic value is reached. This dependence was reflected in the non-linearity of Bagley's plots. The asymptotic value was attained at lower L/D values for semirigid molecules than for rigid ones, showing the influence of the molecular conformation on the flow field development due to the different modes of relaxation for each type of molecule. (Author)

  2. PMMA-g-OEtOx Graft Copolymers: Influence of Grafting Degree and Side Chain Length on the Conformation in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Irina Muljajew

    2018-03-01

    Full Text Available Depending on the degree of grafting (DG and the side chain degree of polymerization (DP, graft copolymers may feature properties similar to statistical copolymers or to block copolymers. This issue is approached by studying aqueous solutions of PMMA-g-OEtOx graft copolymers comprising a hydrophobic poly(methyl methacrylate (PMMA backbone and hydrophilic oligo(2-ethyl-2-oxazoline (OEtOx side chains. The graft copolymers were synthesized via reversible addition-fragmentation chain transfer (RAFT copolymerization of methyl methacrylate (MMA and OEtOx-methacrylate macromonomers of varying DP. All aqueous solutions of PMMA-g-OEtOx (9% ≤ DG ≤ 34%; 5 ≤ side chain DP ≤ 24 revealed lower critical solution temperature behavior. The graft copolymer architecture significantly influenced the aggregation behavior, the conformation in aqueous solution and the coil to globule transition, as verified by means of turbidimetry, dynamic light scattering, nuclear magnetic resonance spectroscopy, and analytical ultracentrifugation. The aggregation behavior of graft copolymers with a side chain DP of 5 was significantly affected by small variations of the DG, occasionally forming mesoglobules above the cloud point temperature (Tcp, which was around human body temperature. On the other hand, PMMA-g-OEtOx with elongated side chains assembled into well-defined structures below the Tcp (apparent aggregation number (Nagg = 10 that were able to solubilize Disperse Orange 3. The thermoresponsive behavior of aqueous solutions thus resembled that of micelles comprising a poly(2-ethyl-2-oxazoline (PEtOx shell (Tcp > 60 °C.

  3. Study on fusion energy conformity with global environmental issues

    International Nuclear Information System (INIS)

    Kurihara, Kenichi

    1998-01-01

    Global environmental conformity has been one of the most important issues discussed recently as being required for all human activities. From this point of view, this report investigates whether nuclear fusion can be a benign energy source for the global environment. First of all, we chose the following global environmental problems: (1) Global warming, (2) Acid rain, (3) Ozonosphere destruction, (4) Air pollution, (5) Environmental hormones, (6) Radiation and radioactive materials, (7) Electromagnetic waves, and (8) Heat drainage from an energy source. Secondly, these problems were fully surveyed in terms of their relationships with proposed nuclear fusion power plant. Finally, as a result of this discussion, it was confirmed that a fusion power plant would not produce any new problems, but would partially contribute to solving some of the environmental problems. (author)

  4. Conformations of Trimethyl Phosphite: a Matrix Isolation Infrared and AB Initio Study

    Science.gov (United States)

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

    2011-06-01

    Hyperconjugative interactions have received considerable attention because of its importance in determining structure and reactivity in organic compounds. In all these molecules, our studies, as many others in the literature, indicated that the O-P-O and O-C-O segments played a crucial role in conformational preferences. In the case of the organic phosphates, in addition to the O-P-O segments, the P=O group was also found to influence the structures. To address this issue further, it was thought interesting to study the conformations of trimethylphosphite (TMPhite), which lacks a P=O group. A comparison of the conformations of trimethylphosphate (TMP) and TMPhite was expected to highlight the role of the P=O group in the conformational preference of organic phosphates, which is the motivation for the present work. The conformations of TMPhite were studied using matrix isolation infrared spectroscopy. TMPhite was trapped in a nitrogen matrix using an effusive source maintained at 298 K and 410 K and also a supersonic source. These experiments were designed to enable us to assign the infrared features of the higher energy conformer(s). As a result of these experiments, infrared spectra of the conformations of TMPhite were obtained. The experimental studies were supported by ab initio computations performed at the B3LYP/6-31++G** level. Computations indicated four minima corresponding to conformers with the following symmetries: C_1, C_s, C1a and C_3, given in order of increasing energy. This conformational picture was clearly different from that of TMP, in which the C_3 was the lowest energy structure, thereby clearly indicating the role of the P=O group in structural preferences in these systems. We also performed a photochemical insertion of oxygen in TMPhite to produce TMP in the matrix, in an effort to correlate the conformers of the two molecules. These experiments also gave rise to interesting side reactions, where in addition to TMP, we also observed the

  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. 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.

  7. Accessibility of nucleic acid-complexed biomolecules to hydroxyl radicals correlates with their conformation: a fluorescence polarization spectroscopy study

    International Nuclear Information System (INIS)

    Makrigiorgos, G.M.; Bump, E.; Huang, C.; Kassis, A.I.; Baranowska-Kortylewicz, J.

    1994-01-01

    A fluorescence methodology has been developed to examine the relationship between the conformational state of specific biomolecules in simple chromatin models and their accessibility to hydroxyl radicals ( . OH). Polylysine and histone H1 were labelled with SECCA, the succinimidyl ester of coumarin-3-carboxylic acid, which generates the fluorescent derivative 7-OH-SECCA following its interaction with radiation-induced . OH in aqueous solution. The fluorescence induced per unit γ-ray dose reflecting the accessibility of . OH to such SECCA-conjugated biomolecules was recorded. The biomolecules were also labelled with the fluorescent derivative 7-OH-SECCA in trace amounts to study their conformation under identical conditions via fluorescence polarization spectroscopy. (author)

  8. Conformational study on cyclic melanocortin ligands and new insight into their binding mode at the MC4 receptor.

    Science.gov (United States)

    Grieco, Paolo; Brancaccio, Diego; Novellino, Ettore; Hruby, Victor J; Carotenuto, Alfonso

    2011-09-01

    The melanocortin receptors are involved in many physiological functions, including pigmentation, sexual function, feeding behavior, and energy homeostasis, making them potential targets to treat obesity, sexual dysfunction, etc. Understanding the basis of the ligand-receptor interactions is crucial for the design of potent and selective ligands for these receptors. The conformational preferences of the cyclic melanocortin ligands MTII (Ac-Nle(4)-c[Asp(5)-His(6)-DPhe(7)-Arg(8)-Trp(9)-Lys(10)]-NH(2)) and SHU9119 (Ac-Nle(4)-c[Asp(5)-His(6)-DNal(2')(7)-Arg(8)-Trp(9)-Lys(10)]-NH(2)), which show agonist and antagonist activity at the h-MC4R, respectively, were comprehensively investigated by solution NMR spectroscopy in different environments. In particular, water and water/DMSO (8:2) solutions were used as isotropic solutions and an aqueous solution of DPC (dodecylphosphocholine) micelles was used as a membrane mimetic environment. NMR-derived conformations of these two ligands were docked within h-MC4R models. NMR and docking studies revealed intriguing differences which can help explain the different activities of these two ligands. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  9. Conformational reduction of DOPA in the gas phase studied by laser desorption supersonic jet laser spectroscopy.

    Science.gov (United States)

    Ishiuchi, Shun-ichi; Mitsuda, Haruhiko; Asakawa, Toshiro; Miyazaki, Mitsuhiko; Fujii, Masaaki

    2011-05-07

    The conformational reduction in catecholamine neurotransmitters was studied by resonance enhanced multi photon ionization (REMPI), ultraviolet-ultraviolet (UV-UV) hole burning and infrared (IR) dip spectroscopy with applying a laser desorption supersonic jet technique to DOPA, which is one of the catecholamine neurotransmitters and has one more phenolic OH group than tyrosine. It is concluded that DOPA has a single observable conformer in the gas phase at low temperature. Quantum chemical calculations at several levels with or without the dispersion correction were also carried out to study stable conformations. From the comparison between the computational IR spectra and the experimental ones, the most stable structure was determined. It is strongly suggested that the conformational reduction is caused by electrostatic interactions, such as a dipole-dipole interaction, between the chain and OH groups. This journal is © the Owner Societies 2011

  10. DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule.

    Science.gov (United States)

    Pandey, Urmila; Srivastava, Mayuri; Singh, R P; Yadav, R A

    2014-08-14

    The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G(**) level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G(**) method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. 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.

  12. Self-assembly, Dynamics and Chirality of Conformational Switches on Metal Surfaces Studied by UHV-STM

    DEFF Research Database (Denmark)

    Nuermaimaiti, Ajiguli

    2013-01-01

    structures formed by the conformational switches and statistical analysis of conformational states, a detailed study of dynamic processes is performed by acquiring time-resolved STM data. Furthermore, one of the possible applications of conformational switches towards inducing chirality in surface assemblies...

  13. Conformation radiotherapy and conformal radiotherapy

    International Nuclear Information System (INIS)

    Morita, Kozo

    1999-01-01

    In order to coincide the high dose region to the target volume, the 'Conformation Radiotherapy Technique' using the multileaf collimator and the device for 'hollow-out technique' was developed by Prof. S. Takahashi in 1960. This technique can be classified a type of 2D-dynamic conformal RT techniques. By the clinical application of this technique, the late complications of the lens, the intestine and the urinary bladder after radiotherapy for the maxillary cancer and the cervical cancer decreased. Since 1980's the exact position and shape of the tumor and the surrounding normal tissues can be easily obtained by the tremendous development of the CT/MRI imaging technique. As a result, various kinds of new conformal techniques such as the 3D-CRT, the dose intensity modulation, the tomotherapy have been developed since the beginning of 1990'. Several 'dose escalation study with 2D-/3D conformal RT' is now under way to improve the treatment results. (author)

  14. Computational Replication of the Primary Isotope Dependence of Secondary Kinetic Isotope Effects in Solution Hydride-Transfer Reactions: Supporting the Isotopically Different Tunneling Ready State Conformations.

    Science.gov (United States)

    Derakhshani-Molayousefi, Mortaza; Kashefolgheta, Sadra; Eilers, James E; Lu, Yun

    2016-06-30

    We recently reported a study of the steric effect on the 1° isotope dependence of 2° KIEs for several hydride-transfer reactions in solution (J. Am. Chem. Soc. 2015, 137, 6653). The unusual 2° KIEs decrease as the 1° isotope changes from H to D, and more in the sterically hindered systems. These were explained in terms of a more crowded tunneling ready state (TRS) conformation in D-tunneling, which has a shorter donor-acceptor distance (DAD) than in H-tunneling. To examine the isotopic DAD difference explanation, in this paper, following an activated motion-assisted H-tunneling model that requires a shorter DAD in a heavier isotope transfer process, we computed the 2° KIEs at various H/D positions at different DADs (2.9 Å to 3.5 Å) for the hydride-transfer reactions from 2-propanol to the xanthylium and thioxanthylium ions (Xn(+) and TXn(+)) and their 9-phenyl substituted derivatives (Ph(T)Xn(+)). The calculated 2° KIEs match the experiments and the calculated DAD effect on the 2° KIEs fits the observed 1° isotope effect on the 2° KIEs. These support the motion-assisted H-tunneling model and the isotopically different TRS conformations. Furthermore, it was found that the TRS of the sterically hindered Ph(T)Xn(+) system does not possess a longer DAD than that of the (T)Xn(+) system. This predicts a no larger 1° KIE in the former system than in the latter. The observed 1° KIE order is, however, contrary to the prediction. This implicates the stronger DAD-compression vibrations coupled to the bulky Ph(T)Xn(+) reaction coordinate.

  15. Conformable Fractional Bessel Equation and Bessel Functions

    OpenAIRE

    Gökdoğan, Ahmet; Ünal, Emrah; Çelik, Ercan

    2015-01-01

    In this work, we study the fractional power series solutions around regular singular point x=0 of conformable fractional Bessel differential equation and fractional Bessel functions. Then, we compare fractional solutions with ordinary solutions. In addition, we present certain property of fractional Bessel functions.

  16. The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution.

    Science.gov (United States)

    Silva, Daniel L; Murugan, N Arul; Kongsted, Jacob; Rinkevicius, Zilvinas; Canuto, Sylvio; Ågren, Hans

    2012-07-19

    Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

  17. Stability studies of oxytetracycline in methanol solution

    Science.gov (United States)

    Wang, Wei; Wu, Nan; Yang, Jinghui; Zeng, Ming; Xu, Chenshan; Li, Lun; Zhang, Meng; Li, Liting

    2018-02-01

    As one kind of typical tetracycline antibiotics, antibiotic residues of oxytetracycline have been frequently detected in many environmental media. In this study, the stability of oxytetracycline in methanol solution was investigated by high-performance liquid chromatography combined with UV-vis (HPLC-UV). The results show that the stability of oxytetracycline in methanol solution is highly related to its initial concentration and the preserved temperature. Under low temperature condition, the solution was more stable than under room temperature preservation. Under the same temperature preservation condition, high concentrations of stock solutions are more stable than low concentrations. The study provides a foundation for preserving the oxytetracycline-methanol solution.

  18. Methodologies for conformational studies of oligo- and poly-glucans: crystallography and molecular mechanics

    International Nuclear Information System (INIS)

    Tran, Huu Vinh

    1983-01-01

    After some considerations on the conformational analysis of polysaccharides, this research thesis outlines the interest of molecular mechanics as a method to study these components. Technical aspects are presented. The author reports the prediction of the conformations of some specific cyclic oligomers (glucans, glucore), the use of X-ray diffraction to study glucides (and the limitations of this method). He reports the search for another investigation method: relationships between X rays and molecular mechanics, situation with respect to other crystallographic methods, presentation of principle of the 'Packing' method, and applications. He reports the study of regular conformations of polysaccharides, the study of the statistic configuration of polymer chains and the application to alpha-glucans

  19. Conformational stabilization of the membrane embedded targeting domain of the lysosomal peptide transporter TAPL for solution NMR

    Energy Technology Data Exchange (ETDEWEB)

    Tumulka, Franz [Goethe-University Frankfurt, Institute of Biochemistry, Biocenter (Germany); Roos, Christian; Loehr, Frank [Goethe-University Frankfurt, Institute of Biophysical Chemistry, Biocenter (Germany); Bock, Christoph [Goethe-University Frankfurt, Institute of Biochemistry, Biocenter (Germany); Bernhard, Frank; Doetsch, Volker [Goethe-University Frankfurt, Institute of Biophysical Chemistry, Biocenter (Germany); Abele, Rupert, E-mail: abele@em.uni-frankfurt.de [Goethe-University Frankfurt, Institute of Biochemistry, Biocenter (Germany)

    2013-10-15

    The ATP binding cassette transporter TAPL translocates cytosolic peptides into the lumen of lysosomes driven by the hydrolysis of ATP. Functionally, this transporter can be divided into coreTAPL, comprising the transport function, and an additional N-terminal transmembrane domain called TMD0, which is essential for lysosomal targeting and mediates the interaction with the lysosomal associated membrane proteins LAMP-1 and LAMP-2. To elucidate the structure of this unique domain, we developed protocols for the production of high quantities of cell-free expressed TMD0 by screening different N-terminal expression tags. Independently of the amino acid sequence, high expression was detected for AU-rich sequences in the first seven codons, decreasing the free energy of RNA secondary structure formation at translation initiation. Furthermore, avoiding NGG codons in the region of translation initiation demonstrated a positive effect on expression. For NMR studies, conditions were optimized for high solubilization efficiency, long-term stability, and high quality spectra. A most critical step was the careful exchange of the detergent used for solubilization by the detergent dihexanoylphosphatidylcholine. Several constructs of different size were tested in order to stabilize the fold of TMD0 as well as to reduce the conformation exchange. NMR spectra with sufficient resolution and homogeneity were finally obtained with a TMD0 derivative only modified by a C-terminal His{sub 10}-tag and containing a codon optimized AT-rich sequence.

  20. 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.

  1. 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

    2015-02-01

    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.

  2. 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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

  4. 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.

  5. 3D Conformal radiotherapy for gastric cancer-results of a comparative planning study

    International Nuclear Information System (INIS)

    Leong, Trevor; Willis, David; Joon, Daryl Lim; Condron, Sara; Hui, Andrew; Ngan, Samuel Y.K.

    2005-01-01

    Background and purpose: Many radiation oncologists are reluctant to use anteroposterior-posteroanterior (AP-PA) field arrangements when treating gastric cancer with adjuvant postoperative radiotherapy due to concerns about normal tissue toxicity, particularly in relation to the kidneys and spinal cord. In this report, we describe a multiple-field conformal radiotherapy technique, and compare this technique to the more commonly used AP-PA technique that was used in the recently reported Intergroup study (INT0116). Materials and methods: Fifteen patients with stages II-IV adenocarcinoma of the stomach were treated with adjuvant postoperative chemoradiotherapy using a standardised 3D conformal radiotherapy technique that consisted of a 'split-field', mono-isocentric arrangement employing 6 radiation fields. For each patient, a second radiotherapy treatment plan was generated utilising AP-PA fields. The two techniques were then compared for target volume coverage and dose to normal tissues using dose volume histogram (DVH) analysis. Results: The conformal technique provides more adequate coverage of the target volume with 99% of the planning target volume (PTV) receiving 95% of the prescribed dose, compared to 93% using AP-PA fields. Comparative DVHs for the right kidney, left kidney and spinal cord demonstrate lower radiation doses using the conformal technique, and although the liver dose is higher, it is still well below liver tolerance. Conclusions: 3D conformal radiotherapy produces superior dose distributions and reduced radiation doses to the kidneys and spinal cord compared to AP-PA techniques, with the potential to reduce treatment toxicity

  6. 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

  7. 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.

  8. 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.

  9. Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules

    Science.gov (United States)

    Hache, F.

    2010-06-01

    Circular dichroism (CD) is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.

  10. Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules

    Directory of Open Access Journals (Sweden)

    Hache F.

    2010-06-01

    Full Text Available Circular dichroism (CD is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.

  11. The Fab Conformations in the Solution Structure of Human Immunoglobulin G4 (IgG4) Restrict Access to Its Fc Region

    Science.gov (United States)

    Rayner, Lucy E.; Hui, Gar Kay; Gor, Jayesh; Heenan, Richard K.; Dalby, Paul A.; Perkins, Stephen J.

    2014-01-01

    Human IgG4 antibody shows therapeutically useful properties compared with the IgG1, IgG2, and IgG3 subclasses. Thus IgG4 does not activate complement and shows conformational variability. These properties are attributable to its hinge region, which is the shortest of the four IgG subclasses. Using high throughput scattering methods, we studied the solution structure of wild-type IgG4(Ser222) and a hinge mutant IgG4(Pro222) in different buffers and temperatures where the proline substitution suppresses the formation of half-antibody. Analytical ultracentrifugation showed that both IgG4 forms were principally monomeric with sedimentation coefficients s20,w0 of 6.6–6.8 S. A monomer-dimer equilibrium was observed in heavy water buffer at low temperature. Scattering showed that the x-ray radius of gyration Rg was unchanged with concentration in 50–250 mm NaCl buffers, whereas the neutron Rg values showed a concentration-dependent increase as the temperature decreased in heavy water buffers. The distance distribution curves (P(r)) revealed two peaks, M1 and M2, that shifted below 2 mg/ml to indicate concentration-dependent IgG4 structures in addition to IgG4 dimer formation at high concentration in heavy water. Constrained x-ray and neutron scattering modeling revealed asymmetric solution structures for IgG4(Ser222) with extended hinge structures. The IgG4(Pro222) structure was similar. Both IgG4 structures showed that their Fab regions were positioned close enough to the Fc region to restrict C1q binding. Our new molecular models for IgG4 explain its inability to activate complement and clarify aspects of its stability and function for therapeutic applications. PMID:24876381

  12. 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.

  13. Moessbauer and positron annihilation studies of structural modifications of hemoglobin in solution

    International Nuclear Information System (INIS)

    Oshtrakh, M.I.; Kopelyan, E.A.; Semionkin, V.A.

    1995-01-01

    Structural modifications of human adult oxyhemoglobin in concentrated solution were studied by Moessbauer and positron life-time spectroscopies. The effects of non-sterile degradation and irradiation by γ-rays were compared by both techniques. It was found that positron annihilation parameters were sensitive to the structural modifications of hemoglobin molecules in solution and could be related with the conformational states of hemoglobin. (author)15 refs.; 3 tabs

  14. Interaction of pepsin-[C16mim]Br system: interfacial dilational rheology and conformational studies.

    Science.gov (United States)

    Huang, Tian; Cao, Chong; Liu, Zi-lin; Li, Yang; Du, Feng-pei

    2014-09-21

    The interfacial rheological property is closely related to the stabilities of foams and emulsions, yet there have been limited studies on the interaction between proteins with ionic liquid-type imidazolium surfactants at the decane-water interface as well as in the bulk. Herein, we investigated the interfacial and bulk properties of pepsin (PEP) and an ionic liquid (IL), 1-hexadecyl-3-methylimidazolium bromide, [C(16)mim]Br. The interfacial pressure and dilational rheology studies were performed to describe the formation of [C(16)mim]Br-pepsin complexes. The influence of the oscillating frequency and the bulk concentration of [C(16)mim]Br on the dilational properties were explored. The conformational changes were studied by monitoring the fluorescence and far UV-CD spectra. The results reveal that the globular structure of pepsin is one of the decisive factors controlling the nature of the interfacial film. The monotonous increase in the dilational elastic modulus of pepsin-[C(16)mim]Br solutions with the surface age indicates that no loops and tails had formed. Interestingly, with an increase in the concentration of [C(16)mim]Br, the εd-c curve first passes through a plateau value due to steric hindrance and the electrostatic barrier of already absorbed tenacious pepsin-[C(16)mim]Br complexes. With the further addition of [C(16)mim]Br, the remarkable decrease in dilational elastic modulus indicates that the compact structure is destroyed gradually. The results of the fluorescence spectra and far UV-CD spectra confirm that [C(16)mim]Br did not produce perceptible changes in pepsin at the concentrations studied in the dilational experiment. Possible schematic programs of the pepsin-[C(16)mim]Br interaction model at the interface and in bulk phase are proposed.

  15. CONFORMATIONAL STUDIES OF LIGNANS FROM Durio oxleyanus Griff. (

    Directory of Open Access Journals (Sweden)

    Rudiyansyah Rudiyansyah

    2010-06-01

    Full Text Available Searching for secondary metabolites from the wood bark of Durio oxleyanus has afforded two new lignans, namely threo-carolignan Y (1 and erythro-carolignan Y (2 together with three other known lignans erythro-carolignan X (3, boehmenan X (4 and boehmenan (5. The relative configurations of compounds 1 and 2 were established by J-based configurational analysis and 2D NOESY studies.   Keywords: carolignan, threo, erythro, Durio, Bombacaceae

  16. 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.

  17. A nuclear magnetic resonance study of conformational transmission in phosphorylated pyranosides

    International Nuclear Information System (INIS)

    Vries, N.K. de.

    1987-01-01

    This thesis describes an experimental NMR study, combined with MNDO calculations, on the conformational preferences of the exocyclic bond of 6-phosphorylated pyranosides and tetrahydropyran-2-methyl compounds. The various factors influencing the rotamer population distribution around this O-C-C-O fragment, e.g. solvent polarity, stereoelectronic effects and coordination of phosphorus, are analysed. 150 refs.; 25 figs.; 16 tabs

  18. Can a combination of the conformal thin-sandwich and puncture methods yield binary black hole solutions in quasiequilibrium?

    International Nuclear Information System (INIS)

    Hannam, Mark D.; Evans, Charles R.; Cook, Gregory B.; Baumgarte, Thomas W.

    2003-01-01

    We consider combining two important methods for constructing quasiequilibrium initial data for binary black holes: the conformal thin-sandwich formalism and the puncture method. The former seeks to enforce stationarity in the conformal three-metric and the latter attempts to avoid internal boundaries, like minimal surfaces or apparent horizons. We show that these two methods make partially conflicting requirements on the boundary conditions that determine the time slices. In particular, it does not seem possible to construct slices that are quasistationary and that avoid physical singularities while simultaneously are connected by an everywhere positive lapse function, a condition which must be obtained if internal boundaries are to be avoided. Some relaxation of these conflicting requirements may yield a soluble system, but some of the advantages that were sought in combining these approaches will be lost

  19. Conformally connected universes

    International Nuclear Information System (INIS)

    Cantor, M.; Piran, T.

    1983-01-01

    A well-known difficulty associated with the conformal method for the solution of the general relativistic Hamiltonian constraint is the appearance of an aphysical ''bag of gold'' singularity at the nodal surface of the conformal factor. This happens whenever the background Ricci scalar is too large. Using a simple model, it is demonstrated that some of these singular solutions do have a physical meaning, and that these can be considered as initial data for Universe containing black holes, which are connected, in a conformally nonsingular way with each other. The relation between the ADM mass and the horizon area in this solution supports the cosmic censorship conjecture. (author)

  20. Neutron scattering study of dilute supercritical solutions

    International Nuclear Information System (INIS)

    Cochran, H.D.; Wignall, G.D.; Shah, V.M.; Londono, J.D.; Bienkowski, P.R.

    1994-01-01

    Dilute solutions in supercritical solvents exhibit interesting microstructures that are related to their dramatic macroscopic behavior. In typical attractive solutions, solutes are believed to be surrounded by clusters of solvent molecules, and solute molecules are believed to congregate in the vicinity of one another. Repulsive solutions, on the other hand, exhibit a local region of reduced solvent density around the solute with solute-solute congregation. Such microstructures influence solubility, partial molar volume, reaction kinetics, and many other properties. We have undertaken to observe these interesting microstructures directly by neutron scattering experiments on dilute noble gas systems including Ar. The three partial structure factors for such systems and the corresponding pair correlation functions can be determined by using the isotope substitution technique. The systems studied are uniquely suited for our objectives because of the large coherent neutron scattering length of the isotope 36 Ar and because of the accurate potential energy functions that are available for use in molecular simulations and theoretical calculations to be compared with the scattering results. We will describe our experiment, the unique apparatus we have built for it, and the neutron scattering results from our initial allocations of beam time. We will also describe planned scattering experiments to follow those with noble gases, including study of long-chain molecules in supercritical solvents. Such studies will involve hydrocarbon mixtures with and without deuteration to provide contrast

  1. 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.

  2. Exploratory conformational study of (+)-catechin. Modeling of the polarizability and electric dipole moment.

    Science.gov (United States)

    Bentz, Erika N; Pomilio, Alicia B; Lobayan, Rosana M

    2014-12-01

    The extension of the study of the conformational space of the structure of (+)-catechin at the B3LYP/6-31G(d,p) level of theory is presented in this paper. (+)-Catechin belongs to the family of the flavan-3-ols, which is one of the five largest phenolic groups widely distributed in nature, and whose biological activity and pharmaceutical utility are related to the antioxidant activity due to their ability to scavenge free radicals. The effects of free rotation around all C-O bonds of the OH substituents at different rings are taken into account, obtaining as the most stable conformer, one that had not been previously reported. One hundred seven structures, and a study of the effects of charge delocalization and stereoelectronic effects at the B3LYP/6-311++G(d,p) level are reported by natural bond orbital analysis, streamlining the order of these structures. For further analysis of the structural and molecular properties of this compound in a biological environment, the calculation of polarizabilities, and the study of the electric dipole moment are performed considering the whole conformational space described. The results are analyzed in terms of accumulated knowledge for (4α → 6″, 2α → O → 1″)-phenylflavans and (+)-catechin in previous works, enriching the study of both types of structures, and taking into account the importance of considering the whole conformational space in modeling both the polarizability and the electric dipole moment, also proposing to define a descriptive subspace of only 16 conformers.

  3. Proton magnetic resonance studies of 5,6-saturated thymidine derivatives produced by ionizing radiation. Conformational analysis of 6-hydroxylated diastereoisomers

    Energy Technology Data Exchange (ETDEWEB)

    Cadet, J; Ducolomb, R [CEA Centre d' Etudes Nucleaires de Grenoble, 38 (France). Lab. de Radiobiologie; Hruska, F E [Manitoba Univ., Winnipeg (Canada). Dept. of Chemistry

    1979-06-20

    The conformational properties of ten 6-hydroxylated dihydrothymidine derivatives including the various diastereoisomers of 5,6-dihydroxy-5,6-dihydrothymidine, 6-hydroxy-5,6-dihydrothymidine and 5-bromo-6-hydroxy-5,6-dihydrothymidine have been studied by 250 MHz proton magnetic resonance in aqueous solutions. A close correlation has been established between the carbon-6 configuration and the osidic conformation. The increase in the amplitude of the puckering within the furanose ring compared to that of thymidine or 2'-deoxyuridine is more pronounced for the levortatory (6S) nucleosides than for the dextrorotatory (6R) diastereoisomers. The importance of the 2'endo conformer population decreases in the following order: (-)> (+)>thymidine. The absence of destabilizing effects on the g/sup +/ rotameric population about the C(4')-C(5') bond denotes the lack of any interaction between exocyclic hydroxymethyl group and the 6-hydroxyl function or the 2-keto group. The 5,6-saturated nucleosides adopt a preferential anti conformation. The comparison has been extended to syn nucleosides which show opposite trends in the sugar conformation and g/sup +/ distribution.

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

    International Nuclear Information System (INIS)

    Birdsall, B.; Andrews, J.; Ostler, G.; Tendler, S.J.B.; Feeney, J.; Roberts, G.C.K.; Davies, R.W.; Cheung, H.T.A.

    1989-01-01

    Two mutants of Lactobacillus casei dihydrofolate reductase, Trp 21 → Leu and Asp 26 → 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. 1 H, 13 C, and 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. 1 H NMR studies of the Trp 21 → 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 → 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

  5. Solute redistribution studies in oxidised zirconium alloys

    Energy Technology Data Exchange (ETDEWEB)

    Khera, S K; Kale, G B; Gadiyar, H S [Bhabha Atomic Research Centre, Bombay (India). Metallurgy Div.

    1977-01-01

    Electron microprobe studies on solute distribution in oxide layers and in the regions near oxide metal interface have been carried out in the case of zircaloy-2 and zirconium binary alloys containing niobium, tin, iron, copper, chromium and nickel and oxidised in steam at 550 deg C. In the case of alloys having higher oxidation rates, the oxide of solute element was found to dissolve in ZrO/sub 2/ without any composition variation. However, for solute addition with limited solubility like Cr, Cu and Fe, solute enrichment at metal/oxide interface and depletion of the same matrix has been observed. The intensity profiles for nickel distribution were also found to be identical to Fe or Cr distribution. The mode of solute distribution has been discussed in relation to oxidation behaviour of these alloys.

  6. Conformational study of sarcosine as probed by matrix-isolation FT-IR spectroscopy and molecular orbital calculations

    OpenAIRE

    Gómez-Zavaglia, Andrea; Fausto, R.

    2003-01-01

    Sarcosine (N-methylglycine) has been studied by matrix-isolation FT-IR spectroscopy and molecular orbital calculations undertaken at the DFT/B3LYP and MP2 levels of theory with the 6-311++G(d, p) and 6-31++G(d, p) basis set, respectively. Eleven different conformers were located in the potential energy surface (PES) of sarcosine, with the ASC conformer being the ground conformational state. This form is analogous to the glycine most stable conformer and is characterized by a NH...O= intramole...

  7. A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains.

    Science.gov (United States)

    Fox, Stephen J; Gourdain, Stephanie; Coulthurst, Anton; Fox, Clare; Kuprov, Ilya; Essex, Jonathan W; Skylaris, Chris-Kriton; Linclau, Bruno

    2015-01-19

    A comprehensive conformational analysis of both 2,3-difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2-difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3-difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn-difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 3-D conformal HDR brachytherapy as monotherapy for localized prostate cancer. A pilot study

    International Nuclear Information System (INIS)

    Martin, T.; Baltas, D.; Kurek, R.; Roeddiger, S.; Kontova, M.; Anagnostopoulos, G.; Skazikis, G.; Zamboglou, N.; Dannenberg, T.; Buhleier, T.; Tunn, U.

    2004-01-01

    Purpose: pilot study to evaluate feasibility, acute toxicity and conformal quality of three-dimensional (3-D) conformal high-dose-rate (HDR) brachytherapy as monotherapy for localized prostate cancer using intraoperative real-time planning. Patients and methods: between 05/2002 and 05/2003, 52 patients with prostate cancer, prostate-specific antigen (PSA) ≤ 10 ng/ml, Gleason score ≤ 7 and clinical stage ≤ T2a were treated. Median PSA was 6.4 ng/ml and median Gleason score 5. 24/52 patients had stage T1c and 28/52 stage T2a. For transrectal ultrasound-(TRUS-)guided transperineal implantation of flexible plastic needles into the prostate, the real-time HDR planning system SWIFT trademark was used. After implantation, CT-based 3-D postplanning was performed. All patients received one implant for four fractions of HDR brachytherapy in 48 h using a reference dose (D ref ) of 9.5 Gy to a total dose of 38.0 Gy. Dose-volume histograms (DVHs) were analyzed to evaluate the conformal quality of each implant using D 90 , D 10 urethra, and D 10 rectum. Acute toxicity was evaluated using the CTC (common toxicity criteria) scales. Results: median D 90 was 106% of D ref (range: 93-115%), median D 10 urethra 159% of D ref (range: 127-192%), and median D 10 rectum 55% of D ref (range: 35-68%). Median follow-up is currently 8 months. In 2/52 patients acute grade 3 genitourinary toxicity was observed. No gastrointestinal toxicity > grade 1 occurred. Conclusion: 3-D conformal HDR brachytherapy as monotherapy using intraoperative real-time planning is a feasible and highly conformal treatment for localized prostate cancer associated with minimal acute toxicity. Longer follow-up is needed to evaluate late toxicity and biochemical control. (orig.)

  9. Adaptive solution of the multigroup diffusion equation on irregular structured grids using a conforming finite element method formulation

    International Nuclear Information System (INIS)

    Ragusa, J. C.

    2004-01-01

    In this paper, a method for performing spatially adaptive computations in the framework of multigroup diffusion on 2-D and 3-D Cartesian grids is investigated. The numerical error, intrinsic to any computer simulation of physical phenomena, is monitored through an a posteriori error estimator. In a posteriori analysis, the computed solution itself is used to assess the accuracy. By efficiently estimating the spatial error, the entire computational process is controlled through successively adapted grids. Our analysis is based on a finite element solution of the diffusion equation. Bilinear test functions are used. The derived a posteriori error estimator is therefore based on the Hessian of the numerical solution. (authors)

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

    OpenAIRE

    Ammar Saleem Khazaal; Nizar N Ismeel; Abdel fattah K. Hussein

    2018-01-01

    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,...

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

    International Nuclear Information System (INIS)

    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 + 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 -10 (year) -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

  12. 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.

  13. 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.

  14. 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.

  15. Spectroscopic and theoretical studies on the aromaticity of pyrrol-2-yl-carbonyl conformers

    Science.gov (United States)

    Dubis, Alina T.; Wojtulewski, Sławomir; Filipkowski, Karol

    2013-06-01

    The aromaticity of s-cis and s-trans pyrrol-2-yl carbonyl conformers was studied by FT-IR, 1H NMR spectroscopy and DFT calculations at the B3LYP/6-311++G(d,p) level of theory. The Harmonic Oscillator Model of Aromaticity (HOMA) and Nucleus Independent Chemical Shift (NICS) indices were calculated to estimate π-electron delocalization in the pyrrole ring. The usefulness of infrared spectroscopy in the evaluation of the aromaticity of the homogeneous set of pyrroles is discussed. The influence of 2-substitution on different aspects of aromaticity and stability of the pyrrol-2-yl carbonyl conformers is also discussed. It is concluded that the substitution effect of the title pyrrole derivatives can be explained on the basis of theoretical and experimental measurements of π-electron delocalization, including IR data.

  16. Design of ET(B) receptor agonists: NMR spectroscopic and conformational studies of ET7-21[Leu7, Aib11, Cys(Acm)15].

    Science.gov (United States)

    Hewage, Chandralal M; Jiang, Lu; Parkinson, John A; Ramage, Robert; Sadler, Ian H

    2002-03-01

    In a previous report we have shown that the endothelin-B receptor-selective linear endothelin peptide, ET-1[Cys (Acm)1,15, Ala3, Leu7, Aib11], folds into an alpha-helical conformation in a methanol-d3/water co-solvent [Hewage et al. (1998) FEBS Lett., 425, 234-238]. To study the requirements for the structure-activity relationships, truncated analogues of this peptide were subjected to further studies. Here we report the solution conformation of ET7-21[Leu7, Aib11, Cys(Acm)15], in a methanol-d3/water co-solvent at pH 3.6, by NMR spectroscopic and molecular modelling studies. Further truncation of this short peptide results in it displaying poor agonist activity. The modelled structure shows that the peptide folds into an alpha-helical conformation between residues Lys9-His16, whereas the C-terminus prefers no fixed conformation. This truncated linear endothelin analogue is pivotal for designing endothelin-B receptor agonists.

  17. 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.)

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

    International Nuclear Information System (INIS)

    Azreg-Ainou, Mustapha

    2014-01-01

    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.)

  19. Biotransformation of Geniposide into Genipin by Immobilized Trichoderma reesei and Conformational Study of Genipin

    Directory of Open Access Journals (Sweden)

    Yishun Yang

    2018-01-01

    Full Text Available Trichoderma reesei QM9414, Trichoderma viride 3.316, Aspergillus niger M85, and Aspergillus niger M92 were screened for hydrolyzing geniposide into genipin. T. reesei was selected according to the β-glucosidase activity of the fermentation broths using geniposide as a substrate. T. reesei was immobilized by embedding method using sodium alginate as the carrier. Geniposide was hydrolyzed by immobilized T. reesei at 28°C (200 rpm for 34 h, and the yield of genipin was 89%. The product was purified and identified by UV, IR, EIMS, and 1H-NMR. Since there were two sets of signals in 1H-NMR spectra, a series of experiments were performed and verified that the existence of two conformations was the main reason. Generally, biotransformation of geniposide into genipin by immobilized T. reesei provides a promising solution to the genipin production.

  20. Representation theory of current algebra and conformal field theory on Riemann surfaces

    International Nuclear Information System (INIS)

    Yamada, Yasuhiko

    1989-01-01

    We study conformal field theories with current algebra (WZW-model) on general Riemann surfaces based on the integrable representation theory of current algebra. The space of chiral conformal blocks defined as solutions of current and conformal Ward identities is shown to be finite dimensional and satisfies the factorization properties. (author)

  1. Regulated bioanalysis of conformers - A case study with ASP2151 in dog plasma and urine.

    Science.gov (United States)

    Ohtsu, Yoshiaki; Otsuka, Shohei; Nakamura, Takeshi; Noguchi, Kiyoshi

    2015-08-01

    We developed and validated bioanalytical methods for a potent helicase-primase inhibitor ASP2151 that has two conformers. These conformers elute as unseparated broad peaks under ordinary high-performance liquid chromatographic conditions, indicating discernable differences in hydrophobicity. We observed that column temperature and mobile phase pH have no effect on these peaks and that conformers form a single symmetrical peak when tetrahydrofuran is added to the mobile phase. In addition, we needed to develop semi-automated methods where inter-conversion of the conformers is unlikely to cause sample-to-sample extraction variability. Briefly, following the addition of deuterium-labeled ASP2151 as an internal standard (IS), dog plasma samples or acetonitrile-added urine samples were filtrated. The filtrates were then injected into a column-switching liquid chromatography-tandem mass spectrometry (LC-MS/MS) system and trapped onto an extraction column. Extracts were back-flushed onto an analytical C18 column (4.6×50mm, 3μm) with a mobile phase consisting of methanol, tetrahydrofuran, and 20mmol/L ammonium acetate (45:5:50, v/v/v). The eluent was monitored in the negative atmospheric pressure chemical ionization mode. The calibration curve was linear over a range of 5-1000ng/mL for plasma and 0.5-100μg/mL for urine. Validation data met the acceptance criteria in accordance with regulatory guidance and demonstrated that these methods were selective, accurate, and reproducible. In addition, the present methods were successfully applied to a pharmacokinetic study in dogs. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. 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 fo...... in industry. Graphical Abstract ᅟ....

  3. 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...

  4. A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria.

    Science.gov (United States)

    Javornik, Uroš; Plavec, Janez; Wang, Baifan; Graham, Steven M

    2018-01-02

    A combined variable temperature 600 MHz NMR/molecular dynamics study of the Ca 2+ -release agent cyclic adenosine 5'-diphosphate ribose (cADPR) was conducted. In addition to elucidating the major and minor orientations of the conformationally flexible furanose rings, γ- (C4'-C5'), and β- (C5'-O5') bonds, the thermodynamics (ΔH o , ΔS o ) associated with each of these conformational equilibria were determined. Both furanose rings were biased towards a south conformation (64-74%) and both β-bonds heavily favored trans conformations. The R-ring γ-bond was found to exist almost exclusively as the γ + conformer, whereas the A-ring γ-bond was a mixture of the γ + and γ t conformers, with the trans conformer being slightly favored. Enthalpic factors accounted for most of the observed conformational preferences, although the R-ring furanose exists as its major conformation based solely on entropic factors. There was excellent agreement between the NMR and MD results, particularly with regard to the conformer identities, but the MD showed a bias towards γ + conformers. The MD results showed that both N-glycosidic χ-bonds are exclusively syn. Collectively the data allowed for the construction of a model for cADPR in which many of the conformationally flexible units in fact effectively adopt single orientations and where most of the conformational diversity resides in its A-ring furanose and γ-bond. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Rheological study of chitosan in solution

    International Nuclear Information System (INIS)

    Silva, Italo Guimaraes Medeiros da; Alves, Keila dos Santos; Balaban, Rosangela de Carvalho

    2009-01-01

    Chitosan is an abundant biopolymer with remarkable physicochemical and biological properties, usually employed in a wide range of applications. It acts as a cationic polyelectrolyte in aqueous acid solutions, leading to unique characteristics. In this work, chitosan was characterized by 1 H NMR and its rheological behavior were studied as function of chitosan sample, shear rate, polymer concentration, ionic strength, time and temperature. In order to calculate rheological parameters and to understand the macromolecular dynamic in solution, the Otswald-de Waele model was fitted. (author)

  6. 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...

  7. Quantum Conformal Algebras and Closed Conformal Field Theory

    CERN Document Server

    Anselmi, D

    1999-01-01

    We investigate the quantum conformal algebras of N=2 and N=1 supersymmetric gauge theories. Phenomena occurring at strong coupling are analysed using the Nachtmann theorem and very general, model-independent, arguments. The results lead us to introduce a novel class of conformal field theories, identified by a closed quantum conformal algebra. We conjecture that they are the exact solution to the strongly coupled large-N_c limit of the open conformal field theories. We study the basic properties of closed conformal field theory and work out the operator product expansion of the conserved current multiplet T. The OPE structure is uniquely determined by two central charges, c and a. The multiplet T does not contain just the stress-tensor, but also R-currents and finite mass operators. For this reason, the ratio c/a is different from 1. On the other hand, an open algebra contains an infinite tower of non-conserved currents, organized in pairs and singlets with respect to renormalization mixing. T mixes with a se...

  8. 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

  9. 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

  10. Conformational effect on small angle neutron scattering behavior of interacting polyelectrolyte solutions: a perspective of integral equation theory.

    Science.gov (United States)

    Shew, Chwen-Yang; Do, Changwoo; Hong, Kunlun; Liu, Yun; Porcar, Lionel; Smith, Gregory S; Chen, Wei-Ren

    2012-07-14

    We present small angle neutron scattering (SANS) measurements of deuterium oxide (D(2)O) solutions of linear and star sodium poly(styrene sulfonate) (NaPSS) as a function of polyelectrolyte concentration. Emphasis is on understanding the dependence of their SANS coherent scattering cross section I(Q) on the molecular architecture of single polyelectrolyte. The key finding is that for a given concentration, star polyelectrolytes exhibit more pronounced characteristic peaks in I(Q), and the position of the first peak occurs at a smaller Q compared to their linear counterparts. Based on a model of integral equation theory, we first compare the SANS experimental I(Q) of salt-free polyelectrolyte solutions with that predicted theoretically. Having seen their satisfactory qualitative agreement, the dependence of counterion association behavior on polyelectrolyte geometry and concentration is further explored. Our predictions reveal that the ionic environment of polyelectrolyte exhibits a strong dependence on polyelectrolyte geometry at lower polyelectrolyte concentration. However, when both linear and star polyelectrolytes exceed their overlap concentrations, the spatial distribution of counterion is found to be essentially insensitive to polyelectrolyte geometry due to the steric effect.

  11. 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.

  12. 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.

  13. Glycation and secondary conformational changes of human serum albumin: study of the FTIR spectroscopic curve-fitting technique

    Directory of Open Access Journals (Sweden)

    Yu-Ting Huang

    2016-05-01

    Full Text Available The aim of this study was attempted to investigate both the glycation kinetics and protein secondary conformational changes of human serum albumin (HSA after the reaction with ribose. The browning and fluorescence determinations as well as Fourier transform infrared (FTIR microspectroscopy with a curve-fitting technique were applied. Various concentrations of ribose were incubated over a 12-week period at 37 ± 0.5 oC under dark conditions. The results clearly shows that the glycation occurred in HSA-ribose reaction mixtures was markedly increased with the amount of ribose used and incubation time, leading to marked alterations of protein conformation of HSA after FTIR determination. In addition, the browning intensity of reaction solutions were colored from light to deep brown, as determined by optical observation. The increase in fluorescence intensity from HSA–ribose mixtures seemed to occur more quickly than browning, suggesting that the fluorescence products were produced earlier on in the process than compounds causing browning. Moreover, the predominant α-helical composition of HSA decreased with an increase in ribose concentration and incubation time, whereas total β-structure and random coil composition increased, as determined by curve-fitted FTIR microspectroscopy analysis. We also found that the peak intensity ratios at 1044 cm−1/1542 cm−1 markedly decreased prior to 4 weeks of incubation, then almost plateaued, implying that the consumption of ribose in the glycation reaction might have been accelerated over the first 4 weeks of incubation, and gradually decreased. This study first evidences that two unique IR peaks at 1710 cm−1 [carbonyl groups of irreversible products produced by the reaction and deposition of advanced glycation end products (AGEs] and 1621 cm−1 (aggregated HSA molecules were clearly observed from the curve-fitted FTIR spectra of HSA-ribose mixtures over the course of incubation time. This study

  14. 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.

  15. 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.

  16. 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.

  17. Comparative dosimetric study of three-dimensional conformal, dynamic conformal arc, and intensity-modulated radiotherapy for brain tumor treatment using Novalis system

    International Nuclear Information System (INIS)

    Ding Meisong; Newman, Francis M.S.; Kavanagh, Brian D.; Stuhr, Kelly M.S.; Johnson, Tim K.; Gaspar, Laurie E.

    2006-01-01

    Purpose: To investigate the dosimetric differences among three-dimensional conformal radiotherapy (3D-CRT), dynamic conformal arc therapy (DCAT), and intensity-modulated radiotherapy (IMRT) for brain tumor treatment. Methods and Materials: Fifteen patients treated with Novalis were selected. We performed 3D-CRT, DCAT, and IMRT plans for all patients. The margin for the planning target volume (PTV) was 1 mm, and the specific prescription dose was 90% for all plans. The target coverage at the prescription dose, conformity index (CI), and heterogeneity index were analyzed for all plans. Results: For small tumors (PTV ≤2 cm 3 ), the three dosimetric parameters had approximate values for both 3D-CRT and DCAT plans. The CI for the IMRT plans was high. For medium tumors (PTV >2 to ≤100 cm 3 ), the three plans were competitive with each other. The IMRT plans had a greater CI, better target coverage at the prescription dose, and a better heterogeneity index. For large tumors (PTV >100 cm 3 ), the IMRT plan had good target coverage at the prescription dose and heterogeneity index and approximate CI values as those in the 3D-CRT and DCAT plans. Conclusion: The results of our study have shown that DCAT is suitable for most cases in the treatment of brain tumors. For a small target, 3D-CRT is useful, and IMRT is not recommended. For larger tumors, IMRT is superior to 3D-CRT and very competitive in sparing critical structures, especially for big tumors

  18. Study on protein conformation and adsorption behaviors in nanodiamond particle-protein complexes

    International Nuclear Information System (INIS)

    Wang Haidong; Niu, Catherine Hui; Yang Qiaoqin; Badea, Ildiko

    2011-01-01

    In the present research, the conformation of bovine serum albumin (BSA) in the nanodiamond particle (ND)-BSA complex was studied by Fourier transform infrared spectroscopy, fluorescence spectroscopy, UV-vis spectroscopy, and circular dichroism spectroscopy. The spectroscopic study revealed that most BSA structural features could be preserved in the complex though the BSA underwent conformational changes in the complex due to ND-BSA interaction. In addition, BSA adsorption isotherms and zeta-potential measurements were employed to investigate the pH dependence of the ND-BSA interaction. The changes in surface charge of the ND-BSA complex with pH variations indicated that the binding of BSA to ND might lead to not only the adsorption of BSA onto the ND surface but also the partial breakup of ND aggregates into relatively small ND-BSA aggregates because of the strong binding force between ND and BSA. The results show that ND is an excellent platform for protein immobilization with high affinity and holds great potential to be used for biosensor applications.

  19. Study on protein conformation and adsorption behaviors in nanodiamond particle-protein complexes

    Energy Technology Data Exchange (ETDEWEB)

    Wang Haidong [Department of Biomedical Engineering, University of Saskatchewan, Saskatoon, S7N 5A9 (Canada); Niu, Catherine Hui [Department of Chemical Engineering, University of Saskatchewan, Saskatoon, S7N 5A9 (Canada); Yang Qiaoqin [Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, S7N 5A9 (Canada); Badea, Ildiko, E-mail: catherine.niu@usask.ca [Drug Design and Discovery Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9 (Canada)

    2011-04-08

    In the present research, the conformation of bovine serum albumin (BSA) in the nanodiamond particle (ND)-BSA complex was studied by Fourier transform infrared spectroscopy, fluorescence spectroscopy, UV-vis spectroscopy, and circular dichroism spectroscopy. The spectroscopic study revealed that most BSA structural features could be preserved in the complex though the BSA underwent conformational changes in the complex due to ND-BSA interaction. In addition, BSA adsorption isotherms and zeta-potential measurements were employed to investigate the pH dependence of the ND-BSA interaction. The changes in surface charge of the ND-BSA complex with pH variations indicated that the binding of BSA to ND might lead to not only the adsorption of BSA onto the ND surface but also the partial breakup of ND aggregates into relatively small ND-BSA aggregates because of the strong binding force between ND and BSA. The results show that ND is an excellent platform for protein immobilization with high affinity and holds great potential to be used for biosensor applications.

  20. Benchmarking Experimental and Computational Thermochemical Data: A Case Study of the Butane Conformers.

    Science.gov (United States)

    Barna, Dóra; Nagy, Balázs; Csontos, József; Császár, Attila G; Tasi, Gyula

    2012-02-14

    Due to its crucial importance, numerous studies have been conducted to determine the enthalpy difference between the conformers of butane. However, it is shown here that the most reliable experimental values are biased due to the statistical model utilized during the evaluation of the raw experimental data. In this study, using the appropriate statistical model, both the experimental expectation values and the associated uncertainties are revised. For the 133-196 and 223-297 K temperature ranges, 668 ± 20 and 653 ± 125 cal mol(-1), respectively, are recommended as reference values. Furthermore, to show that present-day quantum chemistry is a favorable alternative to experimental techniques in the determination of enthalpy differences of conformers, a focal-point analysis, based on coupled-cluster electronic structure computations, has been performed that included contributions of up to perturbative quadruple excitations as well as small correction terms beyond the Born-Oppenheimer and nonrelativistic approximations. For the 133-196 and 223-297 K temperature ranges, in exceptional agreement with the corresponding revised experimental data, our computations yielded 668 ± 3 and 650 ± 6 cal mol(-1), respectively. The most reliable enthalpy difference values for 0 and 298.15 K are also provided by the computational approach, 680.9 ± 2.5 and 647.4 ± 7.0 cal mol(-1), respectively.

  1. Conformational analysis of the Sda determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations

    International Nuclear Information System (INIS)

    Blanco, Jose L. Jimenez; Rooijen, Johannes J.M. van; Erbel, Paul J.A.; Leeflang, Bas R.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G.

    2000-01-01

    The conformational behaviour of the spacer-linked synthetic Sd a tetrasaccharide β-d-GalpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (1) and the two mimics β-d-Galp-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O)(CH 2 ) 5 NH 2 (2) and β-d-GlcpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (3) were investigated by 1 H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1 H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the β-d-Hex(NAc)-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp fragments. The α- Neu5-Ac-(2 → 3)-β-d-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

  2. FLUORESCENCE SPECTROSCOPIC STUDY OF THE FORMATION OF HYDROPHOBIC MICRODOMAINS IN AQUEOUS-SOLUTIONS OF POLY(ALKYLMETHYLDIALLYLAMMONIUM BROMIDES)

    NARCIS (Netherlands)

    YANG, YJ; Engberts, Jan B F N

    The conformational state of poly(alkylmethyldiallylammonium bromides) was studied in aqueous solutions using pyrene as a fluorescence probe. The results are indicative for the formation of hydrophobic microdomains in the case of several copolymers which possess sufficiently hydrophobic alkyl side

  3. 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

  4. Study of PDMS conformation in PDMS-based hybrid materials prepared by gamma irradiation

    International Nuclear Information System (INIS)

    Lancastre, J.J.H.; Fernandes, N.; Margaça, F.M.A.; Miranda Salvado, I.M.; Ferreira, L.M.; Falcão, A.N.; Casimiro, M.H.

    2012-01-01

    Polydimethylsiloxane-silicate based hybrid materials have recognized properties (high flexibility, low elastic modulus or high mechanical strength) for which there are a large number of applications in development, such as for the bioapplications field. The hybrids addressed in the present study were prepared by gamma irradiation of a mixture of polydimethylsiloxane (PDMS) with tetraethylorthosilicate (TEOS) and zirconium propoxide (PrZr) without addition of any solvent or other product. The materials are homogeneous, transparent, monolithic and flexible. The structure dependence on the PrZr content is addressed. A combination of X-ray diffraction (XRD) and Infrared Spectroscopy (IR) was used. The results reveal that the polymer in the hybrids prepared with PrZr, in a content≤5 wt%, shows a structure similar to that in the irradiated pure polymer sample. In these samples the presence of ordered polymer regions is clearly found. For samples prepared with higher content of Zr almost no ordered polymer regions are observed. The addition of PrZr plays an important role on polymer conformation in these hybrid materials. - Highlights: ► PDMS-based hybrid materials were prepared by γ-irradiation. ► FTIR, ATR/FT-IR and XRD techniques were used to characterize the materials. ► Changes in FTIR bands reflect growth of crosslinking network. ► Above certain Zr concentration regions of Zr-silicate oxide are formed. ► Zr content determines conformation of the polymer chain network.

  5. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  6. Controlling non-conformities propagation in manufacturing. Case study in an electromechanical assembly plant.

    OpenAIRE

    Fiegenwald , Valérie; Bassetto , Samuel; Tollenaere , Michel

    2011-01-01

    International audience; The purpose of this paper is to control the propagation of non-conformities. The control methods implemented to ensure the quality performance of a production system present weaknesses, inherent to their constitution, which can let non-conformities propagate along the value stream. This propagation cannot be avoided, but it can be mastered. This paper presents a method to master non-conformities propagation in a production system by building the associated control char...

  7. Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Jensen, T.R.; Kjær, Kristian

    2002-01-01

    Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely...... characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a Computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different...

  8. Conformational study of the protegrin-1 (PG-1 dimer interaction with lipid bilayers and its effect

    Directory of Open Access Journals (Sweden)

    Nussinov Ruth

    2007-04-01

    Full Text Available Abstract Background Protegrin-1 (PG-1 is known as a potent antibiotic peptide; it prevents infection via an attack on the membrane surface of invading microorganisms. In the membrane, the peptide forms a pore/channel through oligomerization of multiple subunits. Recent experimental and computational studies have increasingly unraveled the molecular-level mechanisms underlying the interactions of the PG-1 β-sheet motifs with the membrane. The PG-1 dimer is important for the formation of oligomers, ordered aggregates, and for membrane damaging effects. Yet, experimentally, different dimeric behavior has been observed depending on the environment: antiparallel in the micelle environment, and parallel in the POPC bilayer. The experimental structure of the PG-1 dimer is currently unavailable. Results Although the β-sheet structures of the PG-1 dimer are less stable in the bulk water environment, the dimer interface is retained by two intermolecular hydrogen bonds. The formation of the dimer in the water environment implies that the pathway of the dimer invasion into the membrane can originate from the bulk region. In the initial contact with the membrane, both the antiparallel and parallel β-sheet conformations of the PG-1 dimer are well preserved at the amphipathic interface of the lipid bilayer. These β-sheet structures illustrate the conformations of PG-1 dimer in the early stage of the membrane attack. Here we observed that the activity of PG-1 β-sheets on the bilayer surface is strongly correlated with the dimer conformation. Our long-term goal is to provide a detailed mechanism of the membrane-disrupting effects by PG-1 β-sheets which are able to attack the membrane and eventually assemble into the ordered aggregates. Conclusion In order to understand the dimeric effects leading to membrane damage, extensive molecular dynamics (MD simulations were performed for the β-sheets of the PG-1 dimer in explicit water, salt, and lipid bilayers

  9. Study of actinide paramagnetism in solution

    International Nuclear Information System (INIS)

    Autillo, Matthieu

    2015-01-01

    The physiochemical properties of actinide (An) solutions are still difficult to explain, particularly the behavioral differences between An(III) and Ln(III). The study of actinide paramagnetic behavior may be a 'simple' method to analyze the electronic properties of actinide elements and to obtain information on the ligand-actinide interaction. The objective of this PhD thesis is to understand the paramagnetic properties of these elements by magnetic susceptibility measurements and chemical shift studies. Studies on actinide electronic properties at various oxidation states in solution were carried out by magnetic susceptibility measurements in solution according to the Evans method. Unlike Ln(III) elements, there is no specific theory describing the magnetic properties of these ions in solution. To obtain accurate data, the influence of experimental measurement technique and radioactivity of these elements was analyzed. Then, to describe the electronic structure of their low energy states, the experimental results were complemented with quantum chemical calculations from which the influence of the ligand field was studied. Finally, these interpretations were applied to better understand the variations in the magnetic properties of actinide cations in chloride and nitrate media. Information about ligand-actinide interactions may be determined from an NMR chemical shift study of actinide complexes. Indeed, modifications induced by a paramagnetic complex can be separated into two components. The first component, a Fermi contact contribution (δ_c) is related to the degree of covalency in coordination bonds with the actinide ions and the second, a dipolar contribution (δ_p_c) is related to the structure of the complex. The paramagnetic induced shift can be used only if we can isolate these two terms. To achieve this study on actinide elements, we chose to work with the complexes of dipicolinic acid (DPA). Firstly, to characterize the geometrical parameters, a

  10. Conformal symmetry and string theories

    International Nuclear Information System (INIS)

    Kumar, A.

    1987-01-01

    This thesis is devoted to the study of various aspects of the 2-dimensional conformal field theory and its applications to strings. We make a short review of the conformal field theory and its supersymmetric extension, called superconformal field theory. We present an elegant superspace formulation of these theories and solve the condition for the closure of the superconformal algebra. The we go on to classify the superconformal field theories according to these solutions. We prove that N ≥ 5 superconformal algebra, with N being the number of supersymmetries, does not have central charge. We find the primary representations of all the interesting superconformal algebra. We study the quantization of the superconformal theories and derive the constraints on the central charge of the algebra that has to be satisfied for a consistent quantum theory. This quantization process also determines the ground state energy of the system and the spectrum of the model. We study the global aspects of the conformal symmetry and its role in the construction of consistent heterotic string theories. We prove the uniqueness of heterotic superstring theories in 10 dimensions in the fermionic constructions. We show how the vertex operators are closely associated with the primary field representation of the conformal algebra. We utilize these vertex operator constructions to obtain tree amplitudes in the 10-dimensional heterotic string theory. We show by explicit calculation at the 3-point level that the scattering amplitudes derived from the heterotic superstring are same as the ones obtained from 10-dimensional supergravity theories

  11. Conformationally Preorganized Diastereomeric Norbornane-Based Maltosides for Membrane Protein Study

    DEFF Research Database (Denmark)

    Das, Manabendra; Du, Yang; Ribeiro, Orquidea

    2017-01-01

    were generally better at stabilizing membrane proteins than short alkyl chain agents. Furthermore, use of one well-behaving NBM enabled us to attain a marked stabilization and clear visualization of a challenging membrane protein complex using electron microscopy. Thus, this study not only describes......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 properties....... Here, a novel class of diastereomeric agents with a preorganized conformation, designated norbornane-based maltosides (NBMs), were prepared and evaluated for their ability to solubilize and stabilize membrane proteins. Representative NBMs displayed enhanced behaviors compared to n...

  12. Conformation, orientation and interaction in molecular monolayers: A surface second harmonic and sum frequency generation study

    International Nuclear Information System (INIS)

    Superfine, R.; Huang, J.Y.; Shen, Y.R.

    1988-12-01

    We have used sum frequency generation (SFG) to study the order in a silane monolayer before and after the deposition of a coadsorbed liquid crystal monolayer. We observe an increase in the order of the chain of the silane molecule induced by the interpenetration of the liquid crystal molecules. By using second harmonic generation (SHG) and SFG, we have studied the orientation and conformation of the liquid crystal molecule on clean and silane coated glass surfaces. On both surfaces, the biphenyl group is tilted by 70 degree with the alkyl chain end pointing away from the surface. The shift in the C-H stretch frequencies in the coadsorbed system indicates a significant interaction between molecules. 9 refs., 3 figs

  13. Small angle neutron scattering (SANS) study of gastric mucin solutions

    Science.gov (United States)

    Hong, Z.; Bansil, R.; Waigh, T.; Turner, B.; Bhaskar, K. R.; Afdhal, N.; Lal, J.

    2002-03-01

    We report the first results from a SANS study of purified porcine gastric mucin solutions in D2O. The ability of this glycoprotein to protect the stomach epithelium from acid damage, may be due to a pH dependent conformational transition which leads to gelation at low pH Cao et. al. (Biophysical. J. 76, 1250, 1999). SANS measurements were made over the concentration range of 1 -15 mg/ml at pH 7, 4 and 2. The data indicate that at pH 7 the excluded volume exponent is 1.7, characteristic of swollen chains whereas at pH 2 this exponent increases to 2, indicating theta or poor solvent conditions, consistent with the hydrophobic interactions increasing at lower pH. From a Guinier analysis of the 1mg/ml data at low q's (0.003- 0.007 Å-1) we estimate the cross section radius of the effective cylinder to be 23nm and its length as 96nm in an unbuffered sample, i.e. close to pH 7. In the intermediate q-range (0.01 -0.1Å-1) at pH 7 a fit to the Debye chain gives radius of gyration Rg of 16nm. Mucin is best modelled as an elongated micelle with a cylindrical or worm-like chain to represent the protein core and the sugar chains forming the corona. Results of such calculations will be presented.

  14. Static and dynamic light scattering studies on dilute polyrotaxane solutions

    Science.gov (United States)

    Kume, Tetsuya; Araki, Jun; Sakai, Yasuhiro; Mayumi, Koichi; Kidowaki, Masatoshi; Yokoyama, Hideaki; Ito, Kohzo

    2009-08-01

    Static and dynamic light scattering measurements were performed for dilute polyrotaxane solutions in different types of solvent systems, i.e. dimethylacetamide (DMAc) or dimethylformamide (DMF) containing 1-6 wt% lithium chloride (LiCl), 1 M aqueous sodium hydroxide (NaOH) and dimethylsulfoxide (DMSO). No aggregation of the polyrotaxane in DMF/LiCl was confirmed in the present study. Radius of gyration of the dissolved polyrotaxane was largest in NaOHaq., followed by values in amide solvents/LiCl and that in DMSO, and was probably dominated not by Coulombic repulsion but by the mutual affinity between solvent and polyrotaxane. Ratio of radius of gyration to hydrodynamic radius suggested the flexible random-coiled conformation in DMSO and relatively more extended, semi-flexible ones in amide solvents/LiCl and NaOHaq. The obtained values of second virial coefficient and weight average molecular weight seemed to be affected by a potential change in differential refractive index increments, caused by selective macrocationization or ionization.

  15. Static and dynamic light scattering studies on dilute polyrotaxane solutions

    International Nuclear Information System (INIS)

    Kume, Tetsuya; Sakai, Yasuhiro; Mayumi, Koichi; Kidowaki, Masatoshi; Yokoyama, Hideaki; Ito, Kohzo; Araki, Jun

    2009-01-01

    Static and dynamic light scattering measurements were performed for dilute polyrotaxane solutions in different types of solvent systems, i.e. dimethylacetamide (DMAc) or dimethylformamide (DMF) containing 1-6 wt% lithium chloride (LiCl), 1 M aqueous sodium hydroxide (NaOH) and dimethylsulfoxide (DMSO). No aggregation of the polyrotaxane in DMF/LiCl was confirmed in the present study. Radius of gyration of the dissolved polyrotaxane was largest in NaOHaq., followed by values in amide solvents/LiCl and that in DMSO, and was probably dominated not by Coulombic repulsion but by the mutual affinity between solvent and polyrotaxane. Ratio of radius of gyration to hydrodynamic radius suggested the flexible random-coiled conformation in DMSO and relatively more extended, semi-flexible ones in amide solvents/LiCl and NaOHaq. The obtained values of second virial coefficient and weight average molecular weight seemed to be affected by a potential change in differential refractive index increments, caused by selective macrocationization or ionization.

  16. Hyperfractionated conformal radiotherapy in locally advanced prostate cancer: results of a dose escalation study

    International Nuclear Information System (INIS)

    Forman, Jeffrey D.; Duclos, Marie; Shamsa, Falah; Porter, Arthur T.; Orton, Colin

    1996-01-01

    Purpose: This study was initiated to assess the incidence of chronic complications and histologic and biochemical control following hyperfractionated conformal radiotherapy in patients with locally advanced prostate cancer. Methods and Materials: Between October 1991 and October 1994, 49 patients with locally advanced prostate cancer were entered on the first two dose levels of a prospective dose-escalation study using hyperfractionated three dimensional conformal radiotherapy. The first 25 patients received a minimum tumor dose of 78 Gy to the prostate and seminal vesicles in 6 weeks at 1.3 Gy, b.i.d. No increase in chronic toxicity compared with conventional radiotherapy was noted; therefore, an additional 24 patients were treated to a minimum tumor dose of 82.8 Gy to the prostate and seminal vesicles in 7 weeks at 1.15 Gy, b.i.d. Toxicity was scored according to the Radiation Therapy Oncology Group morbidity grading scale. Efficacy was assessed through scheduled postradiation prostate specific antigen values and ultrasound-guided biopsies. The median follow-up for the entire group was 20 months. Results: The hyperfractionated external radiation was well tolerated with minimal acute morbidity. At 30 months, the actuarial probability of Grade 2 gastrointestinal toxicity was 17%. At 30 months, the actuarial probability of Grade 2 genitourinary toxicity was 16%. There was no statistically significant difference between the two dose levels. No Grade 3 or 4 gastrointestinal or genitourinary toxicity was noted. At 12 months, 84% of patients had a prostate specific antigen ≤ 4; and 53%; ≤ 1 ng/ml. At 12 months, 71% of patients had post radiation biopsies that were either negative (55%) or showed a marked therapeutic effect (16%). Conclusion: The use of hyperfractionated conformal radiotherapy facilitated dose escalation with no increase in chronic toxicity compared to standard doses. The initial tumor response based on prostate specific antigen measurements and

  17. 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.

  18. Conformational stability and self-association equilibrium in biologics.

    Science.gov (United States)

    Clarkson, Benjamin R; Schön, Arne; Freire, Ernesto

    2016-02-01

    Biologics exist in equilibrium between native, partially denatured, and denatured conformational states. The population of any of these states is dictated by their Gibbs energy and can be altered by changes in physical and solution conditions. Some conformations have a tendency to self-associate and aggregate, an undesirable phenomenon in protein therapeutics. Conformational equilibrium and self-association are linked thermodynamic functions. Given that any associative reaction is concentration dependent, conformational stability studies performed at different protein concentrations can provide early clues to future aggregation problems. This analysis can be applied to the selection of protein variants or the identification of better formulation solutions. In this review, we discuss three different aggregation situations and their manifestation in the observed conformational equilibrium of a protein. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. 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.

  20. Study of conformation and dynamic of surfactant molecules in graphite oxide via NMR

    Energy Technology Data Exchange (ETDEWEB)

    Ai, X.Q. [Jiangsu Second Normal University, College of Physics and Electronic Engineering, Nanjing (China); Ma, L.G. [Nanjing Xiaozhuang University, School of Electronic Engineering, Nanjing (China)

    2016-08-15

    The conformation and dynamic of surfactant in graphite oxide (GO) was investigated by solid-state {sup 13}C magic-angle-spinning NMR and {sup 1}H-{sup 13}C cross-polarization/magic-angle-spinning NMR spectra. The conformation ordering of the alkyl chains in the confined system shows strong dependence on its orientation. While the alkyl chains parallel to the GO layer in lateral monolayer arrangement are in gauche conformation in addition to a small amount of all-trans conformation, those with orientation radiating away from the GO in paraffin bilayer arrangement is in all-trans conformation in addition to some gauche conformation even though high-order diffraction peaks appears. NMR results suggest that the least mobile segment is located at the GO-surfactant interface corresponding to the N-methylene group. Further from it, the mobility of the alkyl chain increases. The terminal methyl and N-methyl carbon groups have the highest mobile. The chains in all-trans conformational state are characterized as more rigid than chains with gauche conformation; each segment of the confined alkyl chains with the lateral monolayer arrangement exhibits less mobility as compared to that with the paraffin bilayer arrangement. (orig.)

  1. Ego Development and Conformity: A Construct Validity Study of the Washington University Sentence Completion Test

    Science.gov (United States)

    Hoppe, Carl F.; Loevinger, Jane

    1977-01-01

    Self and peer evaluations and experimental measures of conformity were given to 107 adolescent private school boys. Student discipline records also indicated the number of demerits. The self-report measures and the demerits showed maximum conformity between the self-protective and conscientious ego stages as measured by the Sentence Completion…

  2. Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach

    Energy Technology Data Exchange (ETDEWEB)

    Sinnige, Tessa; Houben, Klaartje [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Pritisanac, Iva [Physical and Theoretical Chemistry Laboratory (United Kingdom); Renault, Marie [Institute of Pharmacology and Structural Biology (France); Boelens, Rolf; Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

    2015-04-15

    The β-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a “divide and conquer” approach in which we first obtained resonance assignments for BamA’s periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.

  3. 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...

  4. Determination of a PWR key neutron parameters uncertainties and conformity studies applications

    International Nuclear Information System (INIS)

    Bernard, D.

    2002-01-01

    The aim of this thesis was to evaluate uncertainties of key neutron parameters of slab reactors. Uncertainties sources have many origins, technologic origin for parameters of fabrication and physical origin for nuclear data. First, each contribution of uncertainties is calculated and finally, a factor of uncertainties is associated to key slab parameter like reactivity, isotherm reactivity coefficient, control rod efficiency, power form factor before irradiation and lifetime. This factors of uncertainties were computed by Generalized Perturbations Theory in case of step 0 and by directs calculations in case of irradiation problems. One of neutronic conformity applications was about fabrication and nuclear data targets precision adjustments. Statistic (uncertainties) and deterministic (deviations) approaches were studied. Then neutronics key slab parameters uncertainties were reduced and so nuclear performances were optimised. (author)

  5. Steric effects on the primary isotope dependence of secondary kinetic isotope effects in hydride transfer reactions in solution: caused by the isotopically different tunneling ready state conformations?

    Science.gov (United States)

    Maharjan, Binita; Raghibi Boroujeni, Mahdi; Lefton, Jonathan; White, Ormacinda R; Razzaghi, Mortezaali; Hammann, Blake A; Derakhshani-Molayousefi, Mortaza; Eilers, James E; Lu, Yun

    2015-05-27

    The observed 1° isotope effect on 2° KIEs in H-transfer reactions has recently been explained on the basis of a H-tunneling mechanism that uses the concept that the tunneling of a heavier isotope requires a shorter donor-acceptor distance (DAD) than that of a lighter isotope. The shorter DAD in D-tunneling, as compared to H-tunneling, could bring about significant spatial crowding effect that stiffens the 2° H/D vibrations, thus decreasing the 2° KIE. This leads to a new physical organic research direction that examines how structure affects the 1° isotope dependence of 2° KIEs and how this dependence provides information about the structure of the tunneling ready states (TRSs). The hypothesis is that H- and D-tunneling have TRS structures which have different DADs, and pronounced 1° isotope effect on 2° KIEs should be observed in tunneling systems that are sterically hindered. This paper investigates the hypothesis by determining the 1° isotope effect on α- and β-2° KIEs for hydride transfer reactions from various hydride donors to different carbocationic hydride acceptors in solution. The systems were designed to include the interactions of the steric groups and the targeted 2° H/D's in the TRSs. The results substantiate our hypothesis, and they are not consistent with the traditional model of H-tunneling and 1°/2° H coupled motions that has been widely used to explain the 1° isotope dependence of 2° KIEs in the enzyme-catalyzed H-transfer reactions. The behaviors of the 1° isotope dependence of 2° KIEs in solution are compared to those with alcohol dehydrogenases, and sources of the observed "puzzling" 2° KIE behaviors in these enzymes are discussed using the concept of the isotopically different TRS conformations.

  6. A study of the conformation and stability of nitroxide free radicals

    International Nuclear Information System (INIS)

    Briere, R.

    1969-03-01

    The first part of this study is an application of nuclear magnetic resonance to the determination of the sign and magnitude of the long range nuclear-electron spin-spin couplings in the free radical nitroxide derived from piperidine. It has been shown that the coupling constants of the protons γ to the nitrogen atom have a pronounced spatial dependence as do the protons in the β position, a point which has not been brought out by previous investigations. Conformational analysis of these compounds has been carried out by measurement of the effect of temperature on the NMR spectra at 310 MHz. The synthesis of di-t-Bu nitroxide labelled with C 13 in the α-position made possible the unambiguous determination of the corresponding 13 C nuclear-electron spin-spin coupling constant, a parameter which had not previously been measured. The coupling constants measured in the 2,2,6,6-tetramethyl piperidine series could then be attributed to the 13 C atoms in the β-position and their variation related to the conformations of the heterocycles. This constitutes the second part of the work reported here. The final section is devoted to a study of the decomposition of an unstable nitroxide having a hydrogen atom in the p-position. This decomposition is bimolecular and the primary isotope effect shows that the rupture. of the C-H bond is involved. From this one can conclude that a nitroxide is stable when the different groups attached to the nitrogen atom cannot give rise to a decomposition either intra molecularly, if the molecular geometry is suitable, or inter molecularly by dimerisation through attack on a different center of a neighbouring molecule thus leading to a fragmentation or a disproportionation. (author) [fr

  7. Time-resolved Fourier transform infrared spectrometry using a microfabricated continuous flow mixer: application to protein conformation study using the example of ubiquitin.

    Science.gov (United States)

    Kakuta, Masaya; Hinsmann, Peter; Manz, Andreas; Lendl, Bernhard

    2003-05-01

    We report on the use of time-resolved Fourier transform infrared spectroscopy (FT-IR) to study chemically induced conformational changes of proteins using the example of ubiquitin. For this purpose a micromachined mixer is coupled to a conventional IR transmission cell with a pathlength of 25 microm and operated in both the continuous and the stopped-flow mode. This experimental set-up allows the elucidation of reaction pathways in the time frame of about 500 milliseconds to seconds with little reagent consumption and low pressure. For continuous flow measurements employed in the time frame from 0.5 to 1.4 s the reaction time is determined by the flow rate used as the connection between the point of confluence in the micromixer and the flow cell was kept constant in all experiments. For stopped-flow experiments (>1.4 s) the time is determined by data acquisition of the rapid scanning infrared spectrometer. Ubiquitin, a small well-known protein with 76 amino acid residues, changes its conformation from native to A-state with the addition of methanol under low pH conditions. We investigated the conformational change in the time frame from 0.5 to 10 s by mixing ubiquitin (20% methanol-d(4)) with an 80% methanol-d(4) solution at pD 2 by evaluating the time dependent changes in the amide I band of the protein.

  8. 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

  9. On the linear conformal gravitation

    International Nuclear Information System (INIS)

    Pal'chik, M.Ya.; Fradkin, E.S.

    1984-01-01

    Conformal gravitation is analyzed under the assumption that its solution possesses the property of conformal symmetry. This assumption has sense in the case of small distances and only for definite types of matter fields, namely: at special choice of matter fields and their interactions, providing a lack of conformal anomalies; or at definite magnitudes of binding constants, coinciding with the zeroes of the Gell-Mann-Low function. The field equations, of the group-theoretical natura are obtained

  10. 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.

  11. Pulse radiolysis study of aqueous cyanamide solutions

    International Nuclear Information System (INIS)

    Draganic, I.G.; Draganic, Z.D.; Sehested, K.

    1978-01-01

    The radiolysis of oxygen-free, aqueous solutions of cyanamide was studied by fast kinetic spectrophotometry. Computer simulation of the reaction mechanisms was used to evaluate the experimental data. Four different species are identified: (1) the radical anion (NH 2 CN) - absorbing light in the UV with lambda/sub max/ 240 = 1500 M -1 cm -1 ; the disappearance is a second-order process with 2k = 1.3 x 10 9 M -1 s -1 ; (2) the hydrogen adduct, NH 2 C(H) double bond N (or NH 2 C double bond NH), with lambda/sub max/ 300 nm and epsilon 300 = 150 M -1 cm -1 decaying by second-order kinetics with 2k = 3.1 x 10 9 M -1 s -1 ; (3) the hydroxyl radical preferentially adds to the cyano group, NH 2 C(OH) double bond N (or NH 2 C double bond NOH). This species rearranges in the submicrosecond scale to NH 2 C ( double bond O) NH (lambda/sub max/ 325 nm and epsilon/sub 325 = 1900 M -1 cm -1 ) and disappears by a second-order process with 2k = 6.3 x 10 9 M -1 s -1 . (4) It is estimated that about 10% of OH radicals attack the substituent group and by H abstraction produce the NHCN radical (lambda/sub max/ 370 nm and epsilon 370 = 1800 M -1 cm -1 ); it disappears by a pseudo-first-order process attributed to a hydrolysis reaction. At increasing acidities, protonation of this radical takes place, NHCN + H + → + NH 2 CN; the protonated form decays faster and absorbs more strongly. In a cyanamide solution containing S 2 O 8 2- , the SO - 4 . radicals react with cyanamide, k = 1 x 10 8 M -1 s -1 , producing + NH 2 CN radicals. The dependence of the optical density at 325 nm on the dose rate and solute concentration are quantitatively consistent with the assumption that the OH radicals react with the NH 2 C(=O)NH species with k = 4 x 10 9 M -1 s -1

  12. Conformational analysis and vibrational studies of ethylenediamine-d4, using DFT method

    International Nuclear Information System (INIS)

    Catikkas, B.

    2010-01-01

    In this work, conformational analysis and quantum chemical calculations of ethylenediamine-d4 were carried out. The geometry optimization and the geometric parameters (bond length, bond angle and tortion angle) were calculated. The Infrared and Raman frequencies of fundamental modes of the most stable conformer were determined. Calculations were carried out by using the MPW1PW91/6-311+G(d,p) method and Gaussian03 and GaussView3.0 programs. Populations of the conformers was calculated. Vibrational assignments of the title molecule were calculated by using Scaled Quantum Mechanical (SQM) analysis. Calculated values were compared with the experimental ones.

  13. Structural study of concentrated micellar solutions

    International Nuclear Information System (INIS)

    Zemb, Thomas

    1985-01-01

    This research thesis reports the study of the structure of concentrated soap-water binary micelles with a comparison of measurements of light, neutrons and X-ray scattering, and the relaxation induced by paramagnetic ions adsorbed at the interface. In the first part, the author discusses the specific sensitivity ranges of different experimental techniques, outlines the resolution which can be obtained with scattering experiments, and proposes a critical analysis of results published in the relevant literature. In a second part, the author discusses the compared results of the application of various techniques (magnetic resonance, X-light and neutron scattering) on the two most used model systems: sodium octanoate and sodium dodecyl sulfate (SDS) in solution. Then, the author addresses the case of ternary systems: study of the influence of the presence of a co-surfactant on the structure, study of the effect of interfacial charge on the micellar structure, use of the same previous quantitative methods to study the disturbances brought to the structure due to the presence of reactants [fr

  14. 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.

  15. Study of the chain conformation of thermotropic nematic main chain polyesters

    Science.gov (United States)

    Li, M. H.; Brûlet, A.; Cotton, J. P.; Davidson, P.; Strazielle, C.; Keller, P.

    1994-10-01

    The conformation of main chain mesomorphic polyesters is studied by small angle neutron scattering (SANS) in the isotropic and in the nematic phases, by using mixtures of deuterated and undeuterated polymers. Particular attention is given to neglect the transesterification effects occurring mainly at high temperature for these LC polymers. In the isotropic phase, despite the presence of long rigid mesogenic groups, the LC polyester chains have a Gaussian conformation shown by the variation of the radius of gyration as a function of the molecular weight. This result is confirmed from the scattering variation in the intermediate range of the scattering vector. In the nematic phase, the SANS data are well fitted to a model of cylinder, in which the main chain polymer is confined. In the unoriented phase, the measurements in the intermediate range give the values of the radii of cylinders : they lie in between 10 Å and 19 Å depending on the degree of polymerization of chains. In the oriented nematic phase, the scattering patterns are highly anisotropic : they correspond to very long, thin and well-oriented cylinders. We have calculated the fully extended chain lengths using for the monomer length that measured in situ by X-ray diffraction. Then the comparison of this length with the measured height of the cylinders gives the existence of hairpins and their number per chain. For the short chain, the conformation is almost completely elongated in the nematic direction, whereas hairpin defects appear in longer chains. Their number decreases slightly with decreasing temperature. The orientational fluctuations of cylinders relatively to the nematic director are weak as shown from the high values of their order parameter (P_2 > 0.9). These results are discussed for two spacer lengths as a function of the molecular weight and of the temperature. La conformation de polyesters linéaires mésomorphes est étudiée par diffusion de neutrons aux petits angles (DNPA) dans les

  16. Conformal Infinity

    OpenAIRE

    Frauendiener, J?rg

    2000-01-01

    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...

  17. A treatment planning study comparing whole breast radiation therapy against conformal, IMRT and tomotherapy for accelerated partial breast irradiation

    International Nuclear Information System (INIS)

    Oliver, Mike; Chen, Jeff; Wong, Eugene; Van Dyk, Jake; Perera, Francisco

    2007-01-01

    Purpose and background: Conventional early breast cancer treatment consists of a lumpectomy followed by whole breast radiation therapy. Accelerated partial breast irradiation (APBI) is an investigational approach to post-lumpectomy radiation for early breast cancer. The purpose of this study is to compare four external beam APBI techniques, including tomotherapy, with conventional whole breast irradiation for their radiation conformity index, dose homogeneity index, and dose to organs at risk. Methods and materials: Small-field tangents, three-dimensional conformal radiation therapy, intensity-modulated radiation therapy and helical tomotherapy were compared for each of 15 patients (7 right, 8 left). One radiation conformity and two dose homogeneity indices were used to evaluate the dose to the target. The mean dose to organs at risk was also evaluated. Results: All proposed APBI techniques improved the conformity index significantly over whole breast tangents while maintaining dose homogeneity and without a significant increase in dose to organs at risk. Conclusion: The four-field IMRT plan produced the best dosimetric results; however this technique would require appropriate respiratory motion management. An alternative would be to use a four-field conformal technique that is less sensitive to the effects of respiratory motion

  18. Dynamics and diffusive-conformational coupling in polymer bulk samples and surfaces: a molecular dynamics study

    International Nuclear Information System (INIS)

    Vree, C; Mayr, S G

    2010-01-01

    The impact of free surfaces on the mobility and conformational fluctuations of model polymer chains is investigated with the help of classical molecular dynamics simulations over a broad temperature range. Below a critical temperature, T*, similar to the critical temperature of the mode coupling theory, the center-of-mass displacements and temporal fluctuations of the radius of gyration of individual chains-as a fingerprint of structural reconfigurations-reveal a strong enhancement close to surfaces, while this effect diminishes with increasing temperature and observation time. Interpreting conformational fluctuations as a random walk in conformational space, identical activation enthalpies for structural reconfigurations and diffusion are obtained within the error bars in the bulk and at the surfaces, thus indicating a coupling of diffusive and conformational dynamics.

  19. 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

    .Results: The Illumina BovineSNP50 BeadChip was used to identify single nucleotide polymorphisms (SNPs) that are associated with body conformation traits. A least absolute shrinkage and selection operator (LASSO) was applied to detect multiple SNPs simultaneously for 29 body conformation traits with 1,314 Chinese...... Holstein cattle and 52,166 SNPs. Totally, 59 genome-wide significant SNPs associated with 26 conformation traits were detected by genome-wide association analysis; five SNPs were within previously reported QTL regions (Animal Quantitative Trait Loci (QTL) database) and 11 were very close to the reported...... SNPs. Twenty-two SNPs were located within annotated gene regions, while the remainder were 0.6-826 kb away from known genes. Some of the genes had clear biological functions related to conformation traits. By combining information about the previously reported QTL regions and the biological functions...

  20. Decoloration studies of some fluorescent dye solutions

    International Nuclear Information System (INIS)

    Zafar-uz-Zaman, M.; Ditta, A.

    1997-01-01

    Rhenium-186-(Sn)-l, l hydroxy ethylene diphosphonate (/sup 186/Re-HEDP) has been used for the palliation of metastatic bone pain. /sup 186/Re- has excellent physical properties that may be useful for the formulation of radiotherapeutic agents. It has a short half-life (90.6 hrs) with moderate energy particles (E /sub max/=1.07 MeV) that penetrate over a short range of tissue and gamma ray of 137 keV which is well suited to image. A number of samples of natural rhenium (metal) power were irradiated in PARR-I research reactor at a thermal neutrons flux of the order lx10/sup 14/ n.cm /sup -2/.s/sup -1/ for various time intervals in order to optimize the production yield of /sup 186/Re. The data indicated that 60 mCi/mg of radioactivity could be obtained for an irradiation time of 24 hours. The irradiated target was converted to its ammonium salt which was used for preparation of /sup 186/Re-HEDP complex. Labeling studies of dissolution salt of HEDP with /sup 186/Re were performed by varying the amounts of rhenium, HEDP and Sn. These studies were also carried out at different pH of the solutions. The quality control of /sup 186/Re-HEDP complex was checked by radio chromatographic techniques. These investigations indicated that the complex of optimum yield (approx. 95%) could be obtained by using amounts of Re (0.15 mg), HEDP (10 mg), stannous chloride dihydrate (4mg) and pH range of 4-6. The effect of antioxidant genetic acid was studied on the stability of the complex which was found to be stable up to five days in the presence of 3 mg of genetic acid. The biodistribution studies in rats showed optimum uptake by bone after 2.5 hours. (author)

  1. Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

    Science.gov (United States)

    Sullivan, David C; Lim, Carmay

    2006-08-24

    Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

  2. 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.

  3. 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

  4. A study of the conformation and stability of nitroxide free radicals; Etude de la conformation et de la stabilite de radicaux libres nitroxydes

    Energy Technology Data Exchange (ETDEWEB)

    Briere, R [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

    1969-03-01

    The first part of this study is an application of nuclear magnetic resonance to the determination of the sign and magnitude of the long range nuclear-electron spin-spin couplings in the free radical nitroxide derived from piperidine. It has been shown that the coupling constants of the protons {gamma} to the nitrogen atom have a pronounced spatial dependence as do the protons in the {beta} position, a point which has not been brought out by previous investigations. Conformational analysis of these compounds has been carried out by measurement of the effect of temperature on the NMR spectra at 310 MHz. The synthesis of di-t-Bu nitroxide labelled with C{sup 13} in the {alpha}-position made possible the unambiguous determination of the corresponding {sup 13}C nuclear-electron spin-spin coupling constant, a parameter which had not previously been measured. The coupling constants measured in the 2,2,6,6-tetramethyl piperidine series could then be attributed to the {sup 13}C atoms in the {beta}-position and their variation related to the conformations of the heterocycles. This constitutes the second part of the work reported here. The final section is devoted to a study of the decomposition of an unstable nitroxide having a hydrogen atom in the p-position. This decomposition is bimolecular and the primary isotope effect shows that the rupture. of the C-H bond is involved. From this one can conclude that a nitroxide is stable when the different groups attached to the nitrogen atom cannot give rise to a decomposition either intra molecularly, if the molecular geometry is suitable, or inter molecularly by dimerisation through attack on a different center of a neighbouring molecule thus leading to a fragmentation or a disproportionation. (author) [French] La premiere partie est une application de la resonance magnetique nucleaire a la determination du signe et de la grandeur des couplages a longue distance dans des radicaux libres nitroxydes piperidiniques. Il est montre que

  5. SAXS-WAXS studies of the low-resolution structure in solution of xylose/glucose isomerase from Streptomyces rubiginosus

    Science.gov (United States)

    Kozak, Maciej; Taube, Michał

    2009-10-01

    The structure and conformation of molecule of xylose/glucose isomerase from Streptomyces rubiginosus in solution (at pH 6 and 7.6; with and without the substrate) has been studied by small- and wide-angle scattering of synchrotron radiation (SAXS-WAXS). On the basis of the SAXS-WAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods. A comparison of the models of glucose isomerase shows only small differences between the model in solution and the crystal structure.

  6. High resolution NMR study of cellulose in solid state and in solution

    International Nuclear Information System (INIS)

    Saint-Germain, Jean

    1983-01-01

    This research thesis reports the study of native cellulose (cotton) and wood by nuclear magnetic resonance (NMR). As far as the cotton spectrum is concerned, the author assigned resonances which more specifically corresponded to amorphous or crystalline areas. Wood was studied in its bulk condition, and resonances have been determined for the different wood components. The behaviour of cellulose in solution in a solvent has been studied by liquid high resolution NMR. The solvation mechanism has been determined and a study of model components of the macromolecule allowed a conformational study of cellulose in this solvent to be performed. Bi-dimensional NMR and longitudinal relaxation time measurements highlighted the existence of an intramolecular hydrogen bond in the cellulose in solution [fr

  7. 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 S 1 state, with the aid of relative stabilization energies of each conformer in the S 0 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 S 1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.

  8. 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.

  9. Conformal Gravity

    International Nuclear Information System (INIS)

    Hooft, G.

    2012-01-01

    The dynamical degree of freedom for the gravitational force is the metric tensor, having 10 locally independent degrees of freedom (of which 4 can be used to fix the coordinate choice). In conformal gravity, we split this field into an overall scalar factor and a nine-component remainder. All unrenormalizable infinities are in this remainder, while the scalar component can be handled like any other scalar field such as the Higgs field. In this formalism, conformal symmetry is spontaneously broken. An imperative demand on any healthy quantum gravity theory is that black holes should be described as quantum systems with micro-states as dictated by the Hawking-Bekenstein theory. This requires conformal symmetry that may be broken spontaneously but not explicitly, and this means that all conformal anomalies must cancel out. Cancellation of conformal anomalies yields constraints on the matter sector as described by some universal field theory. Thus black hole physics may eventually be of help in the construction of unified field theories. (author)

  10. Conformal Tachyons

    CERN Document Server

    Tomaschitz, R

    2000-01-01

    We study tachyons conformally coupled to the background geometry of a Milne universe. The causality of superluminal signal transfer is scrutinized in this context. The cosmic time of the comoving frame determines a distinguished time order for events connected by superluminal signals. An observer can relate his rest frame to the galaxy frame, and compare so the time order of events in his proper time to the cosmic time order. All observers can in this way arrive at identical conclusions on the causality of events connected by superluminal signals. An unambiguous energy concept for tachyonic rays is defined by means of the cosmic time of the comoving reference frame, without resorting to an antiparticle interpretation. On that basis we give an explicit proof that no signals can be sent into the past of observers. Causality violating signals are energetically forbidden, as they would have negative energy in the rest frame of the emitting observer. If an observer emits a superluminal signal, the tachyonic respon...

  11. 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

  12. Dosimetry study on the conventional and three dimensional conformal radiation treatment planning protocols for rectal cancer

    International Nuclear Information System (INIS)

    Cai Yong; He Yuxiang; Han Shukui; Wu Hao; Gong Jian; Xu Bo

    2007-01-01

    Objective: To compare the dose distribution of clinical target volume (CTV), in normal tissues and organs for patients with rectal cancer on the conventional radiotherapy (2D) and three dimension- al conformal radiation treatment (3DCRT). Methods: The CT image data of 36 rectal cancer patients treated with 3DCRT were studied. The CTV, small bowel, colon, bladder, pelvic bone marrow, and femoral head and neck were contoured on consecutive axial slices of CT images. Two 3DCRT and three conventional treatment planning protocols were simulated using three dimensional treatment planning system (CMS Focus 2.31), were defined as 3D-3, 3D-4, 2D-2, 2D-3, 2D-4. The difference of five treatment planning protocols on the CTV and normal structure by analysis of dose-volume histograms (DVHs) were compared. Results: The D 95 and V 95 of these five protocols all exceeded 97%. The conformity index(CI) of 3D was obviously larger than that of 2D protocol. The dose inhomogeneity(DI) in 4 DCRT was less than that of 3 DCRT. The 3D as compared with the 2D, significantly reduced the mean dose of 45 Gy to the small bowel and colon. The 3D-3 as compared with the 2D-3, the 3D-4 as compared with the 2D-4, the mean dose of small bowel and colon was reduced by 28.5% and 25.7%, respectively. The 3D-3 as compared with the 2D-2, the 3D-3 as compared with the 2D-3 and the 3D4 as compared with the 2D-4, the percentage volume of small bowel and colon which received 45 Gy was reduced by 80.8% , 51.1% and 54.7% , respectively. Either the mean dose, or the percentage volume receiving 35 Gy and 45 Gy to the pelvic bone and bladder, the 3D planning protocols had advanage over the 2D planning protocols. The V 45 of bladder in 2D-2 planning proto- col was the highest in all planning protocols, exceeding 98%, but the highest V 45 of bladder was only 50% in the other planning protocols. Conclusions: Even though the difference in pelvic CTV of rectal cancer patients between the conventional radiotherapy and 3

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

    International Nuclear Information System (INIS)

    Laurence, Ted Alfred

    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

  14. Small-angle x-ray scattering study on conformation of amorphous polymer chain in the bulk

    International Nuclear Information System (INIS)

    Hayashi, Hisao; Hamada, Fumiyuki; Nakajima, Akio

    1975-01-01

    In a previous paper, the new method for the determination of the conformation of polymer chains in concentrated solution and in bulk by small angle X-ray scattering was reported. The purpose of this paper is to estimate the dimension and conformation of polystyrene chains in bulk by this method. The tagged polymer used was the copolymer of styrene and p-iodostyrene. Excess scattering was obtained by subtracting the intensity of polystyrene matrix from that of a mixture containing polystyrene and a small fraction of the tagged polystyrene. Since the excess scattering originates from the group of iodine atoms in the tagged polystyrene, the radius of gyration of the tagged polystyrene is estimated by Guinier plot. Measurement was made with a Kratky camera, and in order to obtain high scattering intensity, the primary beam with line-shaped cross section was used. The intercepts of two limiting curves in the plotted radius of gyration diagram showed good agreement, and the measured molecular dimension agreed with the unperturbed dimension of this polymer. It was concluded that the molecular chains in bulk are mutually penetrable, and the centers of gravity of the molecules distribute almost randomly. It was suggested from the plot of the excess scattering intensity that the conformation of the tagged molecules is a random coil. The present results did not support the ordered structure revealed by bundle model and meander model. (Kako, I.)

  15. 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.

  16. 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.

  17. 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

  18. Sequence dependent DNA conformations: Raman spectroscopic studies and a model of action of restriction enzymes

    International Nuclear Information System (INIS)

    Nishimura, Y.

    1985-01-01

    Raman spectra have been examined to clarify the polymorphic forms of DNA, A, B, and Z forms. From an analysis the authors found that the guanine ring breathing vibration is sensitive to its local conformation. Examination of nine crystals of guanosine residues in which the local conformations are well established revealed that a guanosine residue with a C3'endo-anti gives a strong line at 666+-2 cm/sup -1/, O4'endo-anti at 682 cm/sup -1/, C1'exo-anti at 673 cm/sup -1/, C2'endo-anti at 677 cm/sup -1/ and syn-forms around 625 cm/sup -1/. Using this characteristic line, they were able to obtain the local conformations of guanosine moieties in poly(dG-dC). Such a sequence derived variation is suggested to be recognized by sequence specific proteins such as restriction enzymes. The authors found a correlation between sequence dependent DNA conformation and a mode of action of restriction enzymes. The cutting mode of restriction enzymes is classified into three groups. The classification of whether the products have blunt ends, two-base-long cohesive ends, or four-base-long cohesive ends depends primarily on the substrate, not on the enzyme. It is suggested that sequence dependent DNA conformation causes such a classification by the use of the Calladine-Dickerson analysis. In the recognition of restriction enzymes, the methyl group in a certain sequence is considered to play an important role by changing the local conformation of DNA

  19. Conformal expansions and renormalons

    Energy Technology Data Exchange (ETDEWEB)

    Rathsman, J.

    2000-02-07

    The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

  20. Fluoroolefins as Peptide Mimetics. 2. A Computational Study of the Conformational Ramifications of Peptide Bond Replacement

    Science.gov (United States)

    2010-01-01

    Calculated Relative Energies and Thermochemical Corrections (in kcal/mol) for the Gas Phase Conformations of DFA ∆E ∆(E+ ZPE ) ∆E(298) ∆H(298) ∆G(298...Thermochemical Corrections (in kcal/mol) for the Aqueous Phase Conformations of DFA ∆E ∆(E+ ZPE ) ∆E(298) ∆Η(298) ∆G(298) DFA1 0.00 0.00 0.00 0.00 0.00 DFA2 0.39

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

    Science.gov (United States)

    Feng, Wei; Wang, Zhigang; Zhang, Wenke

    2017-02-28

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

  2. Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations.

    Science.gov (United States)

    Pechlaner, Maria; Sigel, Roland K O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2013-10-08

    Nuclear magnetic resonance (NMR) nuclear Overhauser enhancement (NOE) data obtained for a 35-nucleotide RNA segment of a bacterial group II intron indicate a helical hairpin structure in which three parts, a terminal pentaloop, a bulge, and a G-A mismatch, display no Watson-Crick base pairing. The 668 NOE upper distance bounds for atom pairs are insufficient to uniquely determine the conformation of these segments. Therefore, molecular dynamics simulations including time-averaged distance restraints have been used to obtain a conformational ensemble compatible with the observed NMR data. The ensemble shows alternating hydrogen bonding patterns for the mentioned segments. In particular, in the pentaloop and in the bulge, the hydrogen bonding networks correspond to distinct conformational clusters that could not be captured by using conventional single-structure refinement techniques. This implies that, to obtain a realistic picture of the conformational ensemble of such flexible biomolecules, it is necessary to properly account for the conformational variability in the structure refinement of RNA fragments.

  3. Dissipative particle dynamics of triblock copolymer melts: A midblock conformational study at moderate segregation

    Science.gov (United States)

    Tallury, Syamal S.; Spontak, Richard J.; Pasquinelli, Melissa A.

    2014-12-01

    As thermoplastic elastomers, triblock copolymers constitute an immensely important class of shape-memory soft materials due to their unique ability to form molecular networks stabilized by physical, rather than chemical, cross-links. The extent to which such networks develop in triblock and higher-order multiblock copolymers is sensitive to the formation of midblock bridges, which serve to connect neighboring microdomains. In addition to bridges, copolymer molecules can likewise form loops and dangling ends upon microphase separation or they can remain unsegregated. While prior theoretical and simulation studies have elucidated the midblock bridging fraction in triblock copolymer melts, most have only considered strongly segregated systems wherein dangling ends and unsegregated chains become relatively insignificant. In this study, simulations based on dissipative particle dynamics are performed to examine the self-assembly and networkability of moderately segregated triblock copolymers. Utilizing a density-based cluster-recognition algorithm, we demonstrate how the simulations can be analyzed to extract information about microdomain formation and permit explicit quantitation of the midblock bridging, looping, dangling, and unsegregated fractions for linear triblock copolymers varying in chain length, molecular composition, and segregation level. We show that midblock conformations can be sensitive to variations in chain length, molecular composition, and bead repulsion, and that a systematic investigation can be used to identify the onset of strong segregation where the presence of dangling and unsegregated fractions are minimal. In addition, because this clustering approach is robust, it can be used with any particle-based simulation method to quantify network formation of different morphologies for a wide range of triblock and higher-order multiblock copolymer systems.

  4. Using fluorescence correlation spectroscopy to study conformational changes in denatured proteins.

    Science.gov (United States)

    Sherman, Eilon; Itkin, Anna; Kuttner, Yosef Yehuda; Rhoades, Elizabeth; Amir, Dan; Haas, Elisha; Haran, Gilad

    2008-06-01

    Fluorescence correlation spectroscopy (FCS) is a sensitive analytical tool that allows dynamics and hydrodynamics of biomolecules to be studied under a broad range of experimental conditions. One application of FCS of current interest is the determination of the size of protein molecules in the various states they sample along their folding reaction coordinate, which can be accessed through the measurement of diffusion coefficients. It has been pointed out that the analysis of FCS curves is prone to artifacts that may lead to erroneous size determination. To set the stage for FCS studies of unfolded proteins, we first show that the diffusion coefficients of small molecules as well as proteins can be determined accurately even in the presence of high concentrations of co-solutes that change the solution refractive index significantly. Indeed, it is found that the Stokes-Einstein relation between the measured diffusion coefficient and solution viscosity holds even in highly concentrated glycerol or guanidinium hydrochloride (GuHCl) solutions. These measurements form the basis for an investigation of the structure of the denatured state of two proteins, the small protein L and the larger, three-domain protein adenylate kinase (AK). FCS is found useful for probing expansion in the denatured state beyond the unfolding transition. It is shown that the denatured state of protein L expands as the denaturant concentration increases, in a process akin to the transition from a globule to a coil in polymers. This process continues at least up to 5 M GuHCl. On the other hand, the denatured state of AK does not seem to expand much beyond 2 M GuHCl, a result that is in qualitative accord with single-molecule fluorescence histograms. Because both the unfolding transition and the coil-globule transition of AK occur at a much lower denaturant concentration than those of protein L, a possible correlation between the two phenomena is suggested.

  5. 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.

  6. Conformational studies on pertrimethylsilyl derivatives of some mono- and disaccharides by 220 MHz PMR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Streefkerk, D.G.; Bie, M.J.A. de

    1973-01-01

    The complete interpretation of 220 MHz PMR spectra and the accurate chemical shifts and coupling constants, obtained after computer simulation of the spectra, of a number of TMS-mono and -disaccharides are given. By means of an adapted Karplus equation the conformation of the derivatives has been

  7. Vibrational absorption spectra, DFT and SCC-DFTB conformational study and analysis of [Leu]enkephalin

    DEFF Research Database (Denmark)

    Abdali, Salim; Niehaus, T.A.; Jalkanen, Karl J.

    2003-01-01

    . Ab initio (DFT at the B3LYP/6-31G* level of theory) and semi-empirical (SCC-DFTB) with and without dispersion correction were applied to simulate the VA spectra of [Leu] enkephalin. In these calculations structures taken from X-ray measurements for different conformers of the molecule were used...

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

    International Nuclear Information System (INIS)

    Asadinezhad, Ahmad; Kelich, Payam

    2017-01-01

    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.

  9. Conformational study of melectin and antapin antimicrobial peptides in model membrane environments

    Czech Academy of Sciences Publication Activity Database

    Kocourková, L.; Novotná, P.; Čujová, Sabína; Čeřovský, Václav; Urbanová, M.; Setnička, V.

    2017-01-01

    Roč. 170, Jan 5 (2017), s. 247-255 ISSN 1386-1425 Institutional support: RVO:61388963 Keywords : antimicrobial peptides * conformation * liposomes * model membranes * circular dichroism * infrared spectroscopy Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 2.536, year: 2016

  10. Conformational analysis of lignin models; Analise conformacional de modelos de lignina

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Helio F. dos [Juiz de Fora Univ., MG (Brazil). Dept. de Quimica]. E-mail: helius@quimica.ufjf.br

    2001-08-01

    The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level. (author)

  11. Superconformal geometry from the Grassmann and harmonic analyticities II: The N=4SU(2) conformal case

    International Nuclear Information System (INIS)

    Saidi, E.H.; Zakkari, M.

    1990-05-01

    N=4SU(2) conformal invariance is studied in harmonic superspace. It is shown that the N=4SU(2) conformal structure is equivalent to the harmonic analyticity. The solutions of the superconformal constraints are worked out in detail and the conformal properties of all objects of interests are given. A realization of the N=4 current in terms of the free (F.S.) hypermultiplet is obtained. (author). 10 refs

  12. Diagonal Limit for Conformal Blocks in d Dimensions

    CERN Document Server

    Hogervorst, Matthijs; Rychkov, Slava

    2013-01-01

    Conformal blocks in any number of dimensions depend on two variables z, zbar. Here we study their restrictions to the special "diagonal" kinematics z = zbar, previously found useful as a starting point for the conformal bootstrap analysis. We show that conformal blocks on the diagonal satisfy ordinary differential equations, third-order for spin zero and fourth-order for the general case. These ODEs determine the blocks uniquely and lead to an efficient numerical evaluation algorithm. For equal external operator dimensions, we find closed-form solutions in terms of finite sums of 3F2 functions.

  13. Rigid supersymmetry from conformal supergravity in five dimensions

    International Nuclear Information System (INIS)

    Pini, Alessandro; Rodriguez-Gomez, Diego; Schmude, Johannes

    2015-01-01

    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.

  14. Conformality lost

    International Nuclear Information System (INIS)

    Kaplan, David B.; Lee, Jong-Wan; Son, Dam T.; Stephanov, Mikhail A.

    2009-01-01

    We consider zero-temperature transitions from conformal to nonconformal phases in quantum theories. We argue that there are three generic mechanisms for the loss of conformality in any number of dimensions: (i) fixed point goes to zero coupling, (ii) fixed point runs off to infinite coupling, or (iii) an IR fixed point annihilates with a UV fixed point and they both disappear into the complex plane. We give both relativistic and nonrelativistic examples of the last case in various dimensions and show that the critical behavior of the mass gap behaves similarly to the correlation length in the finite temperature Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions, ξ∼exp(c/|T-T c | 1/2 ). We speculate that the chiral phase transition in QCD at large number of fermion flavors belongs to this universality class, and attempt to identify the UV fixed point that annihilates with the Banks-Zaks fixed point at the lower end of the conformal window.

  15. An EPR study of positive hole transfer and trapping in irradiated frozen solutions containing aromatic traps

    International Nuclear Information System (INIS)

    Egorov, A.V.; Zezin, A.A.; Feldman, V.I.

    2002-01-01

    Complete text of publication follows. Processes of positive hole migration and trapping are of basic significance for understanding of the primary events in the radiation chemistry of solid molecular systems. Specific interest is concerned with the case, when ionization energies of 'hole traps' are rather close, so one may expect 'fine tuning' effects resulting from variations in conformation, weak interactions, molecular packing, etc. In this contribution we report the results of EPR study of formation of radical cations in irradiated frozen halocarbon solutions containing aromatic molecules of different structure. Using the 'two-trap' model made it possible to obtain an evidence for efficient long-range trap-to-trap positive hole transfer between alkyl benzene molecules with close ionization energies distributed in the matrices with high ionization potentials. The distance of transfer was found to be 2-4 nm. In the case of frozen solutions containing ethylbenzene and toluene, it was found that the efficiency and direction of hole transfer was controlled by the conformation of ethylbenzene radical cation. The study of positive hole localization in 'bridged' diphenyls of Ph(CH 2 ) n Ph type revealed that the structure of radical cations of these species was affected by local environment (type of halocarbon matrix) and the conformational flexibility of 'bridge'. In summary, we may conclude that migration and localization of positive hole in rigid systems containing aromatic 'traps' is quite sensitive to rather subtle effects. This conclusion may be of common significance for the radiation chemistry of systems with physical dispersion of the traps of similar chemical structure (e.g. macromolecules, adsorbed molecules, etc.)

  16. Study of Bovine Serum Albumin Solubility in Aqueous Solutions by Intrinsic Viscosity Measurements

    Directory of Open Access Journals (Sweden)

    Martin Alberto Masuelli

    2013-01-01

    Full Text Available The behavior of bovine serum albumin (BSA in water is scarcely studied, and the thermodynamic properties arising from the experimental measurements have not been reported. Intrinsic viscosity measurements are very useful in assessing the interaction between the solute and solvent. This work discussed in a simple determination of the enthalpy of BSA in aqueous solution when the concentration ranges from 0.2 to 36.71% wt. and the temperature from 35 to 40°C. The relationship between the concentration and intrinsic viscosity is determined according to the method of Huggins. The temperature increase reduces the ratio between inherent viscosity and concentration (ηi/c. This is reflected in the Van't Hoff curve. Furthermore, this work proposes hydrodynamic cohesion value as an indicator of the degree of affinity of protein with water and thermodynamic implications in conformational changes.

  17. Conformational analysis by intersection: CONAN.

    Science.gov (United States)

    Smellie, Andrew; Stanton, Robert; Henne, Randy; Teig, Steve

    2003-01-15

    As high throughput techniques in chemical synthesis and screening improve, more demands are placed on computer assisted design and virtual screening. Many of these computational methods require one or more three-dimensional conformations for molecules, creating a demand for a conformational analysis tool that can rapidly and robustly cover the low-energy conformational spaces of small molecules. A new algorithm of intersection is presented here, which quickly generates (on average heuristics are applied after intersection to generate a small representative collection of conformations that span the conformational space. In a study of approximately 97,000 randomly selected molecules from the MDDR, results are presented that explore these conformations and their ability to cover low-energy conformational space. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 24: 10-20, 2003

  18. Three-dimensional (3D) real-time conformal brachytherapy - a novel solution for prostate cancer treatment Part I. Rationale and method

    International Nuclear Information System (INIS)

    Fijalkowski, M.; Bialas, B.; Maciejewski, B.; Bystrzycka, J.; Slosarek, K.

    2005-01-01

    Recently, the system for conformal real-time high-dose-rate brachytherapy has been developed and dedicated in general for the treatment of prostate cancer. The aim of this paper is to present the 3D-conformal real-time brachytherapy technique introduced to clinical practice at the Institute of Oncology in Gliwice. Equipment and technique of 3D-conformal real time brachytherapy (3D-CBRT) is presented in detail and compared with conventional high-dose-rate brachytherapy. Step-by-step procedures of treatment planning are described, including own modifications. The 3D-CBRT offers the following advantages: (1) on-line continuous visualization of the prostate and acquisition of the series of NS images during the entire procedure of planning and treatment; (2) high precision of definition and contouring the target volume and the healthy organs at risk (urethra, rectum, bladder) based on 3D transrectal continuous ultrasound images; (3) interactive on-line dose optimization with real-time corrections of the dose-volume histograms (DVHs) till optimal dose distribution is achieved; (4) possibility to overcome internal prostate motion and set-up inaccuracies by stable positioning of the prostate with needles fixed to the template; (5) significant shortening of overall treatment time; (6) cost reduction - the treatment can be provided as an outpatient procedure. The 3D- real time CBRT can be advertised as an ideal conformal boost dose technique integrated or interdigitated with pelvic conformal external beam radiotherapy or as a monotherapy for prostate cancer. (author)

  19. Study of the conformal symmetry breaking in field theories in gravitational background using path integrals

    International Nuclear Information System (INIS)

    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

  20. 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

  1. Conformational change in full-length mouse prion: A site-directed spin-labeling study

    International Nuclear Information System (INIS)

    Inanami, Osamu; Hashida, Shukichi; Iizuka, Daisuke; Horiuchi, Motohiro; Hiraoka, Wakako; Shimoyama, Yuhei; Nakamura, Hideo; Inagaki, Fuyuhiko; Kuwabara, Mikinori

    2005-01-01

    The structure of the mouse prion (moPrP) was studied using site-directed spin-labeling electron spin resonance (SDSL-ESR). Since a previous NMR study by Hornemanna et al., [Hornemanna, Korthb, Oeschb, Rieka, Widera, Wuethricha, Glockshubera, Recombinant full-length murine prion protein, mPrP (23-231): purification and spectroscopic characterization, FEBS Lett. 413 (1997) 277-281] has indicated that N96, D143, and T189 in moPrP are localized in a Cu 2+ binding region, Helix1 and Helix2, respectively, three recombinant moPrP mutations (N96C, D143C, and T189C) were expressed in an Escherichia coli system, and then refolded by dialysis under low pH and purified by reverse-phase HPLC. By using the preparation, we succeeded in preserving a target cystein residue without alteration of the α-helix structure of moPrP and were able to apply SDSL-ESR with a methane thiosulfonate spin label to the full-length prion protein. The rotational correlation times (τ) of 1.1, 3.3, and 4.8 ns were evaluated from the X-band ESR spectra at pH 7.4 and 20 deg C for N96R1, D143R1, and T189R1, respectively. τ reflects the fact that the Cu 2+ binding region is more flexible than Helix1 or Helix2. ESR spectra recorded at various temperatures revealed two phases together with a transition point at around 20 deg C in D143R1 and T189R1, but not in N96R1. With the variation of pH from 4.0 to 7.8, ESR spectra of T189R1 at 20 deg C showed a gradual increase of τ from 2.9 to 4.8 ns. On the other hand, the pH-dependent conformational changes in N96R1 and D143R1 were negligible. These results indicated that T189 located in Helix2 possessed a structure sensitive to physiological pH changes; simultaneously, N96 in the Cu 2+ binding region and D143 in Helix1 were conserved

  2. 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.

  3. Squaraine rotaxanes with boat conformation macrocycles.

    Science.gov (United States)

    Fu, Na; Baumes, Jeffrey M; Arunkumar, Easwaran; Noll, Bruce C; Smith, Bradley D

    2009-09-04

    Mechanical encapsulation of fluorescent, deep-red bis(anilino)squaraine dyes inside Leigh-type tetralactam macrocycles produces interlocked squaraine rotaxanes. The surrounding macrocycles are flexible and undergo rapid exchange of chair and boat conformations in solution. A series of X-ray crystal structures show how the rotaxane co-conformational exchange process involves simultaneous lateral oscillation of the macrocycle about the center of the encapsulated squaraine thread. Rotaxane macrocycles with 1,4-phenylene sidewalls and 2,6-pyridine dicarboxamide bridging units are more likely to adopt boat conformations in the solid state than analogous squaraine rotaxane systems with isophthalamide-containing macrocycles. A truncated squaraine dye, with a secondary amine attached directly to the central C(4)O(2) core, is less electrophilic than the extended bis(anilino)squaraine analogue, but it is still susceptible to chemical and photochemical bleaching. Its stability is greatly enhanced when it is encapsulated as an interlocked squaraine rotaxane. An X-ray crystal structure of this truncated squaraine rotaxane shows the macrocycle in a boat conformation, and NMR studies indicate that the boat is maintained in solution. Encapsulation as a rotaxane increases the dye's brightness by a factor of 6. The encapsulation process appears to constrain the dye and reduce deformation of the chromophore from planarity. This study shows how mechanical encapsulation as a rotaxane can be used as a rational design parameter to fine-tune the chemical and photochemical properties of squaraine dyes.

  4. Adler function and Bjorken polarized sum rule: Perturbation expansions in powers of the S U (Nc) conformal anomaly and studies of the conformal symmetry limit

    Science.gov (United States)

    Cvetič, Gorazd; Kataev, A. L.

    2016-07-01

    We consider a new form of analytical perturbation theory expansion in the massless S U (Nc) theory, for the nonsinglet part of the e+e--annihilation to hadrons Adler function Dn s and of the Bjorken sum rule of the polarized lepton-hadron deep-inelastic scattering Cns B j p, and demonstrate its validity at the O (αs4)-level at least. It is a two-fold series in powers of the conformal anomaly and of S U (Nc) coupling αs. Explicit expressions are obtained for the {β }-expanded perturbation coefficients at O (αs4) level in MS ¯ scheme, for both considered physical quantities. Comparisons of the terms in the {β }-expanded coefficients are made with the corresponding terms obtained by using extra gluino degrees of freedom, or skeleton-motivated expansion, or Rδ-scheme motivated expansion in the Principle of Maximal Conformality. Relations between terms of the {β }-expansion for the Dn s- and Cns B j p-functions, which follow from the conformal symmetry limit and its violation, are presented. The relevance to the possible new analyses of the experimental data for the Adler function and Bjorken sum rule is discussed.

  5. Conformal algebra of Riemann surfaces

    International Nuclear Information System (INIS)

    Vafa, C.

    1988-01-01

    It has become clear over the last few years that 2-dimensional conformal field theories are a crucial ingredient of string theory. Conformal field theories correspond to vacuum solutions of strings; or more precisely we know how to compute string spectrum and scattering amplitudes by starting from a formal theory (with a proper value of central charge of the Virasoro algebra). Certain non-linear sigma models do give rise to conformal theories. A lot of progress has been made in the understanding of conformal theories. The author discusses a different view of conformal theories which was motivated by the development of operator formalism on Riemann surfaces. The author discusses an interesting recent work from this point of view

  6. Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes.

    Science.gov (United States)

    Ruiz-Tórtola, Ángela; Prats-Quílez, Francisco; Gónzalez-Lucas, Daniel; Bañuls, María-José; Maquieira, Ángel; Wheeler, Guy; Dalmay, Tamas; Griol, Amadeu; Hurtado, Juan; Bohlmann, Helge; Götzen, Reiner; García-Rupérez, Jaime

    2018-04-17

    An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin-labeled MB probes were immobilized. This article is protected by copyright. All rights reserved.

  7. General shape and hapten-induced conformational changes of pig anti-dinitrophenyl antibody. A small-angle scattering study

    International Nuclear Information System (INIS)

    Cher, L.; Gladkikh, I.A.; Franek, F.; Kunchenko, A.B.; Ostanevich, Yu.M.

    1980-01-01

    Pig anti-dinitrophenyl antibodies were studied by neutron and X-ray small-angle scattering. Observed scattering curves show that the shapes of two antibody types, precipitating and non-precipitating, are similar, however the latter being more compact. A hapten binding induced conformational change of antibody is observed. This conformational change might be described as a contraction of the whole molecule via similarity transformation. The spatial models of pig antibody molecule based on the existing experimental data were designed. Most probable models have a cavity in the Fsub(c) part and the Fsub(ab) parts are either fully extended or slightly bent down to the Fsub(c) part

  8. Conformally symmetric traversable wormholes

    International Nuclear Information System (INIS)

    Boehmer, Christian G.; Harko, Tiberiu; Lobo, Francisco S. N.

    2007-01-01

    Exact solutions of traversable wormholes are found under the assumption of spherical symmetry and the existence of a nonstatic conformal symmetry, which presents a more systematic approach in searching for exact wormhole solutions. In this work, a wide variety of solutions are deduced by considering choices for the form function, a specific linear equation of state relating the energy density and the pressure anisotropy, and various phantom wormhole geometries are explored. A large class of solutions impose that the spatial distribution of the exotic matter is restricted to the throat neighborhood, with a cutoff of the stress-energy tensor at a finite junction interface, although asymptotically flat exact solutions are also found. Using the 'volume integral quantifier', it is found that the conformally symmetric phantom wormhole geometries may, in principle, be constructed by infinitesimally small amounts of averaged null energy condition violating matter. Considering the tidal acceleration traversability conditions for the phantom wormhole geometry, specific wormhole dimensions and the traversal velocity are also deduced

  9. Conformable covered versus uncovered self-expandable metallic stents for palliation of malignant gastroduodenal obstruction: a randomized prospective study.

    Science.gov (United States)

    Lim, Sun Gyo; Kim, Jin Hong; Lee, Kee Myung; Shin, Sung Jae; Kim, Chan Gyoo; Kim, Kyung Ho; Kim, Ho Gak; Yang, Chang Heon

    2014-07-01

    A conformable self-expandable metallic stent was developed to overcome the limitation of previous self-expandable metallic stents. The aim of this study was to evaluate outcomes after placement of conformable covered and uncovered self-expandable metallic stents for palliation of malignant gastroduodenal obstruction. A single-blind, randomized, parallel-group, prospective study were conducted in 4 medical centres between March 2009 and July 2012. 134 patients with unresectable malignant gastroduodenal obstruction were assigned to a covered double-layered (n=66) or uncovered unfixed-cell braided (n=68) stent placement group. Primary analysis was performed to compare re-intervention rates between two groups. 120 patients were analysed (59 in the covered group and 61 in the uncovered group). Overall rates of re-intervention were not significantly different between the two groups: 13/59 (22.0%) in the covered group vs. 13/61 (21.3%) in the uncovered group, p=0.999. Stent migration was more frequent in the covered group than in the uncovered group (p=0.003). The tumour ingrowth rate was higher in the uncovered group than in the covered group (p=0.016). The rates of re-intervention did not significantly differ between the two stents. Conformable covered double-layered and uncovered unfixed-cell braided stents were associated with different patterns of stent malfunction. Copyright © 2014 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  10. Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanide

    Science.gov (United States)

    Anandan, K.; Kolandaivel, P.; Kumaresan, R.

    Ab initio and density functional theory (DFT) methods have been employed to study the molecular structural conformations and hydrated forms of both salicylamide (SAM) and O-hydroxybenzoyl cyanide (OHBC). Molecular geometries and energetics have been obtained in the gaseous phase by employing the Møller-Plesset type 2 MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The presence of an electron-releasing group (SAM) leads to an increase in the energy of the molecular system, while the presence of an electron-withdrawing group (OHBC) drastically decreases the energy. Chemical reactivity parameters (η and μ) have been calculated using the energy values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained at the Hartree-Fock (HF)/6-311G(2d,2p) level of theory for all the conformers and the principle of maximum hardness (MHP) has been tested. The condensed Fukui functions have been calculated using the atomic charges obtained through the natural bond orbital (NBO) analysis scheme for all the optimized structures at the B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules have been identified. Nuclear magnetic resonance (NMR) studies have been carried out at the B3LYP/6-311G(2d,2p) level of theory for all the conformers in the gaseous phase on the basis of the method of Cheeseman and coworkers. The calculated chemical shift values have been used to discuss the delocalization activity of the electron clouds. The dimeric structures of the most stable conformers of both SAM and OHBC in the gaseous phase have been optimized at the B3LYP/6-311G(2d,2p) level of theory, and the interaction energies have been calculated. The most stable conformers of both compounds bear an intramolecular hydrogen bond, which gives rise to the formation of a pseudo-aromatic ring. These conformers have been allowed to interact with the water molecule. Special emphasis has been given to analysis of the

  11. Conformal potential in N dimensions (N>1)

    Energy Technology Data Exchange (ETDEWEB)

    Barucchi, G [Turin Univ. (Italy). Ist. di Fisica; Istituto di Fisica Matematica dell' Universita, Torino (Italy); Istituto Nazionale di Fisica Nucleare, Turin (Italy))

    1977-07-21

    The conformal invariant model of de Alfaro, Fubini and Furlan is studied in the case of potential V(Q) = g/2Q/sup 2/(Q/sup 2/ = ..sigma..sub(i=1)sup(N) Qsub(i)sup(2), N>1). By means of the invariance under projective transformations and the rotation symmetry of the system in configuration space, explicit solutions are obtained.

  12. Scalar perturbations and conformal transformation

    International Nuclear Information System (INIS)

    Fabris, J.C.; Tossa, J.

    1995-11-01

    The non-minimal coupling of gravity to a scalar field can be transformed into a minimal coupling through a conformal transformation. We show how to connect the results of a perturbation calculation, performed around a Friedman-Robertson-Walker background solution, before and after the conformal transformation. We work in the synchronous gauge, but we discuss the implications of employing other frames. (author). 16 refs

  13. Conformational analysis of 9β,19-cyclopropyl sterols: Detection of the pseudoplanar conformer by nuclear Overhauser effects and its functional implications

    International Nuclear Information System (INIS)

    Nes, W.D.; Benson, M.; Lundin, R.E.; Le, P.H.

    1988-01-01

    Nuclear Overhauser difference spectroscopy and variable temperature studies of the 9β,19-cyclopropyl sterols 24,25-dehydropollinastanol (4,4-desmethyl-5α-cycloart-24-en-3β-ol) and cyclolaudenol [(24S)-24-methyl-5α-cycloart-25(27)-en-3β-ol] have shown the solution conformation of the B/C rings to be twist-chair/twist-boat rather than boat/chair as suggested in the literature. This is very similar to the known crystal structure conformation of 9β,19-cyclopropyl sterols. The effect of these conformations on the molecular shape is highly significant; the first conformation orients into a pseudoplanar or flat shape analogous to lanosterol, whereas the latter conformation exhibits a bent shape. The results are interpreted to imply that, for conformational reasons, cyclopropyl sterols can be expected to maintain the pseudoplanar shape in membrane bilayers

  14. 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.

  15. Dielectric and conformational studies of hydrogen bonded 2-ethoxyethanol and ethyl methyl ketone system

    Science.gov (United States)

    Pattebahadur, Kanchan. L.; Deshmukh, S. D.; Mohod, A. G.; Undre, P. B.; Patil, S. S.; Khirade, P. W.

    2018-05-01

    The Dielectric constant, density and refractive index of binary mixture of 2-ethoxy ethanol (2-EE) with ethyl methyl ketone (EMK) including those of the pure liquids were measured for 11 concentrations at 25°C temperature. The experimental data is used to calculate the Excess molar volume, Excess dielectric constant, Kirkwood correlation factor and Bruggemann factor. The excess parameters results were fitted to the Redlich-Kister type polynomial equation to derive its fitting coefficient. The Kirkwood correlation factor of the mixture has been discussed to yield information about solute solvent interaction. The Bruggeman plot shows a deviation from linearity. The FT-IR spectra of pure and their binary mixtures are also studied.

  16. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase

    Directory of Open Access Journals (Sweden)

    Yanwei Li

    2016-08-01

    Full Text Available The quantum mechanics/molecular mechanics (QM/MM method (e.g., density functional theory (DFT/MM is important in elucidating enzymatic mechanisms. It is indispensable to study “multiple” conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.

  17. Metal binding characterization and conformational studies using Raman microscopy of resin-bound poly(aspartic acid).

    Science.gov (United States)

    Stair, Jacqueline L; Holcombe, James A

    2007-03-01

    The metal binding capacities, conditional stability constants, and secondary structure of immobilized polyaspartic acid (PLAsp) (n = 6, 20, and 30) on TentaGel resin were determined when binding Mg2+, Co2+, Cd2+, and Ni2+. Metal binding to the synthesized peptides was evaluated using breakthrough curves from a packed microcolumn and flame atomic absorption spectrophotometry (FAAS) detection. The metal capacities reached values of 590, 2160, and 3710 mumol of metal/g of resin for the 6-mer, 20-mer, and 30-mer, respectively, and this resulted in 2-3 residues per metal for all peptides and metals tested. Surprisingly, the concentrated environment of the resin along with the spatial distribution of attachment groups allowed for most residues to participate in metal binding regardless of the peptide length. Conditional stability constants calculated using single metal binding isotherms indicated that binding strength decreased as the chain length increased on the resin. Raman microscopy on single beads was used to determine PLAsp secondary structure, and all peptides were of a mixed conformation (i.e., beta-sheets, alpha-helices, random chain, etc.) during neutral conditioning and metal binding. Uniquely, the longer 20-mer and 30-mer peptides showed a distinct change from a mixed conformation to beta-sheets and alpha-helices during metal release with acid. This study confirms that metal release by longer immobilized peptides is often assisted by a conformational change, which easily spoils the binding cavity, while shorter peptides may release metal primarily by H+ displacement.

  18. 4D-Qsar Study of Some Pyrazole Pyridine Carboxylic Acid Derivatives by Electron Conformational-Genetic Algorithm Method.

    Science.gov (United States)

    Tuzun, Burak; Yavuz, Sevtap Caglar; Sabanci, Nazmiye; Saripinar, Emin

    2018-05-13

    In the present work, pharmacophore identification and biological activity prediction for 86 pyrazole pyridine carboxylic acid derivatives were made using the electron conformational genetic algorithm approach which was introduced as a 4D-QSAR analysis by us in recent years. In the light of the data obtained from quantum chemical calculations at HF/6-311 G** level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. Comparing the matrices, electron conformational submatrix of activity (ECSA, Pha) was revealed that are common for these compounds within a minimum tolerance. A parameter pool was generated considering the obtained pharmacophore. To determine the theoretical biological activity of molecules and identify the best subset of variables affecting bioactivities, we used the nonlinear least square regression method and genetic algorithm. The results obtained in this study are in good agreement with the experimental data presented in the literature. The model for training and test sets attained by the optimum 12 parameters gave highly satisfactory results with R2training= 0.889, q2=0.839 and SEtraining=0.066, q2ext1 = 0.770, q2ext2 = 0.750, q2ext3=0.824, ccctr = 0.941, ccctest = 0.869 and cccall = 0.927. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  19. Phase I study of conformal radiotherapy with concurrent gemcitabine in locally advanced bladder cancer

    International Nuclear Information System (INIS)

    Sangar, Vijay K.; McBain, Catherine A.; Lyons, Jeanette; Ramani, Vijay; Logue, John; Wylie, James; Clarke, Noel W.; Cowan, Richard A.

    2005-01-01

    Purpose: A prospective phase I trial was conducted to determine the maximal tolerated dose of gemcitabine given once weekly during hypofractionated conformal radiotherapy to patients with locally advanced transitional cell carcinoma of the bladder. Eight male patients, median age 69 years, with Stage T2 (n = 4) or T3 (n = 4) N0M0, were enrolled in cohorts of 3. Treatment comprised conformal radiotherapy (52.5 Gy in 20 fractions) within 4 weeks, with concurrent gemcitabine once weekly for four cycles. The weekly gemcitabine dose was escalated from 100 mg/m 2 in increments of 50 mg/m 2 per cohort. Dose-limiting toxicity was defined as any acute Radiation Therapy Oncology Group (RTOG) toxicity Grade 3 or greater arising in >1 of 3 patients in each cohort. Tumor response was assessed cystoscopically and radiologically at 3 months. Results: All 8 patients completed radiotherapy, and 6 of 8 completed chemoradiotherapy. No acute toxicity greater than RTOG Grade 1 was seen with gemcitabine at 100 mg/m 2 . Dose-limiting toxicity was observed at 150 mg/m 2 with Grade 3 toxicity seen in 2 of 2 patients (one bladder, one bowel). An additional 3 patients received 100 mg/m 2 with minimal toxicity. No hematologic toxicity was encountered. A complete response was seen in 7 (87.5%) of 8 patients, all of whom were disease free at a median follow-up of 19.5 months (range, 14-23 months). No late toxicity (greater than RTOG Grade 0) has been observed. Conclusion: The maximal tolerated dose for gemcitabine given once weekly with concurrent hypofractionated conformal bladder radiotherapy was 150 mg/m 2 , with a maximal recommended dose of 100 mg/m 2 . This dose regimen has now entered Phase II clinical trials

  20. Supersonic Jet Studies of Benzyl Alcohols: Minimum Energy Conformations and Torsional Motion

    Science.gov (United States)

    1990-05-13

    New York: 1980. (46) Bernstein, E. R.; Law, K.; Schauer, M. J. Chem. Phys. 1984, 80, 207. (47) Hanzlik , R. P.; Schaefer , A. R.; Moon , J. B.; Judson , C...M. J. Am. Chem. Soc. 1987 , 109 , 4926 . -32- Table I. Conformations of substituted benzenes as established by laser jet spectroscopy. jY x 1 ortho T...Chem. Soc. 1987 , 109 , 3453. -29- (11) Breen, P. J.; Bernstein, E. R.; Seeman, J. I. J. Chem, Phys. 1987 , 87, 3269. (12) Breen, P. J.; Warren, J. A

  1. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

    Science.gov (United States)

    Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

    2010-12-30

    Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Förster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(α)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(α)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, β-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an

  2. Conformational effects on the torsional barriers in m-methylanisole studied by microwave spectroscopy

    Science.gov (United States)

    Ferres, Lynn; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

    2018-03-01

    The microwave spectrum of m-methylanisole (also known as 3-methylanisole, or 3-methoxytoluene) was measured using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range of 2-26.5 GHz. Quantum chemical calculations predicted two conformers with the methoxy group in trans or cis position related to the ring methyl group, both of which were assigned in the experimental spectrum. Due to the internal rotation of the ring methyl group, all rotational transitions introduced large A-E splittings up to several GHz, which were analyzed with a newly developed program, called aixPAM, working in the principal axis system. There are significant differences in the V3 potential barriers of 55.7693(90) cm-1 and 36.6342(84) cm-1 determined by fitting 223 and 320 torsional components of the cis and the trans conformer, respectively. These values were compared with those found in other m-substituted toluenes as well as in o- and p-methylanisole. A comparison between the aixPAM and the XIAM code (using a combined axis system) was also performed.

  3. Three-dimensional structural analysis of the group B polysaccharide of Neisseria meningitidis 6275 by two-dimensional NMR: The polysaccharide is suggested to exist in helical conformations in solution

    Energy Technology Data Exchange (ETDEWEB)

    Yamasaki, Ryohei; Bacon, B. (Univ. of California, San Francisco (USA) Veterans Administration Medical Center, San Francisco, CA (USA))

    1991-01-22

    The solution conformations of the group B polysaccharide of Neisseria meningitidis were analyzed by DQF-COSY and pure absorption 2D NOE NMR with three mixing times. The pyranose ring of the sialic acid residue was found to be in the {sup 2}C{sub 5} conformation. The DQF-COSY analysis indicated that the orientations of H6 and H7 and of H7 and H8 are both gauche. In order to overcome the difficulties in analyzing the NOE data due to the two sets of proton overlaps, molecular modeling of {alpha}-2,8-linked sialic acid oligomers was carried out to investigate possible conformers, and theoretical NOE calculations were performed by using CORMA (complete relaxation matrix analysis). The analysis suggests that the polysaccharide adopts helical structures for which the {phi} (defined by O6-C2-O8-C8) and {psi} (C2-O8-C8-C7) angles are in the following ranges: {phi}-60 to 0{degree}, {psi} 115-175{degree} or {phi} 90-120{degree}, {psi}55-175{degree}. The weak affinity of anti-B antibodies for smaller {alpha}-2,8-linked oligosaccharides may be due to the fact that such oligomers are more flexible and may not form an ordered structure as the poly(sialic acid) does.

  4. A study of the radiobiological modeling of the conformal radiation therapy in cancer treatment

    Science.gov (United States)

    Pyakuryal, Anil Prasad

    Cancer is one of the leading causes of mortalities in the world. The precise diagnosis of the disease helps the patients to select the appropriate modality of the treatments such as surgery, chemotherapy and radiation therapy. The physics of X-radiation and the advanced imaging technologies such as positron emission tomography (PET) and computed tomography (CT) plays an important role in the efficient diagnosis and therapeutic treatments in cancer. However, the accuracy of the measurements of the metabolic target volumes (MTVs) in the PET/CT dual-imaging modality is always limited. Similarly the external beam radiation therapy (XRT) such as 3D conformal radiotherapy (3DCRT) and intensity modulated radiation therapy (IMRT) is the most common modality in the radiotherapy treatment. These treatments are simulated and evaluated using the XRT plans and the standard methodologies in the commercial planning system. However, the normal organs are always susceptible to the radiation toxicity in these treatments due to lack of knowledge of the appropriate radiobiological models to estimate the clinical outcomes. We explored several methodologies to estimate MTVs by reviewing various techniques of the target volume delineation using the static phantoms in the PET scans. The review suggests that the more precise and practical method of delineating PET MTV should be an intermediate volume between the volume coverage for the standardized uptake value (SUV; 2.5) of glucose and the 50% (40%) threshold of the maximum SUV for the smaller (larger) volume delineations in the radiotherapy applications. Similarly various types of optimal XRT plans were designed using the CT and PET/CT scans for the treatment of various types of cancer patients. The qualities of these plans were assessed using the universal plan-indices. The dose-volume criteria were also examined in the targets and organs by analyzing the conventional dose-volume histograms (DVHs). The biological models such as tumor

  5. 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 ... dual purpose of helping developing countries achieve sustainable development ... with a view to devising integrated waste management solutions in urban centres ... and disseminate them through national, regional and international networks.

  6. Numerical studies of rotational core collapse in axisymmetry using the conformally flat metric approach

    International Nuclear Information System (INIS)

    Dimmelmeier, H.; Font, J.A.; Mueller, E.

    2001-01-01

    The numerical simulation of hydrodynamic processes in general relativity is a highly complex problem. In order to reduce the complexity of the gravitational field equations, Wilson and coworkers have proposed an approximation scheme, where the 3-metric γ ij is chosen to be conformally flat. In this approximation the Einstein equations reduce to a set of 5 coupled elliptic equations. In this paper we present an axisymmetric general relativistic hydrodynamic code which utilizes this approach together with high-resolution shock-capturing schemes to solve the hydrodynamic equations. We report on tests and preliminary applications of the code to rotating neutron stars and supernova core collapse in axisymmetry. The code promises good applicability to handle a variety of relativistic astrophysical situations, and is prepared to provide information about gravitational radiation from rotating gravitational collapse. (author)

  7. 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.

  8. Protein conformational transitions at the liquid-gas interface as studied by dilational surface rheology.

    Science.gov (United States)

    Noskov, Boris A

    2014-04-01

    Experimental results on the dynamic dilational surface elasticity of protein solutions are analyzed and compared. Short reviews of the protein behavior at the liquid-gas interface and the dilational surface rheology precede the main sections of this work. The kinetic dependencies of the surface elasticity differ strongly for the solutions of globular and non-globular proteins. In the latter case these dependencies are similar to those for solutions of non-ionic amphiphilic polymers and have local maxima corresponding to the formation of the distal region of the surface layer (type I). In the former case the dynamic surface elasticity is much higher (>60 mN/m) and the kinetic dependencies are monotonical and similar to the data for aqueous dispersions of solid nanoparticles (type II). The addition of strong denaturants to solutions of bovine serum albumin and β-lactoglobulin results in an abrupt transition from the type II to type I dependencies if the denaturant concentration exceeds a certain critical value. These results give a strong argument in favor of the preservation of the protein globular structure in the course of adsorption without any denaturants. The addition of cationic surfactants also can lead to the non-monotonical kinetic dependencies of the dynamic surface elasticity indicating destruction of the protein tertiary and secondary structures. The addition of anionic surfactants gives similar results only for the protein solutions of high ionic strength. The influence of cationic surfactants on the local maxima of the kinetic dependencies of the dynamic surface elasticity for solutions of a non-globular protein (β-casein) differs from the influence of anionic surfactants due to the heterogeneity of the charge distribution along the protein chain. In this case one can use small admixtures of ionic surfactants as probes of the adsorption mechanism. The effect of polyelectrolytes on the kinetic dependencies of the dynamic surface elasticity of protein

  9. Analytic study of nonperturbative solutions in open string field theory

    International Nuclear Information System (INIS)

    Bars, I.; Kishimoto, I.; Matsuo, Y.

    2003-01-01

    We propose an analytic framework to study the nonperturbative solutions of Witten's open string field theory. The method is based on the Moyal star formulation where the kinetic term can be split into two parts. The first one describes the spectrum of two identical half strings which are independent from each other. The second one, which we call midpoint correction, shifts the half string spectrum to that of the standard open string. We show that the nonlinear equation of motion of string field theory is exactly solvable at zeroth order in the midpoint correction. An infinite number of solutions are classified in terms of projection operators. Among them, there exists only one stable solution which is identical to the standard butterfly state. We include the effect of the midpoint correction around each exact zeroth order solution as a perturbation expansion which can be formally summed to the complete exact solution

  10. Fluoride removal from aqueous solution by pumice: case study on ...

    African Journals Online (AJOL)

    EJIRO

    conditions, the fluoride removal efficiency from Kuhbonan water by 2.8 mg/L fluoride was 74.64%. Eventually ... industrial wastewater containing fluoride is a key ..... solution using silica ceramic: Adsorption kinetics and equilibrium studies.

  11. Logarithmic conformal field theory through nilpotent conformal dimensions

    International Nuclear Information System (INIS)

    Moghimi-Araghi, S.; Rouhani, S.; Saadat, M.

    2001-01-01

    We study logarithmic conformal field theories (LCFTs) through the introduction of nilpotent conformal weights. Using this device, we derive the properties of LCFTs such as the transformation laws, singular vectors and the structure of correlation functions. We discuss the emergence of an extra energy momentum tensor, which is the logarithmic partner of the energy momentum tensor

  12. Comparative study of four advanced 3d-conformal radiation therapy treatment planning techniques for head and neck cancer

    International Nuclear Information System (INIS)

    Herrassi, Mohamed Yassine; Bentayeb, Farida; Malisan, Maria Rosa

    2013-01-01

    For the head-and-neck cancer bilateral irradiation, intensity-modulated radiation therapy (IMRT) is the most reported technique as it enables both target dose coverage and organ-at-risk (OAR) sparing. However, during the last 20 years, three-dimensional conformal radiotherapy (3DCRT) techniques have been introduced, which are tailored to improve the classic shrinking field technique, as regards both planning target volume (PTV) dose conformality and sparing of OARs, such as parotid glands and spinal cord. In this study, we tested experimentally in a sample of 13 patients, four of these advanced 3DCRT techniques, all using photon beams only and a unique isocentre, namely Bellinzona, Forward-Planned Multisegments (FPMS), ConPas, and field-in-field (FIF) techniques. Statistical analysis of the main dosimetric parameters of PTV and OARs DVHs as well as of homogeneity and conformity indexes was carried out in order to compare the performance of each technique. The results show that the PTV dose coverage is adequate for all the techniques, with the FPMS techniques providing the highest value for D95%; on the other hand, the best sparing of parotid glands is achieved using the FIF and ConPas techniques, with a mean dose of 26 Gy to parotid glands for a PTV prescription dose of 54 Gy. After taking into account both PTV coverage and parotid sparing, the best global performance was achieved by the FIF technique with results comparable to that of IMRT plans. This technique can be proposed as a valid alternative when IMRT equipment is not available or patient is not suitable for IMRT treatment. (author)

  13. Conformation-related exciton localization and charge-pair formation in polythiophenes: ensemble and single-molecule study.

    Science.gov (United States)

    Sugimoto, Toshikazu; Habuchi, Satoshi; Ogino, Kenji; Vacha, Martin

    2009-09-10

    We study conformation-dependent photophysical properties of polythiophene (PT) by molecular dynamics simulations and by ensemble and single-molecule optical experiments. We use a graft copolymer consisting of a polythiophene backbone and long polystyrene branches and compare its properties with those obtained on the same polythiophene derivative without the side chains. Coarse-grain molecular dynamics simulations show that in a poor solvent, the PT without the side chains (PT-R) forms a globulelike conformation in which distances between any two conjugated segments on the chain are within the Forster radius for efficient energy transfer. In the PT with the polystyrene branches (PT-PS), the polymer main PT chain retains an extended coillike conformation, even in a poor solvent, and the calculated distances between conjugated segments favor energy transfer only between a few neighboring chromophores. The theoretical predictions are confirmed by measurements of fluorescence anisotropy and fluorescence blinking of the polymers' single chains. High anisotropy ratios and two-state blinking in PT-R are due to localization of the exciton on a single conjugated segment. These signatures of exciton localization are absent in single chains of PT-PS. Electric-field-induced quenching measured as a function of concentration of PT dispersed in an inert matrix showed that in well-isolated chains of PT-PS, the exciton dissociation is an intrachain process and that aggregation of the PT-R chains causes an increase in quenching due to the onset of interchain interactions. Measurements of the field-induced quenching on single chains indicate that in PT-R, the exciton dissociation is a slower process that takes place only after the exciton is localized on one conjugated segment.

  14. 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

  15. Conformal and covariant Z4 formulation of the Einstein equations: Strongly hyperbolic first-order reduction and solution with discontinuous Galerkin schemes

    Science.gov (United States)

    Dumbser, Michael; Guercilena, Federico; Köppel, Sven; Rezzolla, Luciano; Zanotti, Olindo

    2018-04-01

    We present a strongly hyperbolic first-order formulation of the Einstein equations based on the conformal and covariant Z4 system (CCZ4) with constraint-violation damping, which we refer to as FO-CCZ4. As CCZ4, this formulation combines the advantages of a conformal and traceless formulation, with the suppression of constraint violations given by the damping terms, but being first order in time and space, it is particularly suited for a discontinuous Galerkin (DG) implementation. The strongly hyperbolic first-order formulation has been obtained by making careful use of first and second-order ordering constraints. A proof of strong hyperbolicity is given for a selected choice of standard gauges via an analytical computation of the entire eigenstructure of the FO-CCZ4 system. The resulting governing partial differential equations system is written in nonconservative form and requires the evolution of 58 unknowns. A key feature of our formulation is that the first-order CCZ4 system decouples into a set of pure ordinary differential equations and a reduced hyperbolic system of partial differential equations that contains only linearly degenerate fields. We implement FO-CCZ4 in a high-order path-conservative arbitrary-high-order-method-using-derivatives (ADER)-DG scheme with adaptive mesh refinement and local time-stepping, supplemented with a third-order ADER-WENO subcell finite-volume limiter in order to deal with singularities arising with black holes. We validate the correctness of the formulation through a series of standard tests in vacuum, performed in one, two and three spatial dimensions, and also present preliminary results on the evolution of binary black-hole systems. To the best of our knowledge, these are the first successful three-dimensional simulations of moving punctures carried out with high-order DG schemes using a first-order formulation of the Einstein equations.

  16. Intramolecular tautomerisation and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study

    Directory of Open Access Journals (Sweden)

    Hovorun D. M.

    2011-04-01

    Full Text Available Aim. To determine the lifetime of the mutagenic cytosine derivatives through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atoms in molecules (AIM theory and physicochemical kinetics were used. Results. It is shown that the modification of all investigated compounds, except DCyt, prevents their pairing in both mutagenic and canonical tautomeric forms with a base which is an interacting partner. This effect can inhibit their mutagenic potential. It is also established that Watson-Crick tautomeric hypothesis can be formally expanded for the investigated molecules so far as a lifetime of the mutagenic tautomers much more exceeds characteristic time for the incorporation of one nucleotides pair by DNA biosynthesis machinery. It seems that just within the frame of this hypothesis it will be possible to give an adequate explanation of the mechanisms of mutagenic action of N4-aminocytosine, N4-methoxycytosine, N4-hydroxycytosine and N4dehydrocytosine, which have much more energy advantageous imino form in comparison with amino form. Conclusions. For the first time the comprehensive conformational analysis of a number of classical mutagens, namely cytosine derivatives, has been performed using the methods of non-empirical quantum chemistry at the MP2/6-311++G (2df,pd//B3LYP/6-311++G(d,p level of theory

  17. Longitudinal Study of Intestinal Symptoms and Fecal Continence in Patients With Conformal Radiotherapy for Prostate Cancer

    International Nuclear Information System (INIS)

    Geinitz, Hans; Thamm, Reinhard; Keller, Monika; Astner, Sabrina T.; Heinrich, Christine; Scholz, Christian; Pehl, Christian; Kerndl, Simone; Prause, Nina; Busch, Raymonde; Molls, Michael; Zimmermann, Frank B.

    2011-01-01

    Purpose: To prospectively assess the intestinal symptoms and fecal continence in patients who had undergone conformal radiotherapy (CRT) for prostate cancer. Methods and Materials: A total of 78 men who had undergone definitive CRT for prostate cancer were evaluated. The patients were assessed before, during (treatment Weeks 4 and 6), and 2, 12, and 24 months after CRT completion. The intestinal symptoms and fecal continence were evaluated with comprehensive standardized questionnaires. Results: The intestinal symptoms were mostly intermittent, with only a small minority of patients affected daily. Defecation pain, fecal urge, and rectal mucous discharge increased significantly during therapy. Defecation pain and rectal mucous discharge had returned to baseline levels within 8 weeks and 1 year after CRT, respectively. However, fecal urge remained significantly elevated for ≤1 year and then returned toward the pretreatment values. The prevalence of rectal bleeding was significantly elevated 2 years after CRT. Fecal continence deteriorated during CRT and remained impaired at 1 year after treatment. Incontinence was mostly minor, occurring less than once per week and predominantly affecting incontinence for gas. Conclusion: Intestinal symptoms and fecal incontinence increased during prostate CRT. Except for rectal bleeding, the intestinal symptoms, including fecal incontinence, returned to baseline levels within 1-2 years after CRT. Thus, the rate of long-term late radiation-related intestinal toxicity was low.

  18. Conformational changes of plasma fibronectin detected upon adsorption to solid substrates: A spin-label study

    International Nuclear Information System (INIS)

    Narasimhan, C.; Lai, Chingsan

    1989-01-01

    Changes in local environment of the free sulfhydryl groups in plasma fibronectin upon adsorption of the protein to polystyrene beads have been examined by electron spin resonance (ESR) spin-label spectroscopy. The two free sulfhydryl groups per subunit of plasma fibronectin were modified chemically with an [ 15 N, 2 H]maleimide spin-label. For soluble fibronectin, both free sulfhydryl groups shown to be in confined environments as evidenced from the labeled protein exhibiting a strongly immobilized ESR spectrum as described previously using [ 14 N, 1 H]maleimide spin-labels. When the labeled protein was adsorbed to the beads, half of the strongly immobilized component was found to convert into a weakly immobilized component, a result indicating that one of the two labeled sites becomes exposed and exhibits a fast tumbling motion. Experiments conducted using various spin-labeled fibronectin fragments suggest that the newly exposed labeled site is located between the DNA-binding and the cell-binding regions of the molecule. The data obtained indicate that, upon adsorption to polystyrene beads, plasma fibronectin undergoes a conformational change through which the buried free sulfhydryl group near the cell-binding region of the molecule is exposed. This observation may have important implications regarding the expression of cell adhesive properties of the fibronectin molecule

  19. Vibrational spectroscopy and principal component analysis for conformational study of virus nucleic acids

    Science.gov (United States)

    Dovbeshko, G. I.; Repnytska, O. P.; Pererva, T.; Miruta, A.; Kosenkov, D.

    2004-07-01

    Conformation analysis of mutated DNA-bacteriophages (PLys-23, P23-2, P47- the numbers have been assigned by T. Pererva) induced by MS2 virus incorporated in Ecoli AB 259 Hfr 3000 has been done. Surface enhanced infrared absorption (SEIRA) spectroscopy and principal component analysis has been applied for solving this problem. The nucleic acids isolated from the mutated phages had a form of double stranded DNA with different modifications. The nucleic acid from phage P47 was undergone the structural rearrangement in the most degree. The shape and position ofthe fine structure of the Phosphate asymmetrical band at 1071cm-1 as well as the stretching OH vibration at 3370-3390 cm-1 has indicated to the appearance ofadditional OH-groups. The Z-form feature has been found in the base vibration region (1694 cm-1) and the sugar region (932 cm-1). A supposition about modification of structure of DNA by Z-fragments for P47 phage has been proposed. The P23-2 and PLys-23 phages have showed the numerous minor structural changes also. On the basis of SEIRA spectra we have determined the characteristic parameters of the marker bands of nucleic acid used for construction of principal components. Contribution of different spectral parameters of nucleic acids to principal components has been estimated.

  20. Study on a Novel Gelled Foam for Conformance Control in High Temperature and High Salinity Reservoirs

    Directory of Open Access Journals (Sweden)

    Tong Li

    2018-05-01

    Full Text Available A novel gelled foam for conformance control was investigated for its ability to enhance oil recovery (EOR in high temperature and high salinity reservoirs. The formulation optimization, foaming performance, and core flooding performance of the gelled foam were systematically evaluated under harsh reservoir conditions. The gelled foam formulation was optimized with 0.4% polymer (hydrolyzed polyacrylamide; HPAM, 0.06% cross-linker (phenolic and 0.2% foaming agent (sulphobetaine; SB. The addition of the gel improved the stability of the foam system by 3.8 times that of traditional foam. A stabilization mechanism in the gelled foam was proposed to describe the stabilization process of the foam film. The uniformly distributed three-dimensional network structure of the gel provided a thick protective layer for the foam system that maintained the stability of the foam and improved the strength and thickness of the liquid film. The gelled foam exhibited good formation adaptability, profile control, and EOR performance. The foam flowed into the high permeability layer, plugged the dominant channel, and increased the swept volume. Oil recovery was enhanced by 29.4% under harsh high -temperature and high salinity conditions.

  1. Comparative study of the conformational lock, dissociative thermal inactivation and stability of euphorbia latex and lentil seedling amine oxidases.

    Science.gov (United States)

    Amani, M; Moosavi-Movahedi, A A; Floris, G; Longu, S; Mura, A; Moosavi-Nejad, S Z; Saboury, A A; Ahmad, F

    2005-04-01

    The thermal stability of copper/quinone containing amine oxidases from Euphorbia characias latex (ELAO) and lentil seedlings (LSAO) was measured in 100 mM potassium phosphate buffer (pH 7.0) following changes in absorbance at 292 nm. ELAO was shown to be about 10 degrees C more stable than LSAO. The dissociative thermal inactivation of ELAO was studied using putrescine as substrate at different temperatures in the range 47-70 degrees C, and a "conformational lock" was developed using the theory pertaining to oligomeric enzyme. Moreover ELAO was shown to be more stable towards denaturants than LSAO, as confirmed by dodecyl trimethylammonium bromide denaturation curves. A comparison of the numbers of contact sites in inter-subunits of ELAO relative to LSAO led us to conclude that the higher stability of ELAO to temperature and towards denaturants was due to the presence of larger number of contact sites in the conformational lock of the enzyme. This study also gives a putative common mechanism for thermal inactivation of amine oxidases and explains the importance of C-terminal conserved amino acids residues in this class of enzymes.

  2. [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.

  3. Studies of Protein Solution Properties Using Osmotic Pressure Measurements

    Science.gov (United States)

    Agena, S.; Bogle, David; Pusey, Marc; Agena, S.

    1998-01-01

    Examination of the protein crystallization process involves investigation of the liquid and solid state and a protein's properties in these states. Liquid state studies such as protein self association in solution by light scattering methods or other methods have been used to examine a protein Is properties and therefore its crystallization process and conditions. Likewise can osmotic pressure data be used to examine protein properties and various published osmotic pressure studies were examined by us to correlate osmotic pressure to protein solution properties. The solution behavior of serum albumin, alpha - chymotrypsin, beta - lactoglobulin and ovalbumin was examined over a range of temperatures, pH values and different salt types and concentrations. Using virial expansion and a local composition model the non ideal solution behavior in form of the activity coefficients (thermodynamic) was described for the systems. This protein activity coefficient data was related to a protein's solubility behavior and this process and the results will be presented.

  4. Conformal field theory in conformal space

    International Nuclear Information System (INIS)

    Preitschopf, C.R.; Vasiliev, M.A.

    1999-01-01

    We present a new framework for a Lagrangian description of conformal field theories in various dimensions based on a local version of d + 2-dimensional conformal space. The results include a true gauge theory of conformal gravity in d = (1, 3) and any standard matter coupled to it. An important feature is the automatic derivation of the conformal gravity constraints, which are necessary for the analysis of the matter systems

  5. Myelography Iodinated Contrast Media. 2. Conformational Versatility of Iopamidol in the Solid State.

    Science.gov (United States)

    Bellich, Barbara; Di Fonzo, Silvia; Tavagnacco, Letizia; Paolantoni, Marco; Masciovecchio, Claudio; Bertolotti, Federica; Giannini, Giovanna; De Zorzi, Rita; Geremia, Silvano; Maiocchi, Alessandro; Uggeri, Fulvio; Masciocchi, Norberto; Cesàro, Attilio

    2017-02-06

    The phenomenon of polymorphism is of great relevance in pharmaceutics, since different polymorphs have different physicochemical properties, e.g., solubility, hence, bioavailability. Coupling diffractometric and spectroscopic experiments with thermodynamic analysis and computational work opens to a methodological approach which provides information on both structure and dynamics in the solid as well as in solution. The present work reports on the conformational changes in crystalline iopamidol, which is characterized by atropisomerism, a phenomenon that influences both the solution properties and the distinct crystal phases. The conformation of iopamidol is discussed for three different crystal phases. In the anhydrous and monohydrate crystal forms, iopamidol molecules display a syn conformation of the long branches stemming out from the triiodobenzene ring, while in the pentahydrate phase the anti conformation is found. IR and Raman spectroscopic studies carried out on the three crystal forms, jointly with quantum chemical computations, revealed that the markedly different spectral features can be specifically attributed to the different molecular conformations. Our results on the conformational versatility of iopamidol in different crystalline phases, linking structural and spectroscopic evidence for the solution state and the solid forms, provide a definite protocol for grasping the signals that can be taken as conformational markers. This is the first step for understanding the crystallization mechanism occurring in supersaturated solution of iopamidol molecules.

  6. 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.

  7. Vanillin and isovanillin: Comparative vibrational spectroscopic studies, conformational stability and NLO properties by density functional theory calculations

    Science.gov (United States)

    Balachandran, V.; Parimala, K.

    This study is a comparative analysis of FT-IR and FT-Raman spectra of vanillin (3-methoxy-4-hydroxybenzaldehyde) and isovanillin (3-hydroxy-4-methoxybenzaldehyde). The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for both molecules using the B3LYP density functional theory (DFT) with the standard 6-311++G∗∗ basis set. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. The calculated harmonic vibrational frequencies are compared with experimental FT-IR and FT-Raman spectra. The geometrical parameters and total energies of vanillin and isovanillin were obtained for all the eight conformers (a-h) from DFT/B3LYP method with 6-311++G∗∗ basis set. The computational results identified the most stable conformer of vanillin and isovanillin as in the "a" form. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecules have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules.

  8. Revisiting imidazolium based ionic liquids: Effect of the conformation bias of the [NTf2] anion studied by molecular dynamics simulations

    Science.gov (United States)

    Neumann, Jan; Golub, Benjamin; Odebrecht, Lisa-Marie; Ludwig, Ralf; Paschek, Dietmar

    2018-05-01

    We study ionic liquids composed of 1-alkyl-3-methylimidazolium cations and bis(trifluoromethyl-sulfonyl)imide anions ([CnMIm][NTf2]) with varying chain-length n = 2, 4, 6, 8 by using molecular dynamics simulations. We show that a reparametrization of the dihedral potentials as well as charges of the [NTf2] anion leads to an improvement of the force field model introduced by Köddermann, Paschek, and Ludwig [ChemPhysChem 8, 2464 (2007)] (KPL-force field). A crucial advantage of the new parameter set is that the minimum energy conformations of the anion (trans and gauche), as deduced from ab initio calculations and Raman experiments, are now both well represented by our model. In addition, the results for [CnMIm][NTf2] show that this modification leads to an even better agreement between experiment and molecular dynamics simulation as demonstrated for densities, diffusion coefficients, vaporization enthalpies, reorientational correlation times, and viscosities. Even though we focused on a better representation of the anion conformation, also the alkyl chain-length dependence of the cation behaves closer to the experiment. We strongly encourage to use the new NGOLP (Neumann, Golub, Odebrecht, Ludwig, Paschek) force field for the [NTf2] anion instead of the earlier KPL parameter set for computer simulations aiming to describe the thermodynamics, dynamics, and also structure of imidazolium-based ionic liquids.

  9. Functional and conformational properties of phaseolin (Phaseolus vulgris L.) and kidney bean protein isolate: a comparative study.

    Science.gov (United States)

    Yin, Shou-Wei; Tang, Chuan-He; Wen, Qi-Biao; Yang, Xiao-Quan

    2010-03-15

    Kidney bean (Phaseolus vulgris L.) seed is an underutilised plant protein source with good potential to be applied in the food industry. Phaseolin (also named G1 globulin) represents about 50 g kg(-1) of total storage protein in the seed. The aim of the present study was to characterise physicochemical, functional and conformational properties of phaseolin, and to compare these properties with those of kidney bean protein isolate (KPI). Compared with kidney bean protein isolate (KPI), the acid-extracted phaseolin-rich protein product (PRP) had much lower protein recovery of 320 g kg(-1) (dry weight basis) but higher phaseolin purity (over 950 g kg(-1)). PRP contained much lower sulfhydryl (SH) and disulfide bond contents than KPI. Differential scanning calorimetry analyses showed that the phaseolin in PRP was less denatured than in KPI. Thermal analyses in the presence or absence of dithiothreitol, in combination with SH and SS content analyses showed the contributions of SS to the thermal stability of KPI. The analyses of near-UV circular dichroism and intrinsic fluorescence spectra indicated more compacted tertiary conformation of the proteins in PRP than in KPI. PRP exhibited much better protein solubility, emulsifying activity index, and gel-forming ability than KPI. The relatively poor functional properties of KPI may be associated with protein denaturation/unfolding, with subsequent protein aggregation. The results presented here suggest the potential for acid-extracted PRP to be applied in food formulations, in view of its functional properties.

  10. Nuclear magnetic resonance studies of conformations and molecular interactions in lyotropic mesophases - Applications to solubilization problems

    International Nuclear Information System (INIS)

    Caniparoli, Jean-Philippe

    1988-01-01

    After having determined the structural properties of smectic liquid crystals made from double chain surfactants/water binary systems, residual anisotropic interactions and relaxation times measurements were used to investigate the molecular ordering. Phosphorus, deuterium and nitrogen NMR of the surfactant molecules evidenced their high degree of order and the strong anisotropy of their motions. Quantitative results depended on the surfactant polar head -phosphate or ammonium-, while they displayed little variations with the hydrocarbon tail size. The marked dependence of the order and dynamics of small solutes in a lamellar phase on their hydrophilic or hydrophobic behaviour was shown using the same methods. By means of para-magnetically induced relaxation, it was proved that the non-polar solute benzene is located in the organic domain of the liquid crystalline matrix. (author) [fr

  11. A study of densitometry comparison among three radiographic processing solutions

    International Nuclear Information System (INIS)

    Changizi, V.; Jazayeri, E.; Talaeepour, A.

    2006-01-01

    The radiographic image accuracy depends on the X-ray film information visibility. Good visibility is found by good contrast. Radiation exposure parameters (kVp, mAs) and film processing conditions have impact on contrast. In dentistry radiography machines, exposure time and processing procedure are set by radiographer. No optimized exposure time and processing conditions may lead to incorrect diagnosis and re-exposure of the patient. Therefore, we studied the performance of the three different available processing solutions with dental X-ray film. Materials and Methods: Dental intraoral E-speed films, size 2 (Kodak company, USA) were used in this study. These films were developed in a manual processor using three different brands of processing solution: 1) Taifsaz (Iran), 2) Darutasvir (Iran) and 3) Agfa (Germany) for temperatures of 25 d ig C , 28 d ig C and 30 d ig C at the three different exposure times, 0.2 s, 0.25 s and 0.35 s. Performance was evaluated with respect to base plus fog, relative contrast and relative speed. Results: Darutasvir processing solution as the cheapest one showed higher base plus fog density at 25 d ig C and 30 d ig C than that of Taifsaz and Agfa solutions. Also, Darutasvir solution was found to have better relative contrast than that of the others, except for 30 d ig C at 0.25 s. Relative speed was higher in Darutsavir solution than Agfa for 25 d ig C at three exposure times used in this study, for 28 d ig C at 0.2 s and for 30 d ig C at 0.35 s. Taifsaz Processing solution was in the second order with respect to tested conditions. Conclusion: Comparison among available X-ray film processing solutions for different temperatures at different exposure times can help to maintain image quality while patient exposure and film cost are kept considerably low

  12. Recent advancements in conformal gravity

    International Nuclear Information System (INIS)

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

    2017-01-01

    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. (paper)

  13. Pulse radiolysis studies of iron(I) in aqueous solutions

    International Nuclear Information System (INIS)

    Nenadovic, M.T.; Micic, O.I.; Muk, A.A.

    1980-01-01

    The absorption spectrum and decay kinetics of the products of the reactions of iron(II) ions with hydrated electrons and hydrogen atoms have been studied in aqueous solution using pulse-radiolysis techniques. Iron(I) is formed by reaction with hydrated electrons and its absorption spectrum is reported and discussed. The formation of molecular hydrogen by reaction of Fe + with water is suppressed by other solutes present in the solutions. In acidic solutions containing [SO 4 ] 2- , the intermediates formed in the reaction with H atoms decay by a first-order process and produce molecular hydrogen, but the rate of their decay does not depend only on the oxonium ion concentration but also on intermolecular rearrangement in the [FeSO 4 -H] complex. (author)

  14. Study on Product Innovative Design Process Driven by Ideal Solution

    Science.gov (United States)

    Zhang, Fuying; Lu, Ximei; Wang, Ping; Liu, Hui

    Product innovative design in companies today relies heavily on individual members’ experience and creative ideation as well as their skills of integrating creativity and innovation tools with design methods agilely. Creative ideation and inventive ideas generation are two crucial stages in product innovative design process. Ideal solution is the desire final ideas for given problem, and the striving reaching target for product design. In this paper, a product innovative design process driven by ideal solution is proposed. This design process encourages designers to overcome their psychological inertia, to foster creativity in a systematic way for acquiring breakthrough creative and innovative solutions in a reducing sphere of solution-seeking, and results in effective product innovative design rapidly. A case study example is also presented to illustrate the effectiveness of the proposed design process.

  15. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to Gas-Phase Structures.

    Science.gov (United States)

    Kondalaji, Samaneh Ghassabi; Khakinejad, Mahdiar; Valentine, Stephen J

    2018-06-01

    Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. Graphical Abstract ᅟ.

  16. 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.

  17. A Comparative Dosimetric Study of Adjuvant 3D Conformal Radiotherapy for Operable Stomach Cancer Versus AP-PA Conventional Radiotherapy in NCI-Cairo

    International Nuclear Information System (INIS)

    El-Hossiny, H.A.; Diab, N.A.; El-Taher, M.M.

    2009-01-01

    This study was to compare this multiple field conformal technique to the AP-PA technique with respect to target volume coverage and dose to normal tissues. Materials and Methods: Seventeen patients with stages II-III denocarcinoma of the stomach were treated with adjuvant postoperative chemoradiotherapy presented to radiotherapy department in National Cancer Institute, Cairo in period between February 2009 to March 2010 using 3D conformal radiotherapy technique that consisted of a mono isocentric arrangement employing 4-6 radiation fields. For each patient, a second radiotherapy treatment plan was done using an antroposterior (AP-PA) fields, the two techniques were then compared using dose volume histogram (DVH) analysis. Results: Comparing different DVHs, it was found that the planning target volume (PTV) was adequately covered in both (3D and 2D) plans while the left kidney and spinal cord demonstrate lower radiation doses on using the conformal technique. The liver doses is higher in the 3D tecq, but still well below liver tolerance. Conclusions: Both 3D conformal radiotherapy and AP-PA conventional techniques doses are within range of normal tissues tolerance. Regarding the left kidney and spinal cord the 3D conformal radiotherapy is superior than the AP-PA conventional techniques but with higher doses to the liver in the 3D conformal radiotherapy compared to the AP-PA conventional techniques

  18. Preliminary study on lithium-salt aqueous solution blanket

    International Nuclear Information System (INIS)

    Yoshida, Hiroshi; Naruse, Yuji; Yamaoka, Mitsuaki; Ohara, Atsushi; Ono, Kiyoshi; Kobayashi, Shigetada.

    1992-06-01

    Aqueous solution blanket using lithium salts such as LiNO 3 and LiOH have been studied in the US-TIBER program and ITER conceptual design activity. In the JAERI/LANL collaboration program for the joint operation of TSTA (Tritium Systems Test Assembly), preliminary design work of blanket tritium system for lithium ceramic blanket, aqueous solution blanket and liquid metal blanket, have been performed to investigate technical feasibility of tritium demonstration tests using the TSTA. Detail study of the aqueous solution blanket concept have not been performed in the Japanese fusion program, so that this study was carried out to investigate features of its concept and to evaluated its technical problems. The following are the major items studied in the present work: (i) Neutronics of tritium breeding ratio and shielding performance Lithium concentration, Li-60 enrichment, beryllium or lead, composition of structural material/beryllium/solution, heavy water, different lithium-salts (ii) Physicochemical properties of salts Solubility, corrosion characteristics and compatibility with structural materials, radiolysis (iii) Estimation of radiolysis in ITER aqueous solution blanket. (author)

  19. A study of the effects of internal organ motion on dose escalation in conformal prostate treatments

    International Nuclear Information System (INIS)

    Happersett, Laura; Mageras, Gig S.; Zelefsky, Michael J.; Burman, Chandra M.; Leibel, Steven A.; Chui Chen; Fuks, Zvi; Bull, Sarah; Ling, C. Clifton; Kutcher, Gerald J.

    2003-01-01

    Background and purpose: To assess the effect of internal organ motion on the dose distributions and biological indices for the target and non-target organs for three different conformal prostate treatment techniques. Materials and methods: We examined three types of treatment plans in 20 patients: (1) a six field plan, with a prescribed dose of 75.6 Gy; (2) the same six field plan to 72 Gy followed by a boost to 81 Gy; and (3) a five field plan with intensity modulated beams delivering 81 Gy. Treatment plans were designed using an initial CT data set (planning) and applied to three subsequent CT scans (treatment). The treatment CT contours were used to represent patient specific organ displacement; in addition, the dose distribution was convolved with a Gaussian distribution to model random setup error. Dose-volume histograms were calculated using an organ deformation model in which the movement between scans of individual points interior to the organs was tracked and the dose accumulated. The tumor control probability (TCP) for the prostate and proximal half of seminal vesicles (clinical target volume, CTV), normal tissue complication probability (NTCP) for the rectum and the percent volume of bladder wall receiving at least 75 Gy were calculated. Results: The patient averaged increase in the planned TCP between plan types 2 and 1 and types 3 and 1 was 9.8% (range 4.9-12.5%) for both, whereas the corresponding increases in treatment TCP were 9.0% (1.3-16%) and 8.1% (-1.3-13.8%). In all patients, plans 2 and 3 (81 Gy) exhibited equal or higher treatment TCP than plan 1 (75.6 Gy). The maximum treatment NTCP for rectum never exceeded the planning constraint and percent volume of bladder wall receiving at least 75 Gy was similar in the planning and treatment scans for all three plans. Conclusion: For plans that deliver a uniform prescribed dose to the planning target volume (PTV) (plan 1), current margins are adequate. In plans that further escalate the dose to part

  20. The logarithmic conformal field theories

    International Nuclear Information System (INIS)

    Rahimi Tabar, M.R.; Aghamohammadi, A.; Khorrami, M.

    1997-01-01

    We study the correlation functions of logarithmic conformal field theories. First, assuming conformal invariance, we explicitly calculate two- and three-point functions. This calculation is done for the general case of more than one logarithmic field in a block, and more than one set of logarithmic fields. Then we show that one can regard the logarithmic field as a formal derivative of the ordinary field with respect to its conformal weight. This enables one to calculate any n-point function containing the logarithmic field in terms of ordinary n-point functions. Finally, we calculate the operator product expansion (OPE) coefficients of a logarithmic conformal field theory, and show that these can be obtained from the corresponding coefficients of ordinary conformal theory by a simple derivation. (orig.)

  1. 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.

  2. Biological and analytical studies of peritoneal dialysis solutions

    Directory of Open Access Journals (Sweden)

    N. Hudz

    2018-04-01

    Full Text Available The purpose of our work was to conduct biological and analytical studies of the peritoneal dialysis (PD solutions containing glucose and sodium lactate and establish correlations between cell viability of the Vero cell line and values of analytical indexes of the tested solutions. The results of this study confirm the cytotoxicity of the PD solutions even compared with the isotonic solution of sodium chloride, which may be due to the low pH of the solutions, presence of glucose degradation products (GDPs and high osmolarity of the solutions, and unphysiological concentrations of glucose and sodium lactate. However, it is not yet known what factors or their combination and to what extent cause the cytotoxicity of PD solutions. In the neutral red (NR test the weak, almost middle (r = -0.496 and 0.498, respectively and unexpected correlations were found between reduced viability of monkey kidney cells and increased pH of the PD solutions and between increased cell viability and increased absorbance at 228 nm of the tested PD solutions. These two correlations can be explained by a strong correlation (r = -0.948 between a decrease in pH and an increase in the solution absorbance at 228 nm. The opposite effect was observed in the MTT test. The weak, but expected correlations (r = 0.32 and -0.202, respectively were found between increased cell viability and increased pH in the PD solutions and between decreased cell viability and increased absorbance at 228 nm of the tested PD solutions. The middle and weak correlations (r = 0.56 and 0.29, respectively were detected between increased cell viability and increased lactate concentration in the NR test and MTT test. The data of these correlations can be partially explained by the fact that a correlation with a coefficient r = -0.34 was found between decreased pH in the solutions and increased lactate concentration. The very weak correlations (0.138 and 0.196, respectively were found between increased cell

  3. Study of free acidity determinations in aqueous solution

    International Nuclear Information System (INIS)

    Kergreis, A.

    1966-04-01

    The object of this work is the study of the principal methods which can be applied to the measurement of 'free' acidity. In the first part, we define the various types of acidity which can exist in aqueous solution; then, after having studied some hydrolysis reactions, we compare the value of the neutralisation pH of the hydrated cation and that of the precipitation of the hydroxide. In the second part we have started to study the determination of the acidity of an aqueous solution. After having rapidly considered the 'total' acidity determination, we deal with the problem of the 'free' acidity titration. We have considered in particular certain methods: extrapolation of the equivalent point, colorimetric titrations with or without a complexing agent, and finally the use of ion-exchange resins with mixed aqueous and solvent solutions. (author) [fr

  4. An experimental study on gold precipitation from leach solutions of ...

    African Journals Online (AJOL)

    This paper presents the results of the study dedicated to the determination of the optimum parameters for the electrolytic gold precipitation from thiourea leach solutions. The leaching was carried out using technogenic gold-bearing raw materials (gold-bearing sands) of the Far East of the Russian Federation. The study ...

  5. Equilibrium Sorption Studies of Hg (II) Ions from Aqueous Solution ...

    African Journals Online (AJOL)

    The potential of swamp arum (Lasimorpha senegalensis) seeds as a low-cost adsorbent for the removal of Hg (II) ions from aqueous solution was investigated in this study. The influence of initial metal concentration on the percent adsorption of Hg (II) ions onto powdered swamp arum seeds was studied in a batch system ...

  6. Lanthanide paramagnetic probes for NMR spectroscopic studies of fast molecular conformational dynamics and temperature control. Effective six-site proton exchange in 18-crown-6 by exchange spectroscopy.

    Science.gov (United States)

    Babailov, Sergey P

    2012-02-06

    (1)H and (13)C NMR measurements are reported for the CDCl(3) and CD(2)Cl(2) solutions of [La(18-crown-6)(NO(3))(3)] (I), [Pr(18-crown-6) (NO(3))(3)] (II), [Ce(18-crown-6)(NO(3))(3)] (III), and [Nd(18-crown-6)(NO(3))(3)] (IV) complexes. Temperature dependencies of the (1)H NMR spectra of paramagnetic II-IV have been analyzed using the dynamic NMR (DNMR) methods for six-site exchange. Two types of conformational dynamic processes were identified (the first one is conditioned by interconversion of complex enantiomeric forms and pseudorotation of a macrocycle molecule upon the C(2) symmetry axis; the second one is conditioned by macrocycle molecule inversion). Application of exchange spectroscopy (2D-EXSY) of DNMR for investigation of this dynamic system (II-IV) simplifies the assignment of the NMR signals and represents the first experimental study of multisite exchange. In the present work, the methodology of paramagnetic 4f (Ce, Pr, and Nd) probe applications for the study of free-energy, enthalpy, and entropy changes in chemical exchange processes, as well as the advantages of this method in a comparison with DNMR studies of diamagnetic substances, is discussed. In particular, as a result of paramagnetic chemical shifts in 4f complexes, the range of measurable rate constants expands considerably compared to the analogous range in diamagnetic compounds. Coordination compounds investigated in the paper represent new types of thermometric NMR sensors and lanthanide paramagnetic probes for in situ temperature control in solution.

  7. 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.

  8. Molecular modelling studies of kdr mutations in voltage gated sodium channel revealed significant conformational variations contributing to insecticide resistance.

    Science.gov (United States)

    Yellapu, Nanda Kumar; Gopal, Jeyakodi; Kasinathan, Gunasekaran; Purushothaman, Jambulingam

    2018-06-01

    Voltage gated sodium channels (VGSC) of mosquito vectors are the primary targets of dichlorodiphenyltrichloroethane (DDT) and other synthetic pyrethroids used in public health programmes. The knockdown resistant (kdr) mutations in VGSC are associated with the insecticide resistance especially in Anophelines. The present study is aimed to emphasize and demarcate the impact of three kdr-mutations such as L1014S, L1014F and L1014H on insecticide resistance. The membrane model of sodium transport domain of VGSC (STD-VGSC) was constructed using de novo approach based on domain and trans-membrane predictions. The comparative molecular modelling studies of wild type and mutant models of STD-VGSC revealed that L1014F mutant was observed to be near native to the wild type model in all the respects, but, L1014S and L1014H mutations showed drastic variations in the energy levels, root mean square fluctuations (RMSF) that resulted in conformational variations. The predicted binding sites also showed variable cavity volumes and RMSF in L1014S and L1014H mutants. Further, DDT also found be bound in near native manner to wild type in L1014F mutant and with variable orientation and affinities in L1014S and L1014H mutants. The variations and fluctuations observed in mutant structures explained that each mutation has its specific impact on the conformation of VGSC and its binding with DDT. The study provides new insights into the structure-function-correlations of mutant STD-VGSC structures and demonstrates the role and effects of kdr mutations on insecticide resistance in mosquito vectors.

  9. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    Science.gov (United States)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  10. Bianchi type-I model with conformally invariant scalar and electromagnetic field

    International Nuclear Information System (INIS)

    Accioly, A.J.; Vaidya, A.N.; Som, M.M.

    1983-01-01

    A Bianchi type-I exact solution of the Einstein theory representing the homogeneous anisotropic models with the electromagnetic field and the conformally invariant scalar field is studied. The solution contains Kasner model, pure electromagnetic and pure scalar models as special cases. It is found that the models evolve from an initial Kasner type to a final open Friedmann type universe. (Author) [pt

  11. Synthesis, solid and solution studies of paraquat dichloride calixarene complexes. Molecular modelling

    International Nuclear Information System (INIS)

    Garcia S, I.; Ramirez, F. M.

    2010-01-01

    The interaction of the herbicide paraquat dichloride (P Q, substrate) with p-tert-butylcalix arenas (L, receptor) was investigated in both the solution and solid states. The isolated paraquat calixarene complexes were characterised by UV-visible, 1 H NMR, ESI-Ms, Luminescence and IR spectroscopies and elemental analysis. The stoichiometry of complexes 1 and 2 was 1:1 (1 herbicide: 1 calixarene) and both revealed a biexponential luminescence decay with lifetimes depending on the size and the conformational particularity of the calixarenes. Molecular modelling suggested that both calixarenes interact with the herbicide through cation-π interaction. P Q in included in the p-tert butylcalix a rene cavity, a situation favoured by its pinched conformation in polar solvent while it is partially included in the p-tert butylcalix a rene cavity because of its in-out cone conformation. The theoretical results, in particular using Mopac procedures, were in agreement with the experimental findings. (Author)

  12. Synthesis, solid and solution studies of paraquat dichloride calixarene complexes. Molecular modelling

    Energy Technology Data Exchange (ETDEWEB)

    Garcia S, I.; Ramirez, F. M., E-mail: flor.ramirez@inin.gob.m [ININ, Departamento de Quimica, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2010-07-01

    The interaction of the herbicide paraquat dichloride (P Q, substrate) with p-tert-butylcalix arenas (L, receptor) was investigated in both the solution and solid states. The isolated paraquat calixarene complexes were characterised by UV-visible, {sup 1}H NMR, ESI-Ms, Luminescence and IR spectroscopies and elemental analysis. The stoichiometry of complexes 1 and 2 was 1:1 (1 herbicide: 1 calixarene) and both revealed a biexponential luminescence decay with lifetimes depending on the size and the conformational particularity of the calixarenes. Molecular modelling suggested that both calixarenes interact with the herbicide through cation-{pi} interaction. P Q in included in the p-tert butylcalix a rene cavity, a situation favoured by its pinched conformation in polar solvent while it is partially included in the p-tert butylcalix a rene cavity because of its in-out cone conformation. The theoretical results, in particular using Mopac procedures, were in agreement with the experimental findings. (Author)

  13. Measurements of transuranium trace amounts in solution. Bibliographic study

    International Nuclear Information System (INIS)

    Billon, A.; Gaudez, M.T.

    1986-01-01

    A critical study based on the data of the literature published up to 1984 has been carried out on the measurements of transuranian traces in solution. The general technical aspects of the dosage of transuranian traces in solution and of their speciations were initially reviewed. The second part is devoted to the detailed review of various methods in use in the laboratories. This work has been carried out in the framework of the MIRAGE (migration of radionuclides in the biosphere) Community project. 85 refs

  14. Physicochemical studies on ion-pair amphiphiles: Solution and ...

    Indian Academy of Sciences (India)

    Administrator

    Centre for Surface Science, Department of Chemistry, Jadavpur University, Kolkata 700 032. 2 ... ing systems, drug delivery, nanoparticle synthesis, ... to study the phase behaviours and the interfacial ..... Sections: A, coacervate formation (0⋅10–0⋅19 mol dm ... marked zone – clear solution with precipitate; cross marked.

  15. 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.

  16. Conformational study of red kidney bean (Phaseolus vulgaris L.) protein isolate (KPI) by tryptophan fluorescence and differential scanning calorimetry.

    Science.gov (United States)

    Yin, Shou-Wei; Tang, Chuan-He; Yang, Xiao-Quan; Wen, Qi-Biao

    2011-01-12

    Fluorescence and differential scanning calorimetry (DSC) were used to study changes in the conformation of red kidney bean (Phaseolus vulgaris L.) protein isolate (KPI) under various environmental conditions. The possible relationship between fluorescence data and DSC characteristics was also discussed. Tryptophan fluorescence and fluorescence quenching analyses indicated that the tryptophan residues in KPI, exhibiting multiple fluorophores with different accessibilities to acrylamide, are largely buried in the hydrophobic core of the protein matrix, with positively charged side chains close to at least some of the tryptophan residues. GdnHCl was more effective than urea and SDS in denaturing KPI. SDS and urea caused variable red shifts, 2-5 nm, in the emission λ(max), suggesting the conformational compactness of KPI. The result was further supported by DSC characteristics that a discernible endothermic peak was still detected up to 8 M urea or 30 mM SDS, also evidenced by the absence of any shift in emission maximum (λ(max)) at different pH conditions. Marked decreases in T(d) and enthalpy (ΔH) were observed at extreme alkaline and/or acidic pH, whereas the presence of NaCl resulted in higher T(d) and ΔH, along with greater cooperativity of the transition. Decreases in T(d) and ΔH were observed in the presence of protein perturbants, for example, SDS and urea, indicating partial denaturation and decrease in thermal stability. Dithiothreitol and N-ethylmaleimide have a slight effect on the thermal properties of KPI. Interestingly, a close linear relationship between the T(d) (or ΔH) and the λ(max) was observed for KPI in the presence of 0-6 M urea.

  17. A study of liposome formation using a solution (isoperibol) calorimeter.

    Science.gov (United States)

    Barriocanal, L; Taylor, K M G; Buckton, G

    2004-12-09

    A solution (isoperibol) calorimeter has been employed to study the process of formation of phospholipid vesicles from natural and synthetic phospholipid films. Phospholipid films were hydrated in the solution calorimeter at temperatures exceeding the main phospholipid phase transition temperature, with continuous agitation to ensure conversion of the hydrating bilayers into multilamellar liposomes. It was seen that retention of chloroform in phospholipid films altered the apparent enthalpy change of vesicle formation to a far greater extent than would be expected from the contribution of the enthalpy of solution of chloroform; this indicates that chloroform alters the hydration process of the lipid. The overall measured enthalpy change for the formation of egg phosphatidylcholine vesicles was exothermic, whilst that for dimyristoylphosphatidylcholine was endothermic. This difference, it is suggested, results from the influence of the hydrocarbon chains mostly on the hydration process and also on the process of vesicle formation.

  18. Benchmarking Commercial Conformer Ensemble Generators.

    Science.gov (United States)

    Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

    2017-11-27

    We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import, and OMEGA) and one leading free algorithm, the distance geometry algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms, the median minimum root-mean-square deviations measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit distance geometry algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the midranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parametrize them for best performance in different application scenarios.

  19. Aspect of the conformal invariance

    International Nuclear Information System (INIS)

    Bauer, M.

    1990-11-01

    This thesis is about the study of several physical and mathematical aspects of critical phenomena at two dimensions. These phenomena have remarkable symmetry properties in the coordonnates changes keeping the angles. They are named conformal theories

  20. 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.

  1. 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...

  2. Conformational flexibility of aspartame.

    Science.gov (United States)

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. © 2016 Wiley Periodicals, Inc.

  3. 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.

  4. Picosecond pulse radiolysis study of primary reactions in solutions

    International Nuclear Information System (INIS)

    El-Omar, Abdel Karim

    2013-01-01

    Following the discovery of ionizing radiations and their chemical effects, it was important to study and comprehend the formation mechanisms of short lived free radicals and molecular products. In order to perform such studies, researchers and research groups worked on developing tools allowing both formation and detection of those species at short time scales. Nowadays, pulse radiolysis imposed itself as a fundamental and efficient tool allowing scientists to probe chemical effects as well as reaction mechanisms in studied media. The Laboratoire de Chimie Physique d'Orsay 'LCP' is an interdisciplinary laboratory hosting the platform of fast kinetics known as 'ELYSE'. Due to its femtosecond laser and its picosecond electron accelerator, we have the possibility to study chemical effects of ionizing radiations interaction with media at ultrashort times up to ∼5 ps.Knowing that we are interested in primary reactions induced in aqueous media by ionizing radiations, ELYSE represents the essential tool in performing our studies. The obtained results concern:- First direct determination of hydroxyl radical 'HO*' radiolytic yield as function of time at picosecond time scale;- Direct effect of ionizing radiation in highly concentrated aqueous solutions as well as investigation of the ultrafast electron transfer reaction between solute molecules and positive holes 'H 2 O*+' formed upon water radiolysis;- Study at room temperature of electron transfer reaction between solvated electron (electron donor) and organic solutes (electron acceptors) en viscous medium;- Study at room temperature of electron's solvation dynamics in ethylene glycol and 2-propanol. (author)

  5. Interactions of acidic solutions with sediments: a case study

    International Nuclear Information System (INIS)

    Peterson, S.R.; Serne, R.J.; Felmy, A.R.; Erikson, R.L.; Krupka, K.M.; Gee, G.W.

    1984-01-01

    A methodology is presented for investigating the chemical interactions of acidic solutions with sediments. The MINTEQ geochemical computer code was used to predict solid-phase reactions that might occur when acidic solutions contact neutral sediments which, in turn, may control the concentrations of certain dissolved components. Results of X-ray diffraction analysis of laboratory samples of sediments that have been contacted with acidic uranium mill tailings solutions suggest gypsum and jarosite precipitated. These same mineralogical changes were identified in sediment samples collected from a drained uranium mill evaporation pond (Lucky Mc mine in Wyoming) with a 10-year history of acid attack. Geochemical modeling predicted that these same phases and several amorphous solids not identifiable by X-ray diffraction should have precipitated in the contacted sediments. An equilibrium conceptual model consisting of an assemblage of minerals and amorphous solid phases was then developed to represent a sediment column through which uranium mill tailings solutions were percolated. The MINTEQ code was used to predict effluent solution concentrations resulting from the reactions of the tailings solution with the assemblage of solid phases in the conceptual model. The conceptual model successfully predicted the concentrations of several of the macro-constituents (e.g., Ca, SO 4 , Al, Fe, and Mn), but was not successful in modeling the concentrations of trace elements. The lack of success in predicting the observed trace metal concentrations suggests that other mechanisms, such as adsorption, must be included in future models. The geochemical modeling methodology coupled with the laboratory and field studies should be applicable to a variety of waste disposal problems

  6. Study of solute segregation at interfaces using Auger electron spectroscopy

    International Nuclear Information System (INIS)

    White, C.L.

    1984-01-01

    Interfacial segregation, often confined to within a few atomic distances of the interface, can strongly influence the processing and properties of metals and ceramics. The thinness of such solute-enriched regions can cause them to be particularly suitable for study using surface sensitive microanalytical techniques such as Auger electron spectroscopy (AES). The application of AES to studies of interfacial segregation in metals and ceramics is briefly reviewed, and several examples are presented. 43 references, 14 figures

  7. 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.

  8. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan; Uyaver, Sahin; Sun, Shuyu

    2014-01-01

    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.

  9. Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

    Science.gov (United States)

    Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

    2016-06-02

    Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases.

  10. 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.

  11. Corrosion and impedance studies on magnesium alloy in oxalate solution

    International Nuclear Information System (INIS)

    Fekry, A.M.; Tammam, Riham H.

    2011-01-01

    Highlights: → Corrosion behavior of AZ91E alloy was investigated in 0.1 M Na 2 C 2 O 4 containing different additives as Br - , Cl - or Silicate. → The corrosion rate of 0.1 M oxalate solution containing silicate ion is lower than the blank (0.1 M Na 2 C 2 O 4 ). This was confirmed by scanning electron microscope (SEM) observations. → For the other added ions Br - or Cl - , the corrosion rate is higher than the blank. - Abstract: Corrosion behavior of AZ91E alloy was investigated in oxalate solution using potentiodynamic polarization and electrochemical impedance measurements (EIS). The effect of oxalate concentration was studied, where the corrosion rate increases with increasing oxalate concentration. The effect of added ions (Br - , Cl - or SiO 3 2- ) on the electrochemical behavior of magnesium alloy in 0.1 M Na 2 C 2 O 4 solution at 298 K, was investigated. It was found that the corrosion rate of 0.1 M oxalate solution containing silicate ion is lower than the blank (0.1 M Na 2 C 2 O 4 ). This was confirmed by scanning electron microscope (SEM) observations. However, for the other added ions Br - or Cl - , the corrosion rate is higher than the blank.

  12. Corrosion and impedance studies on magnesium alloy in oxalate solution

    Energy Technology Data Exchange (ETDEWEB)

    Fekry, A.M., E-mail: hham4@hotmail.com [Chemistry Department, Faculty of Science, Cairo University, Gamaa Street, Giza 12613 (Egypt); Tammam, Riham H. [Chemistry Department, Faculty of Science, Cairo University, Gamaa Street, Giza 12613 (Egypt)

    2011-06-15

    Highlights: > Corrosion behavior of AZ91E alloy was investigated in 0.1 M Na{sub 2}C{sub 2}O{sub 4} containing different additives as Br{sup -}, Cl{sup -} or Silicate. > The corrosion rate of 0.1 M oxalate solution containing silicate ion is lower than the blank (0.1 M Na{sub 2}C{sub 2}O{sub 4}). This was confirmed by scanning electron microscope (SEM) observations. > For the other added ions Br{sup -} or Cl{sup -}, the corrosion rate is higher than the blank. - Abstract: Corrosion behavior of AZ91E alloy was investigated in oxalate solution using potentiodynamic polarization and electrochemical impedance measurements (EIS). The effect of oxalate concentration was studied, where the corrosion rate increases with increasing oxalate concentration. The effect of added ions (Br{sup -}, Cl{sup -} or SiO{sub 3}{sup 2-}) on the electrochemical behavior of magnesium alloy in 0.1 M Na{sub 2}C{sub 2}O{sub 4} solution at 298 K, was investigated. It was found that the corrosion rate of 0.1 M oxalate solution containing silicate ion is lower than the blank (0.1 M Na{sub 2}C{sub 2}O{sub 4}). This was confirmed by scanning electron microscope (SEM) observations. However, for the other added ions Br{sup -} or Cl{sup -}, the corrosion rate is higher than the blank.

  13. Electron paramagnetic resonance study of conformational effects in alkyl-substituted 2-cyclohexanonyl radicals in an adamantane matrix

    International Nuclear Information System (INIS)

    Walter, H.F.

    1975-01-01

    Electron paramagnetic resonance spectra have been obtained for radicals produced by x-irradiation of cyclohexanone and various alkyl-substituted cyclohexanones trapped in an adamantane matrix. Temperature variation of these spectra permits determination of the enthalpy and entropy of activation for interconversion between the two half-chair conformations. In those cases where the two conformations have intrinsically different energies, the enthalpy and entropy differences between conformations are determined. For 2-cyclohexanonyl radical, the enthalpy of activation is 3.90 +- 0.07 kcal/mole and the entropy of activation is -2.3 +- 0.3 e.u. Methyl substitution on C 3 or C 5 gives a radical with activation parameters similar to the parent radical, indicating moderate realignment of atoms during the conformational change. Methyl substitution on C 4 gives a radical with lower activation parameters, which are interpreted to indicate conformational change mainly be a folding along the diagonal through the radical site. Larger groups attached to C 3 influence enthalpy and entropy differences between conformations much less than when they are attached to C 5 . Very large groups attached to C 5 apparently flatten the ring; it is not known whether or not this is a matrix effect. Deuteration seems to cause a slight reduction in the activation parameters for 2-cyclohexanonyl radical

  14. Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies

    International Nuclear Information System (INIS)

    Cekan, Pavol; Sigurdsson, Snorri Th.

    2012-01-01

    Highlights: ► Bulges and loops were studied by both EPR and fluorescence spectroscopies using the probe Ç/Ç f . ► One-base bulge was in a temperature-dependent equilibrium between looped-out and stacked states. ► Bases in two- and three-base bulges were stacked at all temperatures, resulting in DNA bending. ► Bases were stacked in symmetrical two- to five-base internal loops, according to EPR data. ► Unexpectedly high fluorescence for the smaller loops indicated local structural perturbations. -- Abstract: The dynamics and conformation of base bulges and internal loops in duplex DNA were studied using the bifunctional spectroscopic probe Ç, which becomes fluorescent (Ç f ) upon reduction of the nitroxide functional group, along with EPR and fluorescence spectroscopies. A one-base bulge was in a conformational equilibrium between looped-out and stacked states, the former favored at higher temperature and the latter at lower temperature. Stacking of bulge bases was favored in two- and three-base bulges, independent of temperature, resulting in DNA bending as evidenced by increased fluorescence of Ç f . EPR spectra of Ç-labeled three-, four- and five-base symmetrical interior DNA bulges at 20 °C showed low mobility, indicating that the spin-label was stacked within the loop. The spin-label mobility at 37 °C increased as the loops became larger. A considerable variation in fluorescence between different loops was observed, as well as a temperature-dependence within constructs. Fluorescence unexpectedly increased as the size of the loop decreased at 2 °C. Fluorescence of the smallest loops, where a single T·T mismatch was located between the stem region and the probe, was even larger than for the single strand, indicating a considerable local structural deformation of these loops from regular B-DNA. These results show the value of combining EPR and fluorescence spectroscopy to study non-helical regions of nucleic acids.

  15. A study of precipitation from pure solutions of uranyl nitrate

    International Nuclear Information System (INIS)

    Decrop, J.; Holder, J.; Sauteron, J.

    1961-01-01

    After its purification by extraction of the uranyl nitrate from the organic solvent, uranium has to be converted into solid form again: uranium trioxide (UO 3 ). It can be done either by thermal decomposition of uranyl nitrate or by precipitation of uranium, followed by filtration and calcination. Only the second method has been studied for now at the Bouchet plant. This paper reports the bench-scale and pilot-scale experiments of the studies of the precipitation of pure solutions of uranyl nitrate using ammonia (gaseous or in solution) or ammonium carbonate. These have been carried out at the Bouchet plant. It investigates the chemical aspect (pH, precipitates chemical composition) and the technical aspect of the different ways of precipitation (conditions of precipitation, decantation and filtration of precipitates). (M.P.)

  16. Phase Behaviour and Miscibility Studies of Collagen/Silk Fibroin Macromolecular System in Dilute Solutions and Solid State.

    Science.gov (United States)

    Ghaeli, Ima; de Moraes, Mariana A; Beppu, Marisa M; Lewandowska, Katarzyna; Sionkowska, Alina; Ferreira-da-Silva, Frederico; Ferraz, Maria P; Monteiro, Fernando J

    2017-08-18

    Miscibility is an important issue in biopolymer blends for analysis of the behavior of polymer pairs through the detection of phase separation and improvement of the mechanical and physical properties of the blend. This study presents the formulation of a stable and one-phase mixture of collagen and regenerated silk fibroin (RSF), with the highest miscibility ratio between these two macromolecules, through inducing electrostatic interactions, using salt ions. For this aim, a ternary phase diagram was experimentally built for the mixtures, based on observations of phase behavior of blend solutions with various ratios. The miscibility behavior of the blend solutions in the miscible zones of the phase diagram was confirmed quantitatively by viscosimetric measurements. Assessing the effects of biopolymer mixing ratio and salt ions, before and after dialysis of blend solutions, revealed the importance of ion-specific interactions in the formation of coacervate-based materials containing collagen and RSF blends that can be used in pharmaceutical, drug delivery, and biomedical applications. Moreover, the conformational change of silk fibroin from random coil to beta sheet, in solution and in the final solid films, was detected by circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR), respectively. Scanning electron microscopy (SEM) exhibited alterations of surface morphology for the biocomposite films with different ratios. Surface contact angle measurement illustrated different hydrophobic properties for the blended film surfaces. Differential scanning calorimetry (DSC) showed that the formation of the beta sheet structure of silk fibroin enhances the thermal stability of the final blend films. Therefore, the novel method presented in this study resulted in the formation of biocomposite films whose physico-chemical properties can be tuned by silk fibroin conformational changes by applying different component mixing ratios.

  17. Conformational, vibrational spectroscopic and quantum chemical studies on 5-methoxyindole-3-carboxaldehyde: A DFT approach

    Science.gov (United States)

    Jeyaseelan, S. Christopher; Hussain, Shamima; Premkumar, R.; Rekha, T. N.; Benial, A. Milton Franklin

    2018-04-01

    Indole and its derivatives are considered as good ligands for various disease causing proteins in human because of presence of the single nitrogen atom. In the present study, the potential energy surface scan was performed for the most stable molecular structure of the 5-Methoxyindole-3-carboxaldehyde (MICA) molecule. The most stable molecular structure was optimized by DFT/B3LYP method with 6-311G++ (d, p) basis set using Gaussian 09 program package. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculations using VEDA 4.0 program. The Frontier molecular orbitals analysis was performed and related molecular propertieswere calculated. The possible electrophilic and nucleophilic reactive sites of the molecule were studied using molecular electrostatic potential analysis, which confirms the bioactivity of the molecule. The natural bond orbital analysis was also performed to confirm the bioactivity of the title molecule.

  18. 4-Mercaptophenylboronic acid: conformation, FT-IR, Raman, OH stretching and theoretical studies.

    Science.gov (United States)

    Parlak, Cemal; Ramasami, Ponnadurai; Tursun, Mahir; Rhyman, Lydia; Kaya, Mehmet Fatih; Atar, Necip; Alver, Özgür; Şenyel, Mustafa

    2015-06-05

    4-Mercaptophenylboronic acid (4-mpba, C6H7BO2S) was investigated experimentally by vibrational spectroscopy. The molecular structure and spectroscopic parameters were studied by computational methods. The molecular dimer was investigated for intermolecular hydrogen bonding. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. The present work provides a simple physical picture of the OH stretch vibrational spectra of 4-mpba and analogues of the compound studied. When the different computational methods are compared, there is a strong evidence of the better performance of the BLYP functional than the popular B3LYP functional to describe hydrogen bonding in the dimer. The findings of this research work should be useful to experimentalists in their quests for functionalised 4-mpba derivatives. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. 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.

  20. A study on the development of regulatory guide to stability conformation and classification criteria of low and intermediate level radioactive waste

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Jae; Paek, Min Hoon; Park, Jong Gil; Han, Byeong Seop; Cheong, Jae Hak; Lee, Hae Chan; Yang, Jin Yeong; Hong, Hei Kwan; Park, Jin Baek [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

    1994-01-15

    The objectives of this study are to examine basic principles and terms and to suggest and recommend definite methods and criteria necessary for the classification and stability conformation of radioactive wastes. In this study, following studies were performed : investigate the domestic regulations related with the stability conformation and classification of radioactive wastes in order to keep mutual relationship and consistency between the regulations, investigate the sources, types and characteristics of domestic radioactive wastes as a basis for this study, investigate the classification criteria and methods of others countries in a general point of view and in the view point of disposal method, select the classification criteria factors for the domestic case and general case in the both general and domestic points of view, investigate the general test items for the stability conformation of radioactive waste forms and analysis on the test items and criteria of others countries for the mined cavity disposal and shallow land disposal in the view point of disposal method, experimental leaching and immersion tests for the borate and spent resin wastes as a study on the stability conformation of waste forms, selection of acceptance criteria for the both of disposal methods in the domestic and general cases.

  1. Conformational interpretation of vescalagin and castalagin physicochemical properties.

    Science.gov (United States)

    Vivas, Nicolas; Laguerre, Michel; Pianet de Boissel, Isabelle; Vivas de Gaulejac, Nathalie; Nonier, Marie-Françoise

    2004-04-07

    Vescalagin and castalagin are two diastereoisomers. The variability of their principal physicochemical properties, compared with their small structural differences, suggests important conformational variations. This study shows, experimentally, that vescalagin has a greater effect on polarity, oxidizability in solution, and thermodegradability than castalagin. Conformational analysis by molecular mechanics demonstrated that vescalagin was more hydrophilic and was more reactive to electrophilic reagents than castalagin. Experimental results were thus explained and demonstrated the distinct behaviors of vescalagin and castalagin. These results were attributed to the C1 position of the two compounds because vescalin and castalin have comparable characteristics. Experimental data were confirmed and interpreted by molecular mechanics. This work represents one of the first attempts to correlate conformation and the properties of phenolic compounds. This step constitutes a predictive method for the pharmacology or chemistry of new compounds.

  2. Hot 56Mn reactions in permanganate solutions: a quasi solution state study [Paper No. NC-6

    International Nuclear Information System (INIS)

    Dedgaonkar, V.G.; Mitra, S.

    1982-01-01

    Neutron activation of aqueous solutions of transition metal and ammonium permanganates over the concentration range 1-10 -3 M has been performed. Retentions for concentrated solutions were much higher than the solid state values, and upon dilution, a limiting value of approx. 4 per cent was attained. Activation of 1-10 -1 M permanganate quasi solutions containing either alumina or a polystyrene cation exchanger allowed continuous extraction of the recoil species before their recombination. (author)

  3. Nuclear Overhauser effect studies of the conformation of Co(NH3)4ATP bound to kidney Na,K-ATPase

    International Nuclear Information System (INIS)

    Stewart, J.M.; Jorgensen, P.L.; Grisham, C.M.

    1989-01-01

    Transferred nuclear Overhauser effect measurements (in the two-dimensional mode) have been used to determine the three-dimensional conformation of an ATP analogue, Co(NH3)4ATP, at the active site of sheep kidney Na,K-ATPase. Previous studies have shown that Co(NH3)4ATP is a competitive inhibitor with respect to MnATP for the Na,K-ATPase. Nine unique proton-proton distances on ATPase-bound Co(NH3)4ATP were determined from the initial build-up rates of the cross-peaks of the 2D-TRNOE data sets. These distances, taken together with previous 31P and 1H relaxation measurements with paramagnetic probes, are consistent with a single nucleotide conformation at the active site. The bound (Co(NH3)4ATP) adopts an anti conformation, with a glycosidic torsion angle of 35 degrees, and the conformation of the ribose ring is slightly N-type (C2'-exo, C3'-endo). The delta and gamma torsional angles in this conformation are 100 degrees and 178 degrees, respectively. The nucleotide adopts a bent configuration, in which the triphosphate chain lies nearly parallel to the adenine moiety. Mn2+ bound to a single, high-affinity site on the ATPase lies above and in the plane of the adenine ring. The distances from enzyme-bound Mn2+ to N6 and N7 are too large for first coordination sphere complexes, but are appropriate for second-sphere complexes involving, for example, intervening hydrogen-bonded water molecules. The NMR data also indicate that the structure of the bound ATP analogue is independent of the conformational state of the enzyme

  4. Nuclear Overhauser effect studies of the conformation of Co(NH3)4ATP bound to kidney Na,K-ATPase

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, J.M.; Jorgensen, P.L.; Grisham, C.M. (Univ. of Virginia, Charlottesville (USA))

    1989-05-30

    Transferred nuclear Overhauser effect measurements (in the two-dimensional mode) have been used to determine the three-dimensional conformation of an ATP analogue, Co(NH3)4ATP, at the active site of sheep kidney Na,K-ATPase. Previous studies have shown that Co(NH3)4ATP is a competitive inhibitor with respect to MnATP for the Na,K-ATPase. Nine unique proton-proton distances on ATPase-bound Co(NH3)4ATP were determined from the initial build-up rates of the cross-peaks of the 2D-TRNOE data sets. These distances, taken together with previous 31P and 1H relaxation measurements with paramagnetic probes, are consistent with a single nucleotide conformation at the active site. The bound (Co(NH3)4ATP) adopts an anti conformation, with a glycosidic torsion angle of 35{degrees}, and the conformation of the ribose ring is slightly N-type (C2'-exo, C3'-endo). The delta and gamma torsional angles in this conformation are 100 degrees and 178 degrees, respectively. The nucleotide adopts a bent configuration, in which the triphosphate chain lies nearly parallel to the adenine moiety. Mn2+ bound to a single, high-affinity site on the ATPase lies above and in the plane of the adenine ring. The distances from enzyme-bound Mn2+ to N6 and N7 are too large for first coordination sphere complexes, but are appropriate for second-sphere complexes involving, for example, intervening hydrogen-bonded water molecules. The NMR data also indicate that the structure of the bound ATP analogue is independent of the conformational state of the enzyme.

  5. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent.

    Science.gov (United States)

    Goyal, Bhupesh; Srivastava, Kinshuk Raj; Durani, Susheel

    2017-06-01

    Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH 2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH 2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH 2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide

  6. [Immortal time bias in pharmacoepidemiological studies: definition, solutions and examples].

    Science.gov (United States)

    Faillie, Jean-Luc; Suissa, Samy

    2015-01-01

    Among the observational studies of drug effects in chronic diseases, many of them have found effects that were exaggerated or wrong. Among bias responsible for these errors, the immortal time bias, concerning the definition of exposure and exposure periods, is relevantly important as it usually tends to wrongly attribute a significant benefit to the study drug (or exaggerate a real benefit). In this article, we define the mechanism of immortal time bias, we present possible solutions and illustrate its consequences through examples of pharmacoepidemiological studies of drug effects. © 2014 Société Française de Pharmacologie et de Thérapeutique.

  7. 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.

  8. Inverse bootstrapping conformal field theories

    Science.gov (United States)

    Li, Wenliang

    2018-01-01

    We propose a novel approach to study conformal field theories (CFTs) in general dimensions. In the conformal bootstrap program, one usually searches for consistent CFT data that satisfy crossing symmetry. In the new method, we reverse the logic and interpret manifestly crossing-symmetric functions as generating functions of conformal data. Physical CFTs can be obtained by scanning the space of crossing-symmetric functions. By truncating the fusion rules, we are able to concentrate on the low-lying operators and derive some approximate relations for their conformal data. It turns out that the free scalar theory, the 2d minimal model CFTs, the ϕ 4 Wilson-Fisher CFT, the Lee-Yang CFTs and the Ising CFTs are consistent with the universal relations from the minimal fusion rule ϕ 1 × ϕ 1 = I + ϕ 2 + T , where ϕ 1 , ϕ 2 are scalar operators, I is the identity operator and T is the stress tensor.

  9. 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

  10. Optimal hypofractionated conformal radiotherapy for large brain metastases in patients with high risk factors: a single-institutional prospective study

    International Nuclear Information System (INIS)

    Inoue, Hiroshi K; Sato, Hiro; Suzuki, Yoshiyuki; Saitoh, Jun-ichi; Noda, Shin-ei; Seto, Ken-ichi; Torikai, Kota; Sakurai, Hideyuki; Nakano, Takashi

    2014-01-01

    A single-institutional prospective study of optimal hypofractionated conformal radiotherapy for large brain metastases with high risk factors was performed based on the risk prediction of radiation-related complications. Eighty-eight patients with large brain metastases ≥10 cm 3 in critical areas treated from January 2010 to February 2014 using the CyberKnife were evaluated. The optimal dose and number of fractions were determined based on the surrounding brain volume circumscribed with a single dose equivalent (SDE) of 14 Gy (V14) to be less than 7 cm 3 for individual lesions. Univariate and multivariate analyses were conducted. As a result of optimal treatment, 92 tumors ranging from 10 to 74.6 cm 3 (median, 16.2 cm 3 ) in volume were treated with a median prescribed isodose of 57% and a median fraction number of five. In order to compare the results according to the tumor volume, the tumors were divided into the following three groups: 1) 10–19.9 cm 3 , 2) 20–29.9 cm 3 and 3) ≥30 cm 3 . The lesions were treated with a median prescribed isodose of 57%, 56% and 55%, respectively, and the median fraction number was five in all three groups. However, all tumors ≥20 cm 3 were treated with ≥ five fractions. The median SDE of the maximum dose in the three groups was 47.2 Gy, 48.5 Gy and 46.5 Gy, respectively. Local tumor control was obtained in 90.2% of the patients, and the median survival was nine months, with a median follow-up period of seven months (range, 3-41 months). There were no significant differences in the survival rates among the three groups. Six tumors exhibited marginal recurrence 7-36 months after treatment. Ten patients developed symptomatic brain edema or recurrence of pre-existing edema, seven of whom required osmo-steroid therapy. No patients developed radiation necrosis requiring surgical resection. Our findings demonstrate that the administration of optimal hypofractionated conformal radiotherapy based on the dose-volume prediction

  11. Conformal Killing vectors in Robertson-Walker spacetimes

    International Nuclear Information System (INIS)

    Maartens, R.; Maharaj, S.d.

    1986-01-01

    It is well known that Robertson-Walker spacetimes admit a conformal Killingl vector normal to the spacelike homogeneous hypersurfaces. Because these spacetimes are conformally flat, there are a further eight conformal Killing vectors, which are neither normal nor tangent to the homogeneous hypersurfaces. The authors find these further conformal Killing vectors and the Lie algebra of the full G 15 of conformal motions. Conditions on the metric scale factor are determined which reduce some of the conformal Killing vectors to homothetic Killing vectors or Killing vectors, allowing one to regain in a unified way the known special geometries. The non-normal conformal Killing vectors provide a counter-example to show that conformal motions do not, in general, map a fluid flow conformally. These non-normal vectors are also used to find the general solution of the null geodesic equation and photon Liouville equation. (author)

  12. An in silico study of the molecular basis of B-RAF activation and conformational stability

    Directory of Open Access Journals (Sweden)

    Jónsdóttir Svava

    2009-07-01

    Full Text Available Abstract Background 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 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. It was found that several mutations, which directly or indirectly destabilized the interactions between these residues within this network, contributed to the changes in B-RAF activity. Conclusion Our results showed that the above mechanisms lead to the disruption of the electrostatic interactions between the A-loop and the αC-helix in the activating mutants, which presumably contribute to the flipping of the activation segment to an active form. Conversely, in the B-RAFD594V mutant that has impaired kinase activity, and in B-RAFWT these interactions were strong and stabilized the kinase inactive form.

  13. Neoadjuvant conformal chemoradiation with induction chemotherapy for rectal adenocarcinoma. A prospective observational study.

    Science.gov (United States)

    Fekete, Zsolt; Muntean, Alina-Simona; Hica, Ştefan; Rancea, Alin; Resiga, Liliana; Csutak, Csaba; Todor, Nicolae; Nagy, Viorica Magdalena

    2014-06-01

    The purpose of this prospective observational study was to evaluate the rate and the prognostic factors for down-staging and complete response for rectal adenocarcinoma after induction chemotherapy and neoadjuvant chemoradiation followed by surgery, and to analyze the rate of sphincter-saving surgery. We included from March 2011 to October 2013 a number of 88 patients hospitalized with locally advanced rectal adenocarcinoma in the Prof. Dr. Ion Chiricuta Institute of Oncology, Cluj. The treatment schedule included 2-4 cycles of Oxaliplatin plus a fluoropyrimidine followed by concomitant chemoradiation with a dose of 50 Gy in 25 fractions combined with a fluoropyrimidine monotherapy. The rate of T down-staging was 49.4% (40/81 evaluable patients). Independent prognostic factors for T down-staging were: age >57 years (p5 cm (p35 days (p5 cm (p=0.03). Sixty-eight patients (79.1%) underwent radical surgery and among them 35 patients (51.5 %) had a sphincter saving procedure. Induction chemotherapy with neoadjuvant chemoradiation produced important down-staging in rectal adenocarcinoma. Independent prognostic factors for T down-staging were: age, cN0, distance from anal verge, initial CEA, the number of Oxaliplatin cycles and duration of radiotherapy; for complete response: cT2, initial tumor size and distance from the anal verge.

  14. 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

    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...... 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...... the A-loop and the alphaC-helix in the activating mutants, which presumably contribute to the flipping of the activation segment to an active form. Conversely, in the B-RAFD594V mutant that has impaired kinase activity, and in B-RAFWT these interactions were strong and stabilized the kinase inactive...

  15. Neutron studies of paramagnetic fullerenols’ assembly in aqueous solutions

    Science.gov (United States)

    Lebedev, V. T.; Szhogina, A. A.; Suyasova, M. V.

    2018-03-01

    Recent results on structural studies of aqueous solutions of water-soluble derivatives of endofullerenes encapsulating 4f- and 3d-elements have been presented. Neutron small angle scattering experiments allowed recognize subtle features of fullerenols assembly as dependent on chemical nature (atomic number) of interior atom, pH-factor and temperature of solutions. It was observed a fractal-type fullerenols’ ordering at the scale of correlation radii ∼ 10-20 nm when molecules with iron atoms are integrated into branched structures at low concentrations (C ≤ 1 % wt.) and organized into globular aggregates at higher amounts (C > 1 % wt.). On the other hand, for Lanthanides captured in carbon cages the supramolecular structures are mostly globular and have larger gyration radii ∼ 30 nm. They demonstrated a good stability in acidic (pH ∼ 3) and neutral (pH ∼ 7) media that is important for forthcoming medical applications.

  16. 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....

  17. Conformal Einstein spaces

    International Nuclear Information System (INIS)

    Kozameh, C.N.; Newman, E.T.; Tod, K.P.

    1985-01-01

    Conformal transformations in four-dimensional. In particular, a new set of two necessary and sufficient conditions for a space to be conformal to an Einstein space is presented. The first condition defines the class of spaces conformal to C spaces, whereas the last one (the vanishing of the Bach tensor) gives the particular subclass of C spaces which are conformally related to Einstein spaces. (author)

  18. Electron paramagnetic resonance studies on conformation states and metal ion exchange properties of vanadium bromoperoxidase

    International Nuclear Information System (INIS)

    de Boer, E.; Boon, K.; Wever, R.

    1988-01-01

    An electron paramagnetic resonance (EPR) study was carried out to examine structural aspects of vanadium-containing bromoperoxidase from the brown seaweed Ascophyllum nodosum. At high pH, the reduced form of bromoperoxidase showed an apparently axially symmetric EPR signal with 16 hyperfine lines. When the pH was lowered, a new EPR spectrum was formed. When EPR spectra of the reduced enzyme were recorded in the pH range from 4.2 to 8.4, it appeared that these changes were linked to a functional group with an apparent pK/sub a/ of about 5.4. In D 2 O this value for the pK/sub a/ was 5.3. It is suggested that these effects arise from protonation of histidine or aspartate/glutamate residues near the metal ion. The values for the isotropic hyperfine coupling constant of the reduced enzyme at both high and low pH are also consistent with a ligand field containing nitrogen and/or oxygen donor atoms. When reduced bromoperoxidase was dissolved in D 2 O or H 2 17 O instead of H 2 16 O, vanadium (IV) hyperfine line widths were markedly affected, demonstrating that water is a ligand of the metal ion. Together with previous work these findings suggest that vanadium (IV) is not involved in catalytic turnover and confirm the model in which the vanadium (V) ion of the native enzyme only serves to bind both hydrogen peroxide and bromide. After excess vanadate was added to a homogeneous preparation of purified bromoperoxidase, the extent of vanadium bound to the protein increased from 0.5 to 1.1, with a concomitant enhancement of enzymic activity. Finally, it is demonstrated that both vanadate (VO 4 3- ) and molybdate (MoO 4 2- ) compete for the same site on apobromoperoxidase

  19. Vibrational, calorimetric, and molecular conformational study on calcein interaction with model lipid membrane

    International Nuclear Information System (INIS)

    Maherani, Behnoush; Arab-Tehrany, Elmira; Rogalska, Ewa; Korchowiec, Beata; Kheirolomoom, Azadeh; Linder, Michel

    2013-01-01

    Nanoliposomes are commonly used as a carrier in controlled release drug delivery systems. Controlled release formulations can be used to reduce the amount of drug necessary to cause the same therapeutic effect in patients. One of the most noticeable factors in release profiles is the strength of the drug-carrier interaction. To adjust the pharmacokinetic and pharmacodynamic properties of therapeutic agents, it is necessary to optimize the drug-carrier interaction. To get a better understanding of this interaction, large unilamellar liposomes containing calcein were prepared using 1,2-dioleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1,2-palmitoyl-sn-glycero-3-phosphocholine, and a mixture of them; calcein was chosen as a model polar molecule of biological interest. The thermodynamic changes induced by calcein and its location in lipid bilayers were determined by differential scanning calorimetry and Raman spectroscopy, respectively. The results reveal that calcein has no significant influence on thermotropic properties of the lipid membrane, but causing the abolition of pre-transition. The decreasing of the pre-transition can be ascribed to the presence of calcein near the hydrophilic cooperative zone of the bilayer. The change in intensity of the Raman peaks represents the interaction of calcein with choline head groups. Moreover, the impact of calcein on phosphoglyceride Langmuir layers spread at the air–water interface was studied using surface pressure-area and surface potential-area isotherms, as well as polarization-modulation infrared reflection–absorption spectroscopy and Brewster angle microscopy. The results obtained indicate that calcein introduce no major modification on the systems prepared with pure lipids

  20. 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)

  1. 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.

  2. 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.

  3. Defining a conformational consensus motif in cotransin-sensitive signal sequences: a proteomic and site-directed mutagenesis study.

    Directory of Open Access Journals (Sweden)

    Wolfgang Klein

    Full Text Available The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity.

  4. Defining a Conformational Consensus Motif in Cotransin-Sensitive Signal Sequences: A Proteomic and Site-Directed Mutagenesis Study

    Science.gov (United States)

    Klein, Wolfgang; Westendorf, Carolin; Schmidt, Antje; Conill-Cortés, Mercè; Rutz, Claudia; Blohs, Marcus; Beyermann, Michael; Protze, Jonas; Krause, Gerd; Krause, Eberhard; Schülein, Ralf

    2015-01-01

    The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar) to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity. PMID:25806945

  5. Conformational analysis, spectroscopic, structure-activity relations and quantum chemical simulation studies of 4-(trifluoromethyl)benzylamine

    Science.gov (United States)

    Arjunan, V.; Devi, L.; Mohan, S.

    2018-05-01

    The FT-IR and FT-Raman spectra of 4-trifluoromethylbenzylamine (TFMBA) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to attain stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers obtained theoretically from the B3LYP gradient calculations employing the standard high level 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. The electronic properties, highest occupied molecular orbital and lowest unoccupied molecular orbital energies are measured by DFT approach. The charges of the atoms by natural bond orbital (NBO) analysis are determined by B3LYP/cc-pVTZ method. The structure-chemical reactivity relations of the compound are determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods.

  6. Studying the perturbed Wess–Zumino–Novikov–Witten SU(2k theory using the truncated conformal spectrum approach

    Directory of Open Access Journals (Sweden)

    R.M. Konik

    2015-10-01

    Full Text Available We study the SU(2k Wess–Zumino–Novikov–Witten (WZNW theory perturbed by the trace of the primary field in the adjoint representation, a theory governing the low-energy behavior of a class of strongly correlated electronic systems. While the model is non-integrable, its dynamics can be investigated using the numerical technique of the truncated conformal spectrum approach combined with numerical and analytical renormalization groups (TCSA+RG. The numerical results so obtained provide support for a semiclassical analysis valid at k≫1. Namely, we find that the low energy behavior is sensitive to the sign of the coupling constant, λ. Moreover, for λ>0 this behavior depends on whether k is even or odd. With k even, we find definitive evidence that the model at low energies is equivalent to the massive O(3 sigma model. For k odd, the numerical evidence is more equivocal, but we find indications that the low energy effective theory is critical.

  7. Conforming to partnership values: a qualitative case study of public–private mix for TB control in Ghana

    Directory of Open Access Journals (Sweden)

    Joshua Amo-Adjei

    2016-01-01

    Full Text Available Background: Public–private mix (PPM can supplement public sector initiatives, including public health. As National Tuberculosis Control Programmes around the world embrace PPM, conforming to the four key principles of partnership values of beneficence, non-maleficence, autonomy, and equity as espoused by the World Health Organization can provide a useful framework to guide successful implementation. Design: This is a qualitative case study of PPM in tuberculosis (TB control, which utilised a purposive sample of 30 key stakeholders involved in TB control in Ghana. Respondents comprised an equal number of respondents from both the public and private sectors. Semi-structured in-depth interviews (IDI were conducted with respondents. Data emanating from the IDIs were analysed deductively. Results: Although the respondents’ perceptions about beneficence were unanimous, their views about non-maleficence, autonomy, and equity appeared incongruous with the underlying meanings of the PPM values. Underlying the unfavourable perceptions were disruptions in funding, project implementers’ failure to follow-up on promised incentives, and private providers lost interest. This was perceived to have negatively affected the smooth implementation of PPM in the country. Conclusions: Going forward, it is imperative that future partnerships are built around utilitarian principles and also adhere to the dictates of agreements, whether they are ‘soft’ or standard contracts.

  8. Small angle X-ray scattering study of thermodynamic and conformational changes in ion-containing symmetric diblock copolymers

    Energy Technology Data Exchange (ETDEWEB)

    Gunkel, Ilja [Max Planck Institute of Microstructure Physics, Halle (Germany); Institute of Physics, Martin Luther University Halle Wittenberg, Halle (Germany); Thurn-Albrecht, Thomas [Institute of Physics, Martin Luther University Halle Wittenberg, Halle (Germany)

    2010-07-01

    We present temperature-dependent SAXS measurements on two different symmetric block copolymers with added salt (lithiumtriflate, LiCF{sub 3}SO{sub 3}). For both studied systems, polystyrene-b-poly-2-vinylpyridine (PS-b-P2VP) and Polystyrene-b-Polyethyleneoxide (PS-b-PEO), the salt selectively dissolved in one block leading to large increases of the order-disorder transition temperatures (T{sub ODT}). In addition, the lamellar thickness of these ion-containing block copolymers nontrivially changed above a certain salt concentration - in PS-b-P2VP the lamellae became thicker whereas their thickness decreased in PS-b-PEO. Using basic arguments of the thermodynamics of block copolymers we were able to separate the ion-induced increase of T{sub ODT} due to a higher incompatibility between the different blocks from changes in the thickness of the lamellae at T{sub ODT} resulting from changes in the conformation of the ion-containing blocks.

  9. Conformational, structural, vibrational and quantum chemical analysis on 4-aminobenzohydrazide and 4-hydroxybenzohydrazide--a comparative study.

    Science.gov (United States)

    Arjunan, V; Jayaprakash, A; Carthigayan, K; Periandy, S; Mohan, S

    2013-05-01

    Experimental and theoretical quantum chemical studies were carried out on 4-hydroxybenzohydrazide (4HBH) and 4-aminobenzohydrazide (4ABH) using FTIR and FT-Raman spectral data. The structural characteristics and vibrational spectroscopic analysis were carried performed by quantum chemical methods with the hybrid exchange-correlation functional B3LYP using 6-31G(**), 6-311++G(**) and aug-cc-pVDZ basis sets. The most stable conformer of the title compounds have been determined from the analysis of potential energy surface. The stable molecular geometries, electronic and thermodynamic parameters, IR intensities, harmonic vibrational frequencies, depolarisation ratio and Raman intensities have been computed. Molecular electrostatic potential and frontier molecular orbitals were constructed to understand the electronic properties. The potential energy distributions (PEDs) were calculated to explain the mixing of fundamental modes. The theoretical geometrical parameters and the fundamental frequencies were compared with the experimental. The interactions of hydroxy and amino group substitutions on the characteristic vibrations of the ring and hydrazide group have been analysed. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Conforming to partnership values: a qualitative case study of public-private mix for TB control in Ghana.

    Science.gov (United States)

    Amo-Adjei, Joshua

    2016-01-01

    Public-private mix (PPM) can supplement public sector initiatives, including public health. As National Tuberculosis Control Programmes around the world embrace PPM, conforming to the four key principles of partnership values of beneficence, non-maleficence, autonomy, and equity as espoused by the World Health Organization can provide a useful framework to guide successful implementation. This is a qualitative case study of PPM in tuberculosis (TB) control, which utilised a purposive sample of 30 key stakeholders involved in TB control in Ghana. Respondents comprised an equal number of respondents from both the public and private sectors. Semi-structured in-depth interviews (IDI) were conducted with respondents. Data emanating from the IDIs were analysed deductively. Although the respondents' perceptions about beneficence were unanimous, their views about non-maleficence, autonomy, and equity appeared incongruous with the underlying meanings of the PPM values. Underlying the unfavourable perceptions were disruptions in funding, project implementers' failure to follow-up on promised incentives, and private providers lost interest. This was perceived to have negatively affected the smooth implementation of PPM in the country. Going forward, it is imperative that future partnerships are built around utilitarian principles and also adhere to the dictates of agreements, whether they are 'soft' or standard contracts.

  11. 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.

  12. Superspace conformal field theory

    International Nuclear Information System (INIS)

    Quella, Thomas

    2013-07-01

    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.

  13. Supersymmetric Janus solutions in four dimensions

    International Nuclear Information System (INIS)

    Bobev, Nikolay; Pilch, Krzysztof; Warner, Nicholas P.

    2014-01-01

    We use maximal gauged supergravity in four dimensions to construct the gravity dual of a class of supersymmetric conformal interfaces in the theory on the world-volume of multiple M2-branes. We study three classes of examples in which the (1+1)-dimensional defects preserve (4,4), (0,2) or (0,1) supersymmetry. Many of the solutions have the maximally supersymmetric AdS 4 vacuum dual to the N=8 ABJM theory on both sides of the interface. We also find new special classes of solutions including one that interpolates between the maximally supersymmetric vacuum and a conformal fixed point with N=1 supersymmetry and G 2 global symmetry. We find another solution that interpolates between two distinct conformal fixed points with N=1 supersymmetry and G 2 global symmetry. In eleven dimensions, this G 2 to G 2 solution corresponds to a domain wall across which a magnetic flux reverses orientation

  14. 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.)

  15. 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.

  16. Diffuse neutron scattering study of metallic interstitial solid solutions

    International Nuclear Information System (INIS)

    Barberis, P.

    1991-10-01

    We studied two interstitial solid solutions (Ni-C(1at%) and Nb-O(2at%) and two stabilized zirconia (ZrO2-CaO(13.6mol%) and ZrO2-Y2O3(9.6mol%) by elastic diffuse neutron scattering. We used polarized neutron scattering in the case of the ferromagnetic Ni-based sample, in order to determine the magnetic perturbation induced by the C atoms. Measurements were made on single crystals in the Laboratoire Leon Brillouin (CEA-CNRS, Saclay, France). An original algorithm to deconvolve time-of-flight spectra improved the separation between elastically and inelastically scattered intensities. In the case of metallic solutions, we used a simple non-linear model, assuming that interstitials are isolated and located in octahedral sites. Results are: - in both compounds, nearest neighbours are widely displaced away from the interstitial, while next nearest neighbours come slightly closer. - the large magnetic perturbation induced by carbon in Nickel decreases with increasing distance on the three first neighbour shells and is in good agreement with the total magnetization variation. - no chemical order between solute atoms could be evidenced. Stabilized zirconia exhibit a strong correlation between chemical order and the large displacements around vacancies and dopants. (Author). 132 refs., 38 figs., 13 tabs

  17. An experimental study on MRI signal intensity of albumin solution

    International Nuclear Information System (INIS)

    Ahn, In Oak; Chang, Kee Hyun; Han, Moon Hee; Song, Chi Sung; Yeon, Kyung Mo

    1990-01-01

    This in vitro study attempted to correlate magnetic resonance (MR) signal intensity with concentration of albumin solution in magnetic field strength of 2.0 Tesla (T) and 0.5T. MR imaging of bovine serum albumin solutions of various concentrations ranging from 0 to 40 g/dl was performed on both 2.0T and 0.5T MR units. The relative (with respect to normal saline) signal intensities of each albumin solution were measured in T1-weighted, proton density-weighted and T2-weighted MR images, correlated with albumin concentration on each pulse sequence, and compared between 2.0T and 0.5T. Additionally, the albumin concentrations showing signal intensities identical to those of white matter, cortical gray matter and cerebrospinal fluid (CSF) of normal brain MRI were determined by visual comparison of those images. 1. On T1-weighted (SE 400-500 msec/30 msec) images under 2.0T and 0.5T field strength, the signal intensity increased with increasing albumin concentrations up to about 30-35 g/dl and the decreased. For the solutions ranging from 0 to about 5 g/dl concentration, the signal intensities appeared isointense to normal saline on visual inspection. 2. On proton density-weighted (SE 2000-2500 msec/30 msec) images under 2.0T and 0.5T field strength, the signal intensity slightly increased with increasing albumin concentrations up to about 7.5-10 g/dl, and then gradually decreased. 3. On T2-weighted (SE 2000-2500 msec/80-100 msec) images under 2.0T and 0.5T field strength, the signal intensity slightly increased with increasing albumin concentrations up to about 7.5-10 g/dl, and then gradually decreased. Above the concentration of about 25-30 g/dl, the signal intensity appeared lower than that of normal saline on visual inspection. 4. Compared with the signal intensities of normal brain structures on T1-weighted images under 2.0T and 0.5T field strength, the signal intensities of the albumin solution below 2.5-5 g/dl concentration were similar to that of CSF, and those of

  18. The ground state hydrogen conformations and vibrational analysis of 2-, 3-, 4- and 5- dihydroxybenzaldehyde: A DFT study

    International Nuclear Information System (INIS)

    Cirak, C.; Saglam, A.; Ucun, F.

    2010-01-01

    The ground state hydrogen conformations of 2-, 3-, 4- and 5-dihydroxybenzaldehyde have been investigated using density functional theory (B3LYP) methods with 6-31G (d,p) basis set. The calculations have indicated that the compounds in the ground state exist with the carbonyl group O atom linked intra molecularly by the two hydrogen bonds of the two hydroxyl groups. The vibrational analyses of the ground state conformers of all the compounds were done and their optimized geometry parameters were given.

  19. Recent progress in irrational conformal field theory

    International Nuclear Information System (INIS)

    Halpern, M.B.

    1993-09-01

    In this talk, I will review the foundations of irrational conformal field theory (ICFT), which includes rational conformal field theory as a small subspace. Highlights of the review include the Virasoro master equation, the Ward identities for the correlators of ICFT and solutions of the Ward identities. In particular, I will discuss the solutions for the correlators of the g/h coset construction and the correlators of the affine-Sugawara nests on g contains h 1 contains hor-ellipsis contains h n . Finally, I will discuss the recent global solution for the correlators of all the ICFT's in the master equation

  20. Multiple spectroscopic studies of the structural conformational changes of human serum albumin—Essential oil based nanoemulsions conjugates

    International Nuclear Information System (INIS)

    Sekar, Gajalakshmi; Sugumar, Saranya; Mukherjee, Amitava; Chandrasekaran, Natarajan

    2015-01-01

    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

  1. 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

  2. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

    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...... the transposition process. We therefore conclude that a stronger focus on an effective sanctioning mechanism is warranted for safeguarding compliance with directives....

  3. Pulse radiolysis for the study of lead salt solutions

    International Nuclear Information System (INIS)

    Breitenkamp, M.

    1976-01-01

    The Pb + ions are produced from Pb 2 + in lead perchlorate solutions by reduction with hydrated electrons, and the absorption spectrum of this ion has been measured together with a time differential observation in the micro- and millisecond range of the disparation of these ions from the solution in the presence of different substances. For these studies the method of pulsed radiolysis has been applied, detecting the short lifed intermediate reaction products by optical absorption and electric conductivity measurements. First an attempt has been made to produce the Pb + ions also by reduction of Pb 2 + with H-atoms. If Pb + and H is produced simultaneously in an aqueous solution the reaction Pb + + H -> PbH + can occur. The absorption spectrum of the short lifed species PbH + has been studied together with the second order evanescence. In addition Pb 2 + has been reduced by i-propanol radicals at high Pb 2 + concentrations. The second order evanescence has been observed and the rate constant of the reaction 2Pb + -> Pb + Pb 2 + has been measured. The Pb 2 + ions can also be reduced by CO 2- radicals, which are formed in the presence of formiate. The observations can be interpreted by the assumption of the primary reaction Pb 2 + + CO 2- -> PbCO 2+ . the spectrum of the product PbCO 2+ has been measured. A second order reaction of PbCO 2+ is observed with a resulting unstable particle of the structure Pb 2 CO 2 2 + . Finally the oxidation of Pb + by the OH-radical and by hydrogen peroxide has been studied. (orig./HK) [de

  4. Thermodynamic properties of aqueous solutions with citrate ions. Compressibility studies in aqueous solutions of citric acid

    International Nuclear Information System (INIS)

    Apelblat, Alexander; Korin, Eli; Manzurola, Emanuel

    2013-01-01

    Highlights: • Over a wide range of concentrations and temperatures sound velocities were measured in aqueous solutions of citric acid. • Compressibility properties of citric acid solutions are thermodynamically characterized. • Changes in the structure of water when citric acid is dissolved are discussed. -- Abstract: Sound velocities in aqueous solutions of citric acid were measured from 15 °C to 50 °C in 5 °C intervals, within the 0.1 mol · kg −1 to 5.0 mol · kg −1 concentration range. These sound velocities served to evaluate the isentropic and isothermal compressibilities, the apparent molar compressibilities, the isochoric thermal pressure coefficients, changes of the cubic expansion coefficients with pressure at constant temperature, the changes of heat capacities with volume and hydration numbers of citric acid in aqueous solutions

  5. 13CHD2–CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins

    International Nuclear Information System (INIS)

    Rennella, Enrico; Huang, Rui; Velyvis, Algirdas; Kay, Lewis E.

    2015-01-01

    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 13 CHD 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 13 CHD 2 13 C–CEST technique can be upwards of a factor of 5 times higher than for a previously published 13 CH 3 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

  6. Conformational analysis of GT1B ganglioside and its interaction with botulinum neurotoxin type B: a study by molecular modeling and molecular dynamics.

    Science.gov (United States)

    Venkateshwari, Sureshkumar; Veluraja, Kasinadar

    2012-01-01

    The conformational property of oligosaccharide GT1B in aqueous environment was studied by molecular dynamics (MD) simulation using all-atom model. Based on the trajectory analysis, three prominent conformational models were proposed for GT1B. Direct and water-mediated hydrogen bonding interactions stabilize these structures. The molecular modeling and 15 ns MD simulation of the Botulinum Neuro Toxin/B (BoNT/B) - GT1B complex revealed that BoNT/B can accommodate the GT1B in the single binding mode. Least mobility was seen for oligo-GT1B in the binding pocket. The bound conformation of GT1B obtained from the MD simulation of the BoNT/B-GT1B complex bear a close conformational similarity with the crystal structure of BoNT/A-GT1B complex. The mobility noticed for Arg 1268 in the dynamics was accounted for its favorable interaction with terminal NeuNAc. The internal NeuNAc1 tends to form 10 hydrogen bonds with BoNT/B, hence specifying this particular site as a crucial space for the therapeutic design that can restrict the pathogenic activity of BoNT/B.

  7. Thermal decomposition studies of aqueous and nitric solutions of hydroxyurea

    International Nuclear Information System (INIS)

    Shekhar Kumar; Pranay Kumar Sinha; Kamachi Mudali, U.; Natarajan, R.

    2012-01-01

    Hydroxyurea and its derivatives are important nonsalt forming reductants in partitioning of uranium and plutonium in the nuclear fuel reprocessing operations. There is no experimental data available in open literature describing pressurization due to the thermal decomposition of aqueous and nitric solutions of hydroxyurea at elevated temperatures. Authors studied thermal decomposition of hydroxyurea-nitric acid system and resultant pressurization at various concentrations of nitric acid in an adiabatic calorimeter in closed-vent conditions. During these experiments, pressurization was observed. In this paper, results of these experiments have been discussed. (author)

  8. The conformal method and the conformal thin-sandwich method are the same

    International Nuclear Information System (INIS)

    Maxwell, David

    2014-01-01

    The conformal method developed in the 1970s and the more recent Lagrangian and Hamiltonian conformal thin-sandwich methods are techniques for finding solutions of the Einstein constraint equations. We show that they are manifestations of a single conformal method: there is a straightforward way to convert back and forth between the parameters for these methods so that the corresponding solutions of the Einstein constraint equations agree. The unifying idea is the need to clearly distinguish tangent and cotangent vectors to the space of conformal classes on a manifold, and we introduce a vocabulary for working with these objects without reference to a particular representative background metric. As a consequence of these conceptual advantages, we demonstrate how to strengthen previous near-CMC (constant mean curvature) existence and non-existence theorems for the original conformal method to include metrics with scalar curvatures that change sign. (paper)

  9. Dissecting the dynamic conformations of the metamorphic protein lymphotactin.

    Science.gov (United States)

    Harvey, Sophie R; Porrini, Massimiliano; Konijnenberg, Albert; Clarke, David J; Tyler, Robert C; Langridge-Smith, Patrick R R; MacPhee, Cait E; Volkman, Brian F; Barran, Perdita E

    2014-10-30

    A mass spectrometer provides an ideal laboratory to probe the structure and stability of isolated protein ions. Interrogation of each discrete mass/charge-separated species enables the determination of the intrinsic stability of a protein fold, gaining snapshots of unfolding pathways. In solution, the metamorphic protein lymphotactin (Ltn) exists in equilibrium between two distinct conformations, a monomeric (Ltn10) and a dimeric (Ltn40) fold. Here, we use electron capture dissociation (ECD) and drift tube ion mobility-mass spectrometry (DT IM-MS) to analyze both forms and use molecular dynamics (MD) to consider how the solution fold alters in a solvent-free environment. DT IM-MS reveals significant conformational flexibility for the monomer, while the dimer appears more conformationally restricted. These findings are supported by MD calculations, which reveal how salt bridges stabilize the conformers in vacuo. Following ECD experiments, a distinctive fragmentation pattern is obtained for both the monomer and dimer. Monomer fragmentation becomes more pronounced with increasing charge state especially in the disordered regions and C-terminal α-helix in the solution fold. Lower levels of fragmentation are seen in the β-sheet regions and in regions that contain salt bridges, identified by MD simulations. The lowest charge state of the dimer for which we obtain ECD data ([D+9H](9+)) exhibits extensive fragmentation with no relationship to the solution fold and has a smaller collision cross section (CCS) than charge states 10-13+, suggesting a "collapsed" encounter complex. Other charge states of the dimer, as for the monomer, are resistant to fragmentation in regions of β-sheets in the solution fold. This study provides evidence for preservation and loss of global fold and secondary structural elements, providing a tantalizing glimpse into the power of the emerging field of native top-down mass spectrometry.

  10. Calculation of the effective chemical shielding anisotropy in L-alanyl-L-alanine, conformational and charge dependence study

    Czech Academy of Sciences Publication Activity Database

    Benda, Ladislav; Bouř, Petr; Buděšínský, Miloš; Müller, N.; Sychrovský, Vladimír

    2007-01-01

    Roč. 14, č. 1 (2007), s. 31-31 ISSN 1211-5894. [Discussions in Structural Molecular Biology /6./. 29.03.2007-31.03.2007, Nové Hrady] Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR cross-correlated relaxations * peptide conformation * ab-initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry

  11. Conformational aspects of proteins at the air/water interface studied by infrared reflection-adsorption spectroscopy

    NARCIS (Netherlands)

    Martin, A.H.; Meinders, M.B.J.; Bos, M.A.; Cohen Stuart, M.A.; Vliet, van T.

    2003-01-01

    From absorption spectra obtained with infrared reflection-absorption spectroscopy (IRRAS), it is possible to obtain information on conformational changes at a secondary folding level of proteins adsorbed at the air/water interface. In addition, information on protein concentration at the interface

  12. Conformational aspects of proteins at the air/water interface studied by infrared reflection-absorption spectroscopy

    NARCIS (Netherlands)

    Martin, A.H.; Meinders, M.B.J.; Bos, M.A.; Cohen Stuart, M.A.; Vliet, T. van

    2003-01-01

    From absorption spectra obtained with infrared reflection - absorption spectroscopy (IRRAS), it is possible to obtain information on conformational changes at a secondary folding level of proteins adsorbed at the air/water interface. In addition, information on protein concentration at the interface

  13. Unconstrained multiplet in N=2 conformal supergravity

    International Nuclear Information System (INIS)

    Hayashi, Masahito; Uehara, Shozo.

    1985-02-01

    An unconstrained (general) multiplet was studied in N = 2 conformal supergravity. Transformation law, embedding formula and multiplication rule are explicitly presented at the linearized level. (author)

  14. Analytic aspects of rational conformal field theories

    International Nuclear Information System (INIS)

    Kiritsis, E.B.; Lawrence Berkeley Lab., CA

    1990-01-01

    The problem of deriving linear differential equations for correlation functions of Rational Conformal Field Theories is considered. Techniques from the theory of fuchsian differential equations are used to show that knowledge of the central charge, dimensions of primary fields and fusion rules are enough to fix the differential equations for one- and two-point functions on the tours. Any other correlation function can be calculated along similar lines. The results settle the issue of 'exact solution' of rational conformal field theories. (orig.)

  15. Conformational and spectroscopic study of xanthogen ethyl formates, ROC(S)SC(O)OCH2CH3. Isolation of CH3CH2OC(O)SH

    Science.gov (United States)

    Juncal, Luciana C.; Cozzarín, Melina V.; Romano, Rosana M.

    2015-03-01

    ROC(S)SC(O)OCH2CH3, with R = CH3sbnd , (CH3)2CHsbnd and CH3(CH2)2sbnd , were obtained through the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. The liquid compounds were identified and characterized by 1H and 13C NMR and mass spectrometry. The conformations adopted by the molecules were studied by DFT methods. 6 conformers were theoretically predicted for R = CH3sbnd and (CH3)2CHsbnd , while the conformational flexibility of the n-propyl substituent increases the total number of feasible rotamers to 21. For the three molecules, the conformers can be associated in 3 groups, being the most stable the AS forms - the Cdbnd S double bond anti (A) with respect to the Csbnd S single bond and the Ssbnd C single bond syn (S) with respect to the Cdbnd O double bond - followed by AA and SS conformers. The vibrational spectra were interpreted in terms of the predicted conformational equilibrium, presenting the ν(Cdbnd O) spectral region signals corresponding to the three groups of conformers. A moderated pre-resonance Raman enhancement of the ν(Cdbnd S) vibrational mode of CH3(CH2)2OC(S)SC(O)OCH2CH3 was detected, when the excitation radiation approaches the energy of a n → π∗ electronic transition associated with the Cdbnd S chromophore. UV-visible spectra in different solvents were measured and interpreted in terms of TD-DFT calculations. The unknown molecule CH3CH2OC(O)SH was isolated by the UV-visible photolysis of CH3OC(S)SC(O)OCH2CH3 isolated in Ar matrix, and also obtained as a side-product of the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3.

  16. Conformational and spectroscopic study of xanthogen ethyl formates, ROC(S)SC(O)OCH₂CH₃. Isolation of CH₃CH₂OC(O)SH.

    Science.gov (United States)

    Juncal, Luciana C; Cozzarín, Melina V; Romano, Rosana M

    2015-03-15

    ROC(S)SC(O)OCH2CH3, with R=CH3-, (CH3)2CH- and CH3(CH2)2-, were obtained through the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. The liquid compounds were identified and characterized by (1)H and (13)C NMR and mass spectrometry. The conformations adopted by the molecules were studied by DFT methods. 6 conformers were theoretically predicted for R=CH3- and (CH3)2CH-, while the conformational flexibility of the n-propyl substituent increases the total number of feasible rotamers to 21. For the three molecules, the conformers can be associated in 3 groups, being the most stable the AS forms - the C=S double bond anti (A) with respect to the C-S single bond and the S-C single bond syn (S) with respect to the C=O double bond - followed by AA and SS conformers. The vibrational spectra were interpreted in terms of the predicted conformational equilibrium, presenting the ν(C=O) spectral region signals corresponding to the three groups of conformers. A moderated pre-resonance Raman enhancement of the ν(C=S) vibrational mode of CH3(CH2)2OC(S)SC(O)OCH2CH3 was detected, when the excitation radiation approaches the energy of a n→π∗ electronic transition associated with the C=S chromophore. UV-visible spectra in different solvents were measured and interpreted in terms of TD-DFT calculations. The unknown molecule CH3CH2OC(O)SH was isolated by the UV-visible photolysis of CH3OC(S)SC(O)OCH2CH3 isolated in Ar matrix, and also obtained as a side-product of the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Corrosion Compatibility Studies on Inconel-600 in NP Decontamination Solution

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sang Yoon; Jung, Jun Young; Won, Huijun; Choi, Wangkyu; Moon, Jeikwon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-05-15

    It is well known that corrosion and contamination process in the primary cooling circuit of nuclear reactors are essentially interrelated: the contaminant isotopes are mostly corrosion products activated in the reactor core, and the contamination takes place on the out-core of Inconel-600 surface. This radionuclide uptake takes place up to the inner oxide layer and oxide/metal interface. So, it is necessary to remove inner oxide layer as well as outer oxide layer for excellent decontamination effects. The outer oxide layers are composed of Fe{sub 3}O{sub 4} and NiFe{sub 2}O{sub 4}. On the other hand, the inner oxide layers are composed of Cr{sub 2}O{sub 3}, (Ni{sub 1-x}Ni{sub x})(Cr{sub 1-y}Fe{sub y}){sub 2}O{sub 4}, and FeCr{sub 2}O{sub 4}. Because of chromium in the trivalent oxidation state which is difficult to dissolve, the oxide layer has an excellent protectiveness and become hard to be decontaminated. Alkaline permanganate (AP) or nitric permanganate (NP) oxidative phase has been used to dissolve the chromium-rich oxide. A disadvantage of AP process is the generation of a large volume of secondary waste. On the other hand, that of NP process is the high corrosion rate for Ni-base alloys. Therefore, for the safe use of oxidative phase in PWR system decontamination, it is necessary to reformulate the NP chemicals for decrease of corrosion rate. This study describes the corrosion compatibility on Inconel-600 and type 304 stainless steel in NP decontamination solution for PWR applications. To evaluate the general corrosion properties, weight change of NP treated specimens was measured. NP treated specimen surface was observed using optical microscope (OM) and scanning electron microscopy (SEM) for the evaluation of the localized corrosion. The effect of additives on the corrosion of the specimens was also evaluated. This study describes the corrosion compatibility on Inconel-600 and type 304 stainless steel in NP decontamination solution for PWR applications

  18. Corrosion Compatibility Studies on Inconel-600 in NP Decontamination Solution

    International Nuclear Information System (INIS)

    Park, Sang Yoon; Jung, Jun Young; Won, Huijun; Choi, Wangkyu; Moon, Jeikwon

    2013-01-01

    It is well known that corrosion and contamination process in the primary cooling circuit of nuclear reactors are essentially interrelated: the contaminant isotopes are mostly corrosion products activated in the reactor core, and the contamination takes place on the out-core of Inconel-600 surface. This radionuclide uptake takes place up to the inner oxide layer and oxide/metal interface. So, it is necessary to remove inner oxide layer as well as outer oxide layer for excellent decontamination effects. The outer oxide layers are composed of Fe 3 O 4 and NiFe 2 O 4 . On the other hand, the inner oxide layers are composed of Cr 2 O 3 , (Ni 1-x Ni x )(Cr 1-y Fe y ) 2 O 4 , and FeCr 2 O 4 . Because of chromium in the trivalent oxidation state which is difficult to dissolve, the oxide layer has an excellent protectiveness and become hard to be decontaminated. Alkaline permanganate (AP) or nitric permanganate (NP) oxidative phase has been used to dissolve the chromium-rich oxide. A disadvantage of AP process is the generation of a large volume of secondary waste. On the other hand, that of NP process is the high corrosion rate for Ni-base alloys. Therefore, for the safe use of oxidative phase in PWR system decontamination, it is necessary to reformulate the NP chemicals for decrease of corrosion rate. This study describes the corrosion compatibility on Inconel-600 and type 304 stainless steel in NP decontamination solution for PWR applications. To evaluate the general corrosion properties, weight change of NP treated specimens was measured. NP treated specimen surface was observed using optical microscope (OM) and scanning electron microscopy (SEM) for the evaluation of the localized corrosion. The effect of additives on the corrosion of the specimens was also evaluated. This study describes the corrosion compatibility on Inconel-600 and type 304 stainless steel in NP decontamination solution for PWR applications. It is revealed that Inconel-600 specimen is more

  19. Design, synthesis, conformational and molecular docking study of some novel acyl hydrazone based molecular hybrids as antimalarial and antimicrobial agents.

    Science.gov (United States)

    Kumar, Parvin; Kadyan, Kulbir; Duhan, Meenakshi; Sindhu, Jayant; Singh, Vineeta; Saharan, Baljeet Singh

    2017-11-14

    Acyl hydrazones are an important class of heterocyclic compounds promising pharmacological characteristics. Malaria is a life-threatening mosquito-borne blood disease caused by a plasmodium parasite. In some places, malaria can be treated and controlled with early diagnosis. However, some countries lack the resources to do this effectively. The present work involves the design and synthesis of some novel acyl hydrazone based molecular hybrids of 1,4-dihydropyridine and pyrazole (5a-g). These molecular hybrids were synthesised by condensation of 1,4-dihydropyridin-4-yl-phenoxyacetohydrazides with differently substituted pyrazole carbaldehyde. The final compound (5) showed two conformations (the major, E, s-cis and the minor, E, s-trans) as revealed by NMR spectral data and further supported by the energy calculations (MOPAC2016 using PM7 method). All the synthesised compounds were screened for their in vitro antimalarial activities against chloroquine-sensitive malaria parasite Plasmodium falciparum (3D7) and antimicrobial activity against Gram positive bacteria i.e. Bacillus cereus, Gram negative bacteria i.e. Escherichia coli and antifungal activity against one yeast i.e. Aspergillus niger. All these compounds were found more potent than chloroquine and clotrimazole, the standard drugs. In vitro antiplasmodial IC 50 value of the most potent compound 5d was found to be 4.40 nM which is even less than all the three reference drugs chloroquine (18.7 nM), pyrimethamine (11 nM) and artimisinin (6 nM). In silico binding study of compound 5d with plasmodial cysteine protease falcipain-2 indicated the inhibition of falcipain-2 as the probable reason for the antimalarial potency of compound 5d. All the compounds had shown good to excellent antimicrobial and antifungal activities.

  20. Treatment Planning Study to Determine Potential Benefit of Intensity-Modulated Radiotherapy Versus Conformal Radiotherapy for Unresectable Hepatic Malignancies

    International Nuclear Information System (INIS)

    Eccles, Cynthia L.; Bissonnette, Jean-Pierre; Craig, Tim; Taremi, Mojgan; Wu Xia; Dawson, Laura A.

    2008-01-01

    Purpose: To compare intensity-modulated radiotherapy (IMRT) with conformal RT (CRT) for hypofractionated isotoxicity liver RT and explore dose escalation using IMRT for the same/improved nominal risk of liver toxicity in a treatment planning study. Methods and Materials: A total of 26 CRT plans were evaluated. Prescription doses (24-54 Gy within six fractions) were individualized on the basis of the effective liver volume irradiated maintaining ≤5% risk of radiation-induced liver disease. The dose constraints included bowel (0.5 cm 3 ) and stomach (0.5 cm 3 ) to ≤30 Gy, spinal cord to ≤25 Gy, and planning target volume (PTV) to ≤140% of the prescribed dose. Two groups were evaluated: (1) PTV overlapping or directly adjacent to serial functioning normal tissues (n = 14), and (2) the liver as the dose-limiting normal tissue (n = 12). IMRT plans using direct machine parameter optimization maintained the CRT plan beam arrangements, an estimated radiation-induced liver disease risk of 5%, and underwent dose escalation, if all normal tissue constraints were maintained. Results: IMRT improved PTV coverage in 19 of 26 plans (73%). Dose escalation was feasible in 9 cases by an average of 3.8 Gy (range, 0.6-13.2) in six fractions. Three of seven plans without improved PTV coverage had small gross tumor volumes (≤105 cm 3 ) already receiving 54 Gy, the maximal prescription dose allowed. In the remaining cases, the PTV range was 9.6-689 cm 3 ; two had overlapped organs at risk; and one had four targets. IMRT did not improve these plans owing to poor target coverage (n = 2) and nonliver (n = 2) dose limits. Conclusion: Direct machine parameter optimization IMRT improved PTV coverage while maintaining normal tissue tolerances in most CRT liver plans. Dose escalation was possible in a minority of patients

  1. T.C.G triplet in an antiparallel purine.purine.pyrimidine DNA triplex. Conformational studies by NMR.

    Science.gov (United States)

    Dittrich, K; Gu, J; Tinder, R; Hogan, M; Gao, X

    1994-04-12

    The antiparallel purine.purine.pyrimidine DNA triplex, RRY6, which contains a T.C.G inverted triplet in the center of the sequence, was examined by proton and phosphorous two-dimensional NMR spectroscopy. The local conformation of the T.C.G triplet (T4.C11.G18) and the effect of this triplet on the global helical structure were analyzed in detail. The formation of the T.C.G triplet is confirmed by a set of cross-strand NOEs, including unusual cross-strand NOEs between the third strand and the pyrimidine strand as opposed to the purine strand of the duplex. NMR data suggest that the T.C.G triplet may be present in an equilibrium between a non-hydrogen-bonded form and a T(O4)-C(NH2) hydrogen-bonded form and that there is a distortion of the in-plane alignment of the three bases. The flanking G.G.C base triplets are well-defined on the 5'-side of T4, but somewhat interrupted on the 3'-side of T4. The effect of the third strand binding on the Watson-Crick duplex was probed by an NMR study of the free duplex RY6. NMR parameters are affected mostly around the T.C.G inversion site. The perturbations extend to at least two adjacent base triplets on either side. The binding of the third purine strand and the accommodation of a central T.C.G inversion in RRY6 does not require a readjustment in sugar pucker, which remains in the range of C2'-endo. 31P resonances of RRY6 distribute over a range of 2.2 ppm. The H-P coupling patterns of the third strand differ from those of the duplex. General spectral patterns defined by the marker protons of the RRY and YRY triplexes are compared.

  2. Lattice models and conformal field theories

    International Nuclear Information System (INIS)

    Saleur, H.

    1988-01-01

    Theoretical studies concerning the connection between critical physical systems and the conformal theories are reviewed. The conformal theory associated to a critical (integrable) lattice model is derived. The obtention of the central charge, critical exponents and torus partition function, using renormalization group arguments, is shown. The quantum group structure, in the integrable lattice models, and the theory of Visaro algebra representations are discussed. The relations between off-critical integrable models and conformal theories, in finite geometries, are studied

  3. A study on quantitative analysis of field size and dose by using gating system in 4D conformal radiation treatment

    Science.gov (United States)

    Ji, Youn-Sang; Dong, Kyung-Rae; Kim, Chang-Bok; Chung, Woon-Kwan; Cho, Jae-Hwan; Lee, Hae-Kag

    2012-10-01

    This study evaluated the gating-based 4-D conformal radiation therapy (4D-CT) treatment planning by a comparison with the common 3-D conformal radiation therapy (3D-CT) treatment planning and examined the change in treatment field size and dose to the tumors and adjacent normal tissues because an unnecessary dose is also included in the 3-D treatment planning for the radiation treatment of tumors in the chest and abdomen. The 3D-CT and gating-based 4D-CT images were obtained from patients who had undergone radiation treatment for chest and abdomen tumors in the oncology department. After establishing a treatment plan, the CT treatment and planning system were used to measure the change in field size for analysis. A dose volume histogram (DVH) was used to calculate the appropriate dose to planning target volume (PTV) tumors and adjacent normal tissue. The difference in the treatment volume of the chest was 0.6 and 0.83 cm on the X- and Y-axis, respectively, for the gross tumor volume (GTV). Accordingly, the values in the 4D-CT treatment planning were smaller and the dose was more concentrated by 2.7% and 0.9% on the GTV and clinical target volume (CTV), respectively. The normal tissues in the surrounding normal tissues were reduced by 3.0%, 7.2%, 0.4%, 1.7%, 2.6% and 0.2% in the bronchus, chest wall, esophagus, heart, lung and spinal cord, respectively. The difference in the treatment volume of the abdomen was 0.72 cm on the X-axis and 0.51 cm on the Y-axis for the GTV; and 1.06 cm on the X-axis and 1.85 cm on the Y-axis for the PTV. Therefore, the values in the 4D-CT treatment planning were smaller. The dose was concentrated by 6.8% and 4.3% on the GTV and PTV, respectively, whereas the adjacent normal tissues in the cord, Lt. kidney, Rt. kidney, small bowels and whole liver were reduced by 3.2%, 4.2%, 1.5%, 6.2% and 12.7%, respectively. The treatment field size was smaller in volume in the case of the 4D-CT treatment planning. In the DVH, the 4D-CT treatment

  4. Universal hydrodynamics of non-conformal branes

    International Nuclear Information System (INIS)

    Kanitscheider, Ingmar; Skenderis, Kostas

    2009-01-01

    We examine the hydrodynamic limit of non-conformal branes using the recently developed precise holographic dictionary. We first streamline the discussion of holography for backgrounds that asymptote locally to non-conformal brane solutions by showing that all such solutions can be obtained from higher dimensional asymptotically locally AdS solutions by suitable dimensional reduction and continuation in the dimension. As a consequence, many holographic results for such backgrounds follow from the corresponding results of the Asymptotically AdS case. In particular, the hydrodynamics of non-conformal branes is fully determined in terms of conformal hydrodynamics. Using previous results on the latter we predict the form of the non-conformal hydrodynamic stress tensor to second order in derivatives. Furthermore we show that the ratio between bulk and shear viscosity is fixed by the generalized conformal structure to be ζ/η = 2(1/(d-1)-c s 2 ), where c s is the speed of sound in the fluid.

  5. 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...

  6. Archiving Primary Data: Solutions for Long-Term Studies.

    Science.gov (United States)

    Mills, James A; Teplitsky, Céline; Arroyo, Beatriz; Charmantier, Anne; Becker, Peter H; Birkhead, Tim R; Bize, Pierre; Blumstein, Daniel T; Bonenfant, Christophe; Boutin, Stan; Bushuev, Andrey; Cam, Emmanuelle; Cockburn, Andrew; Côté, Steeve D; Coulson, John C; Daunt, Francis; Dingemanse, Niels J; Doligez, Blandine; Drummond, Hugh; Espie, Richard H M; Festa-Bianchet, Marco; Frentiu, Francesca; Fitzpatrick, John W; Furness, Robert W; Garant, Dany; Gauthier, Gilles; Grant, Peter R; Griesser, Michael; Gustafsson, Lars; Hansson, Bengt; Harris, Michael P; Jiguet, Frédéric; Kjellander, Petter; Korpimäki, Erkki; Krebs, Charles J; Lens, Luc; Linnell, John D C; Low, Matthew; McAdam, Andrew; Margalida, Antoni; Merilä, Juha; Møller, Anders P; Nakagawa, Shinichi; Nilsson, Jan-Åke; Nisbet, Ian C T; van Noordwijk, Arie J; Oro, Daniel; Pärt, Tomas; Pelletier, Fanie; Potti, Jaime; Pujol, Benoit; Réale, Denis; Rockwell, Robert F; Ropert-Coudert, Yan; Roulin, Alexandre; Sedinger, James S; Swenson, Jon E; Thébaud, Christophe; Visser, Marcel E; Wanless, Sarah; Westneat, David F; Wilson, Alastair J; Zedrosser, Andreas

    2015-10-01

    The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Structure and dynamics of alpha-tocopherol in model membranes and in solution: a broad-line and high-resolution NMR study

    International Nuclear Information System (INIS)

    Ekiel, I.H.; Hughes, L.; Burton, G.W.; Jovall, P.A.; Ingold, K.U.; Smith, I.C.

    1988-01-01

    Nuclear magnetic resonance has been applied to study the conformational dynamics of alpha-tocopherol (vitamin E) in solution and in model membranes. In nonviscous solution, 1 H nuclear magnetic resonance (NMR) showed that alpha-tocopherol is in rapid equilibrium between two or more puckered conformers of its heterocyclic ring. The most likely conformers to be so involved are the two half-chair forms. Deuterium NMR spectra of specifically deuteriated alpha-tocopherol in multilamellar dispersions of egg phosphatidylcholine, measured in the liquid-crystalline state, were characteristic of axially symmetric motional averaging. The orientation of the rotational axis within the molecular framework was determined. Studies on oriented multilamellar membranes revealed that this axis is perpendicular to the surface of the membrane. The profile of quadrupolar splittings along the hydrophobic tail does not have a plateau, in contrast to that of the fatty acyl chains of the membrane lipids. Longitudinal relaxation times (T1) were short. The presence of a minimum in their temperature dependence shows that molecular motion with an effective correlation time tau eff approximately equal to 3 X 10(-9)s is responsible for relaxation. However, the temperatures and absolute values of the minima depend on the position of the deuterium in the molecule, demonstrating that tau eff represents a complex blend of motions

  8. Experimental and theoretical study of solid solution stability under irradiation

    International Nuclear Information System (INIS)

    Cauvin, Richard.

    1981-08-01

    The behavior of dilute alloys (Al-Zn, Al-Ag, Al-Si, Al-Ge and Al-Mg) under 1 MeV electron irradiation has been studied in a high voltage electron microscope. A phenomenon of homogeneous precipitation induced by irradiation in undersaturated solid solutions (Al-Zn, Al-Ag and Al-Si) has been discovered; the observed precipitates are either coherent or incoherent, but never associated with point defect sinks. The solubility limit is a function of irradiation temperature and flux; but, under irradiation, it does not behave as a true thermal solubility limit (without irradiation). The existing theories (kinetic or strictly thermodynamic) do not account for this phenomenon. It is shown that the irreversibility of the mutual recombination between trapped vacancies and mixed interstitials is the driving force of this homogeneous precipitation. Using a dilute solid solution model, we show that, under irradiation, the homogeneous stationary state, stable from a strictly thermodynamic point of view, can be unstable when the recombination reaction is taken into account. The solubility limit under irradiation is calculated with a nucleation-growth model taking account for this effect; it is proportional to the thermal solubility limit without irradiation. This model explains all the experimental observations [fr

  9. Conformal tension in string theories and M-theory

    International Nuclear Information System (INIS)

    Barros, Manuel; Ferrandez, Angel; Lucas, Pascual

    2000-01-01

    This paper deals with string theories and M-theories on backgrounds of the form AdSxM,M being a compact principal U(1)-bundle. These configurations are the natural settings to study Hopf T-dualities (Duff et al., Nucl. Phys. B 544 (1999) 145), and so to define duality chains connecting different string theories and M-theories. There is an increasing great interest in studying those properties (physical or geometrical) which are preserved along the duality chains. For example, it is known that Hopf T-dualities preserve the black hole entropies (Duff et al., Nucl. Phys. B 544 (1999) 145). In this paper we consider a two-parameter family of actions which constitutes a natural variation of the conformal total tension action (also known as Willmore-Chen functional in differential geometry). Then, we show that the existence of wide families of solutions (in particular compact solutions) for the corresponding motion equations is preserved along those duality chains. In particular, we exhibit ample classes of Willmore-Chen submanifolds with a reasonable degree of symmetry in a wide variety of conformal string theories and conformal M-theories, that in addition are solutions of a second variational problem known as the area-volume isoperimetric problem. These are good reasons to refer those submanifolds as the best worlds one can find in a conformal universe. The method we use to obtain this invariant under Hopf T-dualities is based on the principle of symmetric criticality. However, it is used in a two-fold sense. First to break symmetry and so to reduce variables. Second to gain rigidity in direct approaches to integrate the Euler-Lagrange equations. The existence of generalized elastic curves is also important in the explicit exhibition of those configurations. The relationship between solutions and elasticae can be regarded as a holographic property

  10. Hydrolysis-precipitation studies of aluminum (III) solutions. I. Titration of acidified aluminum nitrate solutions

    NARCIS (Netherlands)

    Vermeulen, A.C.; Geus, John W.; Stol, R.J.; Bruyn, P.L. de

    Acidified aluminum nitrate solutions were titrated with alkali (NaOH or KOH) over a temperature range of 24°C to 90°C. A homogeneous distribution of added base was achieved by: (i) in situ decomposition of urea (90°C); and (ii) a novel method involving injection through a capillary submerged in the

  11. 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

  12. Elementary introduction to conformal invariance

    International Nuclear Information System (INIS)

    Grandati, Y.

    1992-01-01

    These notes constitute an elementary introduction to the concept of conformal invariance and its applications to the study of bidimensional critical phenomena. The aim is to give an access as pedestrian as possible to this vast subject. After a brief account of the general properties of conformal transformation in D dimensions, we study more specifically the case D = 2. The center of the discussion is then the consequences of the action of this symmetry group on bidimensional field theories, and in particular the links between the representations of the Virasoro algebra and the structure of the correlation functions of conformal field theories. Finally after showing how the Ising model reduces to a Majorana fermionic field theory, we see how the general formalism previously discussed can be applied to the Ising case at the critical point. (orig.)

  13. Biospectroscopy of Nanodiamond-Induced Alterations in Conformation of Intra- and Extracellular Proteins: A Nanoscale IR Study.

    Science.gov (United States)

    Khanal, Dipesh; Kondyurin, Alexey; Hau, Herman; Knowles, Jonathan C; Levinson, Olga; Ramzan, Iqbal; Fu, Dong; Marcott, Curtis; Chrzanowski, Wojciech

    2016-08-02

    The toxicity of nanomaterials raises major concerns because of the impact that nanomaterials may have on health, which remains poorly understood. We need to explore the fate of individual nanoparticles in cells at nano and molecular levels to establish their safety. Conformational changes in secondary protein structures are one of the main indicators of impaired biological function, and hence, the ability to identify these changes at a nanoscale level offers unique insights into the nanotoxicity of materials. Here, we used nanoscale infrared spectroscopy and demonstrated for the first time that nanodiamond-induced alterations in both extra- and intracellular secondary protein structures lead to the formation of antiparallel β-sheet, β-turns, intermolecular β-sheet, and aggregation of proteins. These conformational changes of the protein structure may result in the loss of functionality of proteins and in turn lead to adverse effects.

  14. 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.

  15. Bronchography in dogs. Comparative study with two barium sulphate solutions

    International Nuclear Information System (INIS)

    Thibaut, J.; Gallardo, P.; Vargas, L.; Deppe, R.; Born, R.

    1998-01-01

    Two solutions of barium sulphate, 60 and 30% w/v, were compared with the ''overflow'' Bronchographic method. Two groups of eight healthy adult does of both sexes, weighing 7 to 18 kg were used for the study. The dogs were anaesthetised with thiopentone sodium 2% (20 mg/kg iv). After intubation, each dog received contrast medium by a catheter connected to a syringe, in a 9 mi dose. Two series of two x-rays plates were taken in left lateral recumbent, 3 and 6 min after administering the contrast medium and in ventrodorsal projection, 30 sec. later. The x-ray plates obtained were analysed and compared intra and inter group considering the advance speed of the contrast medium, the radiographic density and outlines. Adverse reactions were controlled

  16. A study on caregiver burden: stressors, challenges, and possible solutions.

    Science.gov (United States)

    Bialon, Laura Nelson; Coke, Sallie

    2012-05-01

    The purpose of this qualitative study was to explore factors impacting caregiver burden and to explore possible solutions for family caregivers of terminally ill patients. The majority of caregivers reported experiencing role conflict and inadequate stress management. Caregivers who worked outside the home, those who cared for two parents concurrently, those with the least amount of outside assistance, and caregivers who spent a longer period of time caregiving reported the highest levels of health problems and overall burden. Caregivers stated a need for more support from Hospice agencies, more education on caregiver training, and more public education about Hospice services. Faith played a positive role in alleviating caregiver burden. Early identification, intervention, education and coordination of services may help to alleviate caregiver burden, which will improve quality of life for both patient and caregiver.

  17. NMR studies of phase behaviour in polyacrylonitrile solutions

    International Nuclear Information System (INIS)

    Golightly, J.A.

    1998-10-01

    The aim of the thesis was to study the phase behaviour of aqueous polyacrylonitrile/NaSCN solutions using a variety of nuclear magnetic resonance techniques. Polyacrylonitrile (PAN) is the basis of the acrylic fibre industry, as such fibres contain at least 85% PAN. Despite this industrial importance, the available literature describing the phase behaviour of PAN in solution is far from comprehensive. Bulk 1 H NMR relaxation measurements were carried out over a wide range of concentrations and temperatures to probe the molecular dynamics of the PAN and water molecules. The relaxation data was found to be biexponential decay for all samples, the relative amplitudes of which were shown to be equal to the ratio of PAN protons to water protons. Both species were found to be in the regime of rapid molecular motion. Bulk 1 H NMR self diffusion measurements, using the PFGSTE technique, exhibited a bi-exponential decay of the echo amplitudes. By careful selection of the observation time, Δ, it was possible to independently probe the water and PAN translational diffusion. A background gradient, resulting from inhomogeneities of the magnetic field, complicated the analysis of the data and a novel polynomial least squares fitting procedure was devised to overcome this effect. The measured attenuation of the water diffusion coefficients (D∼10 -6 -10 -5 cm 2 s -1 ) with increasing PAN volume fraction was modelled according to various theories, including free volume and scaling laws. The study of the PAN diffusion coefficient (D∼10 -7 -10 -6 cm 2 s -1 ) was limited by the experimental constraints of the NMR spectrometer. A 1 H NMR one-dimensional imaging technique was used to study the non-solvent induced phase separation (coagulation) of a PAN solution. The time dependence of the measured profiles allowed observation of the coagulation process. A diffusion model was developed to fit the experimental data using a semi-infinite diffusion framework. The fitting parameters

  18. Delineation of alternative conformational states in Escherichia coli peptide deformylase via thermodynamic studies for the binding of actinonin.

    Science.gov (United States)

    Berg, Alexander K; Srivastava, D K

    2009-02-24

    We investigated the binding of a naturally occurring antibiotic, actinonin, to the Ni(2+)-reconstituted recombinant form of Escherichia coli peptide deformylase (PDF(Ec)) via isothermal titration microcalorimetry. The binding data conformed to both exothermic and endothermic phases with magnitudes of DeltaG degrees , DeltaH degrees , and TDeltaS degrees being equal to -12, -2.7, and 9.3 kcal/mol and -8.7, 3.9, and 12.6 kcal/mol, respectively. Evidently, although both phases are dominated by favorable entropic changes, the exothermic phase has about 6.7 kcal/mol enthalpic advantage over the endothermic phase. We observed that the removal of bound Ni(2+) from PDF(Ec) abolished the exothermic phase without affecting the endothermic phase, but it was regained upon addition of Zn(2+). In conjunction with metal analysis data, we propose that the recombinant form of PDF(Ec) is expressed in two stable conformational states that yield markedly distinct ITC profiles (i.e., exothermic versus endothermic) upon interaction with actinonin. The existence of two conformational states of PDF(Ec) is further supported by the observation of two distinct and independent transitions during the thermal unfolding of the enzyme. In addition, the thermodynamic data reveal that the formation of the PDF(Ec)-actinonin complex results in the transfer of one H(+) from the enzyme phase to the bulk solvent at pH 6.3. Both exothermic and endothermic phases produce highly negative DeltaC(p) degrees values, but there is no apparent enthalpy-entropy compensation effect upon formation of the PDF(Ec)-actinonin complex. In view of the known structural features of the enzyme, arguments are presented that the alternative conformational states of PDF(Ec) are modulated by the metal ligation at the enzyme site.

  19. Cooling solutions in an operational data centre: A case study

    International Nuclear Information System (INIS)

    Fakhim, B.; Behnia, M.; Armfield, S.W.; Srinarayana, N.

    2011-01-01

    The rapid growth in data centres - large computing infrastructures containing vast quantities of data processing and storage equipment - has resulted in their consumption of up to 100 times more energy per square metre than office accommodation. The decrease in processing server sizes and the more efficient use of space and server processing are challenging data centre facilities to provide more power and cooling, significantly increasing energy demands. Energy consumption of data centres can be severely and unnecessarily high due to inadequate localised cooling and densely packed server rack layouts. However, as heat dissipation in data centres rises by orders of magnitude, inefficiencies such as air recirculation causing hot spots and flow short-circuiting will have a significant impact on the thermal manageability and energy efficiency of the cooling infrastructure. Therefore, an efficient thermal management of high-powered electronic equipment is a significant challenge for cooling of data centres. To highlight the importance of some of these issues, in this project, an operational data centre has been studied. Field measurements of temperature have been performed. Numerical analysis of flow and temperature fields is conducted in order to evaluate the thermal behaviour of the data centre. A number of undesirable hot spots have been identified. To rectify the problem, a few practical design and remedial solutions to improve the cooling effectiveness have been proposed and examined to allow a reduced air-conditioning power requirement. The findings lead to a better understanding of the cooling issues and the respective proposed solutions allow an improved design for future data centres. - Highlights: → Study of flow and temperature distribution in an operational data centre. → Both field measurements and numerical simulations are conducted. → Numerical simulations are validated by field measurements. → Various modifications to improve the thermal

  20. Small angle X-ray scattering study on the conformation of polystyrene in the anti-solvent process of supercritical fluids

    International Nuclear Information System (INIS)

    Liu Yi; Wang Hongli; Zhao Xin; Chen Na; Li Dan; Liu Zhimin; Han Buxing; Rong Lixia; Zhao Hui; Wang Jun; Dong Baozhong

    2003-01-01

    The conformation of polystyrene in the anti-solvent process of supercritical fluids (compressed CO 2 + polystyrene + tetrahydrofuran) is studied by synchrotron radiation X-ray small angle scattering (SAXS). Coil-to-globule transform of polystyrene chain is observed with increasing the concentration of CO 2 . It is found that polystyrene coils at the pressure lower than cloud point pressure (p c ) and changes into globule with uniform density at the pressure higher than p c

  1. Aggregation-primed molten globule conformers of the p53 core domain provide potential tools for studying p53C aggregation in cancer.

    Science.gov (United States)

    Pedrote, Murilo M; de Oliveira, Guilherme A P; Felix, Adriani L; Mota, Michelle F; Marques, Mayra de A; Soares, Iaci N; Iqbal, Anwar; Norberto, Douglas R; Gomes, Andre M O; Gratton, Enrico; Cino, Elio A; Silva, Jerson L

    2018-05-31

    The functionality of the tumor suppressor p53 is altered in more than 50% of human cancers, and many individuals with cancer exhibit amyloid-like buildups of aggregated p53. An understanding of what triggers the pathogenic amyloid conversion of p53 is required for the further development of cancer therapies. Here, perturbation of the p53 core domain (p53C) with sub-denaturing concentrations of guanidine hydrochloride and high hydrostatic pressure revealed native-like molten globule (MG) states, a subset of which were highly prone to amyloidogenic aggregation. We found that MG conformers of p53C, likely representing population-weighted averages of multiple states, have different volumetric properties, as determined by pressure perturbation and size-exclusion chromatography. We also found that they bind the fluorescent dye 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) and have a native-like tertiary structure that occludes the single Trp residue in p53. Fluorescence experiments revealed conformational changes of the single Trp and Tyr residues before p53 unfolding and the presence of MG conformers, some of which were highly prone to aggregation. P53C exhibited marginal unfolding cooperativity, which could be modulated from unfolding to aggregation pathways with chemical or physical forces. We conclude that trapping amyloid precursor states in solution is a promising approach for understanding p53 aggregation in cancer. Our findings support the use of single-Trp fluorescence as a probe for evaluating p53 stability, effects of mutations, and the efficacy of therapeutics designed to stabilize p53. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Study on corrosion of carbon steel in DEA aqueous solutions

    Science.gov (United States)

    Yang, Jun Han; Xie, Jia Lin; Zhang, Li

    2018-02-01

    Corrosion of carbon steel in the CO2 capture process using diethanolamine (DEA) aqueous solutions was investigated. The effects of the mass concentrations of DEA, solution temperature and CO2 loading on the corrosion rate of carbon steel were demonstrated. The experimental results provided comprehensive information on the appropriate concentration range of DEA aqueous solutions under which low corrosion of carbon steel can be achieved.

  3. Radiolysis studies of uranyl nitrate solution in nitric acid medium

    International Nuclear Information System (INIS)

    Siri, Sandra; Mondino, Angel V.

    2005-01-01

    The radiolysis of acidic uranyl nitrate solutions was investigated using Co-60 gamma radiation. Hydrogen peroxide was determined as a function of increasing dose. The UV-vis absorption spectra of the irradiated solutions were measured and the spectral changes were analyzed. The increasing dose increases the absorbance intensities, possibly by an increment in nitrate concentration produced by radiolysis, which can originate the formation of different uranyl complexes in solution. (author)

  4. Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism.

    Science.gov (United States)

    Daidone, Isabella; Magliano, Alessandro; Di Nola, Alfredo; Mignogna, Giuseppina; Clarkson, Matilda Manuela; Lizzi, Anna Rita; Oratore, Arduino; Mazza, Fernando

    2011-04-01

    Lactoferricins are potent antimicrobial peptides released by pepsin cleavage of Lactoferrins. Bovine Lactoferricin (LfcinB) has higher activity than the intact bovine Lactoferrin, and is the most active among the other Lactoferricins of human, murine and caprine origin. In the intact protein the fragment corresponding to LfcinB is in an helical conformation, while in water LfcinB adopts an amphipathic β-hairpin structure. However, whether any of these structural motifs is the antibacterial active conformation, i.e., the one interacting with bacterial membrane components, remains to be seen. Here we present Circular Dichroism (CD) spectra and Molecular Dynamics (MD) simulations indicating that in membrane-mimicking solvents the LfcinB adopts an amphipathic β-hairpin structure similar to that observed in water, but differing in the dynamic behavior of the side-chains of the two tryptophan residues. In the membrane-mimicking solvent these side-chains show a high propensity to point towards the hydrophobic environment, rather than being in the hydrophobic core as seen in water, while the backbone preserves the hairpin conformation as found in water. These results suggest that the tryptophans might act as anchors pulling the stable, solvent-invariant hairpin structure into the membrane.

  5. 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.

  6. Nuclear Overhauser effect studies on the conformation of magnesium adenosine 5'-triphosphate bound to rabbit muscle creatine kinase

    International Nuclear Information System (INIS)

    Rosevear, P.R.; Powers, V.M.; Dowhan, D.; Mildvan, A.S.; Kenyon, G.L.

    1987-01-01

    Nuclear Overhauser effects were used to determine interproton distances on MgATP bound to rabbit muscle creatine kinase. The internuclear distances were used in a distance geometry program that objectively determines both the conformation of the bound MgATP and its uniqueness. Two classes of structures were found that satisfied the measured interproton distances. Both classes had the same anti glycosidic torsional angle (X = 78 +/- 10 0 ) but differed in their ribose ring puckers (O1'-endo or C4'-exo). The uniqueness of the glycosidic torsional angle is consistent with the preference of creatine kinase for adenine nucleotides. One of these conformations of MgATP bound to creatine kinase is indistinguishable from the conformation found for Co(NH 3 ) 4 ATP bound to the catalytic subunit of protein kinase, which also has a high specificity for adenine nucleotides. Distance geometry calculations also suggest that upper limit distances, when low enough (≤ 3.4 A), can be used instead of measured distances to define, within experimental error, the glycosidic torsional angle of bound nucleotides. However, this approach does not permit an evaluation of the ribose ring pucker

  7. Renormalization, conformal ward identities and the origin of a conformal anomaly pole

    Science.gov (United States)

    Corianò, Claudio; Maglio, Matteo Maria

    2018-06-01

    We investigate the emergence of a conformal anomaly pole in conformal field theories in the case of the TJJ correlator. We show how it comes to be generated in dimensional renormalization, using a basis of 13 form factors (the F-basis), where only one of them requires renormalization (F13), extending previous studies. We then combine recent results on the structure of the non-perturbative solutions of the conformal Ward identities (CWI's) for the TJJ in momentum space, expressed in terms of a minimal set of 4 form factors (A-basis), with the properties of the F-basis, and show how the singular behaviour of the corresponding form factors in both basis can be related. The result proves the centrality of such massless effective interactions induced by the anomaly, which have recently found realization in solid state, in the theory of topological insulators and of Weyl semimetals. This pattern is confirmed in massless abelian and nonabelian theories (QED and QCD) investigated at one-loop.

  8. 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

  9. Operator algebras and conformal field theory

    International Nuclear Information System (INIS)

    Gabbiani, F.; Froehlich, J.

    1993-01-01

    We define and study two-dimensional, chiral conformal field theory by the methods of algebraic field theory. We start by characterizing the vacuum sectors of such theories and show that, under very general hypotheses, their algebras of local observables are isomorphic to the unique hyperfinite type III 1 factor. The conformal net determined by the algebras of local observables is proven to satisfy Haag duality. The representation of the Moebius group (and presumably of the entire Virasoro algebra) on the vacuum sector of a conformal field theory is uniquely determined by the Tomita-Takesaki modular operators associated with its vacuum state and its conformal net. We then develop the theory of Mebius covariant representations of a conformal net, using methods of Doplicher, Haag and Roberts. We apply our results to the representation theory of loop groups. Our analysis is motivated by the desire to find a 'background-independent' formulation of conformal field theories. (orig.)

  10. Interdependence of coenzyme-induced conformational work and binding potential in yeast alcohol and porcine heart lactate dehydrogenases: a hydrogen-deuterium exchange study

    International Nuclear Information System (INIS)

    De Weck, Z.; Pande, J.; Kaegi, J.H.R.

    1987-01-01

    Binding of NAD coenzymes to yeast alcohol dehydrogenase (YADH) and porcine heart lactate dehydrogenase (PHLDH) was studied by hydrogen-deuterium exchange with the infrared technique. Conformational changes in the enzymes specific to the coenzymes and their fragments were observed, and the pH dependence of the exchange reaction shows that it conforms to the EX-2 scheme. In both YADH and PHLDH the magnitude of the conformational change as measured by exchange retardation is considerably larger for the NAD + than for NADH. Studies with coenzyme fragments like ADP-ribose, ADP, and AMP also highlight the lack of rigorous correlation between structural features such as charge and size and their influence on exchange behavior. Ternary complexes such as YADH-NAD + -pyrazole, PHLDH-NAD + -oxalate, and PHLDH-NADH-oxamate, which mimic the transition state, have a significantly more pronounced effect on exchange rates than the corresponding binary complexes. The outstanding feature of this study is the demonstration that in the binary enzyme-coenzyme complexes the more loosely bound NAD + is more effective in retarding exchange than the more firmly bound NADH. These differences are attributed to the unequal structural constraints exerted by the two coenzymes upon the enzymes, which translate to unequal expenditure of transconformational work in the formation of the two complexes. The opposing variation in the free energy of binding and the transconformational work expended can be viewed as an unequal partitioning of the net free energy gain resulting from the protein-ligand interaction into a binding term and that required for conformational change

  11. Conformational sensitivity of conjugated poly(ethylene oxide)-poly(amidoamine) molecules to cations adducted upon electrospray ionization – A mass spectrometry, ion mobility and molecular modeling study

    Energy Technology Data Exchange (ETDEWEB)

    Tintaru, Aura [Aix-Marseille Université – CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille (France); Chendo, Christophe [Aix-Marseille Université – CNRS, FR 1739, Fédération des Sciences Chimiques de Marseille, Spectropole, Marseille (France); Wang, Qi [Aix-Marseille Université – CNRS, UMR 6114, Centre Interdisciplinaire de Nanosciences de Marseille, Marseille (France); Viel, Stéphane [Aix-Marseille Université – CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille (France); Quéléver, Gilles; Peng, Ling [Aix-Marseille Université – CNRS, UMR 6114, Centre Interdisciplinaire de Nanosciences de Marseille, Marseille (France); Posocco, Paola [University of Trieste, Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), Trieste (Italy); National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste (Italy); Pricl, Sabrina, E-mail: sabrina.pricl@di3.units.it [University of Trieste, Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), Trieste (Italy); National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste (Italy); Charles, Laurence, E-mail: laurence.charles@univ-amu.fr [Aix-Marseille Université – CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille (France)

    2014-01-15

    Graphical abstract: -- Highlights: •ESI-MS/MS, IMS and molecular modeling were combined to study PEO-PAMAM conformation. •Protonated and lithiated molecules were studied, with charge states from 2 to 4. •Protonation mostly occurred on PAMAM, with PEO units enclosing the protonated group. •Lithium adduction on PEO units lead to more expanded conformations. •Charge location strongly influenced PEO-PAMAM dissociation behavior. -- Abstract: Tandem mass spectrometry and ion mobility spectrometry experiments were performed on multiply charged molecules formed upon conjugation of a poly(amidoamine) (PAMAM) dendrimer with a poly(ethylene oxide) (PEO) linear polymer to evidence any conformational modification as a function of their charge state (2+ to 4+) and of the adducted cation (H{sup +}vs Li{sup +}). Experimental findings were rationalized by molecular dynamics simulations. The G0 PAMAM head-group could accommodate up to three protons, with protonated terminal amine group enclosed in a pseudo 18-crown-6 ring formed by the PEO segment. This particular conformation enabled a hydrogen bond network which allowed long-range proton transfer to occur during collisionally activated dissociation. In contrast, lithium adduction was found to mainly occur onto oxygen atoms of the polyether, each Li{sup +} cation being coordinated by a 12-crown-4 pseudo structure. As a result, for the studied polymeric segment (M{sub n} = 1500 g mol{sup −1}), PEO-PAMAM hybrid molecules exhibited a more expanded shape when adducted to lithium as compared to proton.

  12. A comparative dosimetric study of conventional, conformal and intensity-modulated radiotherapy in postoperative pelvic irradiation of cervical cancer

    International Nuclear Information System (INIS)

    Li Bin; An Jusheng; Wu Lingying; Huang Manni; Gao Juzhen; Xu Yingjie; Dai Jianrong

    2008-01-01

    Objective: To evaluate target-volume coverage and organ at risk (OAR) protection achieved with conventional radiotherapy (CRT), three dimensional conformal radiotherapy (3DCRT), and intensity-modulated radiotherapy(IMRT) through dosimetric comparison in patients with cervical cancer after hysterectomy. Methods: The planning CT scans of 10 patients treated with pelvic radiation after hysterectomy for cervical cancer were used to generate CRT, 3DCRT and IMRT plans for this study. Clinical target volume(CTV) was contoured on the individual axial CT slices of every patient. The CTV was then uniformly expanded by 1.0 cm to create the planning target volume (PTV). The small bowel, rectum, bladder, bone marrow, ovaries, and femoral heads were outlined for the organ at risk (OAR) evaluation. The CRT, 3DCRT and IMRT plans were generated using commercial planning software. CRT plan was prescribed to deliver 45 Gy to the reference point, while IMRT and 3DCRT plans were 45 Gy to 95% of the PTV. Isodose line and dose volume histograms(DVH) were used to evaluate the dose distribution in CTV and OAR. Results: For 10 patients, the average volume of CTV receiving the prescribed dose of CRT was significantly lower than 3DCRT(Q=8.27, P<0.01) and IMRT(Q=8.37, P<0.01), respectively. Comparing with the CRT plan, the 3DCRT and IMRT plans notably reduced the volume of bowel at 30 and 45 Gy levels. The IMRT plan significantly spared rectum and bladder at 30 and 45 Gy levels comparing with the CRT (P<0.01) and 3DCRT(P<0.05) plans, while the 3DCRT plan significantly spared rectum and bladder at 45 Gy level comparing with the CRT(P<0.01) plans. For 4 patients with ovarian transposition, the average doses of ovary over 3 Gy were 2 patients with the 3 DCRT and IMRT plans, and 2 with all three plans. Conclusions: IMRT and 3DCRT are superior to CRT in improving dose coverage of target volume and sparing of OAR, while IMRT being the best. The superiority of IMRT and 3DCRT is obvious in sparing

  13. 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.)

  14. Conformal maps between pseudo-Finsler spaces

    Science.gov (United States)

    Voicu, Nicoleta

    The paper aims to initiate a systematic study of conformal mappings between Finsler spacetimes and, more generally, between pseudo-Finsler spaces. This is done by extending several results in pseudo-Riemannian geometry which are necessary for field-theoretical applications and by proposing a technique that reduces some problems involving pseudo-Finslerian conformal vector fields to their pseudo-Riemannian counterparts. Also, we point out, by constructing classes of examples, that conformal groups of flat (locally Minkowskian) pseudo-Finsler spaces can be much richer than both flat Finslerian and pseudo-Euclidean conformal groups.

  15. A study on the structure of thorium salt solutions

    International Nuclear Information System (INIS)

    Magini, M.; Cabrini, A.; Di Bartolomeo, A.

    1975-01-01

    The structure of highly hydrolyzed thorium salt solutions has been investigated by large and small angle X-ray scattering techniques. The diffraction data obtained with large angle measurements show the presence in solution of microcrystalline particles with the thorium oxide structure. Particles larger than those were discovered by small angle measurements. A possible shape of these colloidal particles has been discussed

  16. 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

  17. Proton NMR studies of Cucurbita maxima trypsin inhibitors: Evidence for pH-dependent conformational change and his25 - try27 interaction

    Energy Technology Data Exchange (ETDEWEB)

    Krishnamoorthi, R.; Chanlan Sun Lin; Yuxi Gong (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States)); Hahn, K. (Univ. of Colorado, Denver (United States))

    1992-01-28

    A pH-dependent His25-Tyr27 interaction was demonstrated in the case of Cucurbita maxima trypsin inhibitors (CMTI-I and CMTI-III) by means of nuclear magnetic resonance (NMR) spectroscopy. pH titration, line widths, peak shapes, deuterium exchange kinetics, and two-dimensional nuclear Overhauser effect spectroscopy (NOESY) were employed to characterize a conformational change involving Tyr27, which was shown to be triggered by deprotonation of His25 around pH 6. A hydrogen bond is proposed to be formed between N{sub {epsilon}} of His25 and OH of Tyr27, as a distance between the atoms, His25 N{epsilon} and Tyr25 OH, of 3.02 {angstrom} is consistent with a model built with NOE-derived distance constraints. The presently characterized relative orientations of His25 and Tyr27 are of functional significance, as these residues make contact with the enzyme in the enzyme-inhibitor complex. Furthermore, trypsin assay and inhibitor-binding studies showed that conformations of trypsin and the squash inhibitor complex. Furthermore, trypsin assay and inhibitor-binding studies showed that conformations of trypsin and the squash inhibitor were functionally relevant only in the pH range 6-8. The pK{sub a} of His25 was determined and found to be influenced by Glu9/Lys substitution and by the hydrolysis of the reactive-site peptide bond between Arg5 and Ile6. As these sites are located far (>10 {angstrom}) from His25, the results point out conformational changes that are propagated to a distant site in the protein molecule.

  18. 1H nuclear magnetic resonance studies of the conformation of an ATP analogue at the active site of Na,K-ATPase from kidney medulla

    International Nuclear Information System (INIS)

    Stewart, J.M.M.; Grisham, C.M.

    1988-01-01

    1 H nuclear magnetic relaxation measurements have been used to determine the three-dimensional conformation of an ATP analogue, Co(NH 3 ) 4 ATP, at the active site of sheep kidney Na,K-ATPase. Previous studies have shown that Co(NH 4 ) 4 ATP is a competitive inhibitor with respect to MnATP for the Na,K-ATPase and that Mn 2+ bound to a single, high-affinity site on the ATPase can be an effective paramagnetic probe for nuclear relaxation studies of the Na-K-ATPase. From the paramagnetic effect of Mn 2+ bound to the APTase on the longitudinal relaxation rates of the protons of Co(NH 3 ) 4 ATP at the substrate site (at 300 and 361 MHz), Mn-H distances to seven protons on the bound nucleotide were determined. Taken together with previous 31 P nuclear relaxation data, these measurements are consistent with a single nucleotide conformation at the active site. The nucleotide adopts a bent configuration, in which the triphosphate chain lies nearly parallel to the adenine moiety. The glycosidic torsion angle is 35 0 , and the conformation of the ribose ring is slightly N-type. The bound Mn 2+ lies above and in the plane of the adenine ring. The distances from Mn 2+ to N 6 and N 7 are too large for first coordination sphere complexes but are appropriate for second-sphere complexes involving, for example, intervening hydrogen-bonded water molecules. The NMR data also indicate that the structure of the bound ATP analogue is independent of the conformational state of the enzyme

  19. /sup 1/H nuclear magnetic resonance studies of the conformation of an ATP analogue at the active site of Na,K-ATPase from kidney medulla

    Energy Technology Data Exchange (ETDEWEB)

    MacD. Stewart, J.M.; Grisham, C.M.

    1988-06-28

    /sup 1/H nuclear magnetic relaxation measurements have been used to determine the three-dimensional conformation of an ATP analogue, Co(NH/sub 3/)/sub 4/ATP, at the active site of sheep kidney Na,K-ATPase. Previous studies have shown that Co(NH/sub 4/)/sub 4/ATP is a competitive inhibitor with respect to MnATP for the Na,K-ATPase and that Mn/sup 2 +/ bound to a single, high-affinity site on the ATPase can be an effective paramagnetic probe for nuclear relaxation studies of the Na-K-ATPase. From the paramagnetic effect of Mn/sup 2 +/ bound to the APTase on the longitudinal relaxation rates of the protons of Co(NH/sub 3/)/sub 4/ATP at the substrate site (at 300 and 361 MHz), Mn-H distances to seven protons on the bound nucleotide were determined. Taken together with previous /sup 31/P nuclear relaxation data, these measurements are consistent with a single nucleotide conformation at the active site. The nucleotide adopts a bent configuration, in which the triphosphate chain lies nearly parallel to the adenine moiety. The glycosidic torsion angle is 35/sup 0/, and the conformation of the ribose ring is slightly N-type. The bound Mn/sup 2 +/ lies above and in the plane of the adenine ring. The distances from Mn/sup 2 +/ to N/sub 6/ and N/sub 7/ are too large for first coordination sphere complexes but are appropriate for second-sphere complexes involving, for example, intervening hydrogen-bonded water molecules. The NMR data also indicate that the structure of the bound ATP analogue is independent of the conformational state of the enzyme.

  20. Topics in conformal field theory

    International Nuclear Information System (INIS)

    Kiritsis, E.B.

    1988-01-01

    In this work two major topics in Conformal Field Theory are discussed. First a detailed investigation of N = 2 Superconformal theories is presented. The structure of the representations of the N = 2 superconformal algebras is investigated and the character formulae are calculated. The general structure of N = 2 superconformal theories is elucidated and the operator algebra of the minimal models is derived. The first minimal system is discussed in more detail. Second, applications of the conformal techniques are studied in the Ashkin-Teller model. The c = 1 as well as the c = 1/2 critical lines are discussed in detail