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Sample records for conformationally non-rigid molecules

  1. Structure and conformational dynamics of molecules in the excited electronic states: theory and experiment

    Science.gov (United States)

    Godunov, I. A.; Bataev, V. A.; Maslov, D. V.; Yakovlev, N. N.

    2017-01-01

    The structure of conformational non-rigid molecules in the excited electronic states are investigated by joint theoretical and experimental methods. The theoretical part of work consist of two stages. In first stage the ab initio quantum-chemical calculations are carried out using high level methods. In second stage the vibrational problems of the various dimensions are solved by variational method for vibrations of large amplitude. In experimental part of work the vibronic spectra are investigated: gas-phase absorption and also, fluorescence excitation spectra of jet-cooled molecules. Some examples are considered.

  2. Metrology of Non-Rigid Objects

    Energy Technology Data Exchange (ETDEWEB)

    Blaedel, K L; Smith, D W; Claudet, A A; Kasper, E P; Patterson, S R

    2002-01-01

    Dimensional characterization of non-rigid parts presents many challenges. For example, when a non-rigid part is mounted in an inspection apparatus the effects of fixturing constraints cause significant deformation of the part. If the part is not used in normal service with the same load conditions as during inspection, the dimensional characteristics in service will deviate from the reported values during inspection. Further, the solution of designing specialized fixturing to duplicate ''as-installed'' conditions does not fully resolve the problem because each inspection requires its own methodology. The goal of this project is to formulate the research problem and propose a method of assessing the dimensional characteristics of non-rigid parts. The measured dimension of a rigid component is traceable at some level of confidence to a single source (NIST in the USA). Hence the measurement of one component of an assembly can be related to the measurement of another component of that assembly. There is no generalized analog to this pedigreed process for dimensionally characterizing non-rigid bodies. For example, a measurement made on a sheet-metal automobile fender is heavily influenced by how it is held during the measurement making it difficult to determine how well that fender will assemble to the rest of the (non-rigid) car body. This problem is often overcome for specific manufacturing problems by constructing rigid fixtures that over-constrain the non-rigid parts to be assembled and then performing the dimensional measurement of the contour of each component to check whether each meets specification. Note that such inspection measurements will yield only an approximation to the assembled shape, which is a function of both the geometry and the compliance of the component parts of the assembly. As a result, non-rigid components are more difficult to specify and inspect and therefore are more difficult to purchase from outside vendors compared

  3. Metrology of Non-Rigid Objects

    Energy Technology Data Exchange (ETDEWEB)

    Blaedel, K; Swift, D; Claudet, A; Kasper, E; Patterson, S

    2002-01-01

    Dimensional characterization of non-rigid parts presents many challenges. For example, when a non-rigid part is mounted in an inspection apparatus the effects of fixturing constraints are significant. If the part is not used in normal service with the same load conditions as during inspection, the dimensional characteristics will deviate from reported values. Further, the solution of designing specialized fixturing to duplicate ''as-installed'' conditions does not fully resolve the problem because each inspection requires its own methodology. The goal of this project is to formulate the research problem and propose a method of assessing the dimensional characteristics of non-rigid parts. The measured dimension of a rigid component is traceable at some level of confidence to a single source (NIST in the USA). Hence the measurement of one component of an assembly can be related to the measurement of another component of that assembly. There is no generalized analog to this pedigreed process for dimensionally characterizing non-rigid bodies. For example, a measurement made on a sheet-metal automobile fender is heavily influenced by how it is held during the measurement making it difficult to determine how well that fender will assemble to the rest of the (non-rigid) car body. This problem is often overcome for specific manufacturing problems by constructing rigid fixtures that over-constrain the non-rigid parts to be assembled and then performing the dimensional measurement of the contour of each component to check whether each meets specification. Note that such inspection measurements will yield only an approximation to the assembled shape, which is a function of both the geometry and the compliance of the component parts of the assembly. As a result, non-rigid components are more difficult to specify and inspect and therefore are more difficult to purchase from outside vendors compared to rigid components. The problems are compounded as the

  4. Conformational States of the Spiropyran Molecule

    Directory of Open Access Journals (Sweden)

    Olha Kovalenko

    2015-01-01

    Full Text Available The form of the potential surface of the ground state was investigated on the basis of indoline spiropyran. As a result of this work the rotamers of an open-ring form of the spiropyran molecule were discovered, and the existence of the most probable rotamers was justified. The 3D potential surface of the ground state of the spiropyran molecule was built. The route of the isomerization of the molecule was discovered and values of barriers for this reaction were found. The part of the isomerization route that is responsible for changing the hybridization of spiroatom from sp3 to sp2 was found.

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

    Science.gov (United States)

    Kobayashi, Eri; Yura, Kei; Nagai, Yoshinori

    2013-01-01

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

  6. Single-Molecule FRET States, Conformational Interchange, and Conformational Selection by Dye Labels in Calmodulin.

    Science.gov (United States)

    DeVore, Matthew S; Braimah, Adebayo; Benson, David R; Johnson, Carey K

    2016-05-19

    We investigate the roles of measurement time scale and the nature of the fluorophores in the FRET states measured for calmodulin, a calcium signaling protein known to undergo pronounced conformational changes. The measured FRET distributions depend markedly on the measurement time scale (nanosecond or microsecond). Comparison of FRET distributions measured by donor fluorescence decay with FRET distributions recovered from single-molecule burst measurements binned over time scales of 90 μs to 1 ms reveals conformational averaging over the intervening time regimes. We find further that, particularly in the presence of saturating Ca(2+), the nature of the measured single-molecule FRET distribution depends markedly on the identity of the FRET pair. The results suggest interchange between conformational states on time scales of hundreds of microseconds or less. Interaction with a fluorophore such as the dye Texas Red alters both the nature of the measured FRET distributions and the dynamics of conformational interchange. The results further suggest that the fluorophore may not be merely a benign reporter of protein conformations in FRET studies, but may in fact alter the conformational landscape.

  7. Non-rigid registration by geometry-constrained diffusion

    DEFF Research Database (Denmark)

    Andresen, Per Rønsholt; Nielsen, Mads

    2001-01-01

    Assume that only partial knowledge about a non-rigid registration is given: certain points, curves, or surfaces in one 3D image are known to map to certain points, curves, or surfaces in another 3D image. In trying to identify the non-rigid registration field, we face a generalized aperture problem...

  8. A robust force field based method for calculating conformational energies of charged drug-like molecules

    DEFF Research Database (Denmark)

    Pøhlsgaard, Jacob; Harpsøe, Kasper; Jørgensen, Flemming Steen

    2012-01-01

    molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force-field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic...

  9. Controlling Protein Conformations to Explore Unprecedented Material Properties by Single-Molecule Surgery

    Science.gov (United States)

    2012-08-17

    Molecule Protein Conformational Dynamics in Enzymatic Reactions,” Single-Molecule Biophysics Meeting, Aspen , CO, Jan. 4-10, 2009. H. P. Lu, “Single...Donor-Acceptor: Cy3-Cy5) pair labeled HPPK molecule tethered between a glass cover-slip surface and a handle (biotin group plus streptavidin), and a...5, 2008. H. P. Lu, “Probing Single-Molecule Protein Conformational Dynamics in Enzymatic Reactions,” Single-Molecule Biophysics Meeting, Aspen

  10. Hamiltonian theory for the non-rigid Earth: Semidiurnal terms

    Science.gov (United States)

    Getino, J.; Ferrándiz, J. M.; Escapa, A.

    2001-04-01

    The purpose of this paper is to determine the contributions to the nutation series arising from the triaxiality of a non-rigid Earth model composed of a rigid mantle and a liquid core. With this aim, the canonical formulation of the rotation of the non-rigid Earth developed by Getino and Ferrándiz is applied in order to study the semidiurnal terms arising from the C22 and S22 geopotential coefficients. Once the corresponding generating function is calculated, analytical expressions of the Andoyer and figure planes are derived. We also provide numerical nutation series based on the analytical formulae.

  11. Non-rigid image registration using bone growth model

    DEFF Research Database (Denmark)

    Bro-Nielsen, Morten; Gramkow, Claus; Kreiborg, Sven

    1997-01-01

    Non-rigid registration has traditionally used physical models like elasticity and fluids. These models are very seldom valid models of the difference between the registered images. This paper presents a non-rigid registration algorithm, which uses a model of bone growth as a model of the change...... between time sequence images of the human mandible. By being able to register the images, this paper at the same time contributes to the validation of the growth model, which is based on the currently available medical theories and knowledge...

  12. Study of polymer molecules and conformations with a nanopore

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-12

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

  13. Study of polymer molecules and conformations with a nanopore

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-03

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

  14. 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.

  15. Single-Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins.

    Science.gov (United States)

    Gauer, J W; LeBlanc, S; Hao, P; Qiu, R; Case, B C; Sakato, M; Hingorani, M M; Erie, D A; Weninger, K R

    2016-01-01

    Single-molecule FRET measurements have a unique sensitivity to protein conformational dynamics. The FRET signals can either be interpreted quantitatively to provide estimates of absolute distance in a molecule configuration or can be qualitatively interpreted as distinct states, from which quantitative kinetic schemes for conformational transitions can be deduced. Here we describe methods utilizing single-molecule FRET to reveal the conformational dynamics of the proteins responsible for DNA mismatch repair. Experimental details about the proteins, DNA substrates, fluorescent labeling, and data analysis are included. The complementarity of single molecule and ensemble kinetic methods is discussed as well. © 2016 Elsevier Inc. All rights reserved.

  16. Joint Space-Time Coherent Vibration Driven Conformational Transitions in a Single Molecule

    Science.gov (United States)

    Li, Shaowei; Chen, Siyu; Li, Jie; Wu, Ruqian; Ho, W.

    2017-10-01

    We report single-molecule conformational transitions with joint angstrom-femtosecond resolution by irradiating the junction of a scanning tunneling microscope with femtosecond laser pulses. An isolated pyrrolidine molecule adsorbed on a Cu(001) surface undergoes reversible transitions between two conformational states. The transition rate decays in time and exhibits sinusoidal oscillations with periods of specific molecular vibrations. The dynamics of this transition depends sensitively on the molecular environment, as exemplified by the effects of another molecule in proximity.

  17. Interplay between quantum interference and conformational fluctuations in single-molecule break junctions.

    Science.gov (United States)

    Berritta, Marco; Manrique, David Zs; Lambert, Colin J

    2015-01-21

    We theoretically explored the combined role of conformational fluctuations and quantum interference in determining the electrical conductance of single-molecule break junctions. In particular we computed the conductance of a family of methylsulfide-functionalized trans-α,ω-diphenyloligoene molecules, with terminal phenyl rings containing meta or para linkages, for which (at least in the absence of fluctuations) destructive interference in the former is expected to decrease their electrical conductance compared with the latter. We compared the predictions of density functional theory (DFT), in which fluctuational effects are absent, with results for the conformationally-averaged conductance obtained from an ensemble of conformations obtained from classical molecular dynamics. We found that junctions formed from these molecules exhibit distinct transport regimes during junction evolution and the signatures of quantum interference in these molecules survive the effect of conformational fluctuations. Furthermore, the agreement between theory and experiment is significantly improved by including conformational averaging.

  18. Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy

    Science.gov (United States)

    Guo, Qing; He, Yufan; Lu, H. Peter

    2015-01-01

    Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2–amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme–substrate interactions, enzyme–substrate active complex formation, and protein folding–binding interactions. PMID:26512103

  19. Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

    KAUST Repository

    Serag, Maged F.

    2014-10-06

    Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

  20. Single molecule insights on conformational selection and induced fit mechanism

    DEFF Research Database (Denmark)

    Hatzakis, Nikos

    2014-01-01

    of unsynchronized molecules, often masking intrinsic dynamic behavior of proteins and biologically significant transient intermediates. Single molecule measurements are emerging as a powerful tool for characterizing protein function. They offer the direct observation and quantification of the activity, abundance...... and lifetime of multiple states and transient intermediates in the energy landscape, that are typically averaged out in non-synchronized ensemble measurements. Here we survey new insights from single molecule studies that advance our understanding of the molecular mechanisms underlying biomolecular recognition....

  1. Bayesian conformational analysis of ring molecules through reversible jump MCMC

    DEFF Research Database (Denmark)

    Nolsøe, Kim; Kessler, Mathieu; Pérez, José

    2005-01-01

    In this paper we address the problem of classifying the conformations of mmembered rings using experimental observations obtained by crystal structure analysis. We formulate a model for the data generation mechanism that consists in a multidimensional mixture model. We perform inference for the p...... for the proportions and the components in a Bayesian framework, implementing an MCMC Reversible Jumps Algorithm to obtain samples of the posterior distributions. The method is illustrated on a simulated data set and on real data corresponding to cyclo-octane structures....

  2. Non-rigid registration by geometry-constrained diffusion

    DEFF Research Database (Denmark)

    Andresen, Per Rønsholt; Nielsen, Mads

    1999-01-01

    Assume that only partial knowledge about a non-rigid registration is given so that certain point, curves, or surfaces in one 3D image map to certain points, curves, or surfaces in another 3D image. We are facing the aperture problem because along the curves and surfaces, point correspondences...... are not given. We will advocate the viewpoint that the aperture and the 3D interpolation problem may be solved simultaneously by finding the simplest displacement field. This is obtained by a geometry-constrained diffusion which yields the simplest displacement field in a precise sense. The point registration...... obtained may be used for growth modelling, shape statistics, or kinematic interpolation. The algorithm applies to geometrical objects of any dimensionality. We may thus keep any number of fiducial points, curves, and/or surfaces fixed while finding the simplest registration. Examples of inferred point...

  3. Probing Protein Multidimensional Conformational Fluctuations by Single-Molecule Multiparameter Photon Stamping Spectroscopy

    Science.gov (United States)

    2015-01-01

    Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental

  4. Conformation of human leucocyte antigen-C molecules at the surface of human trophoblast cells.

    Science.gov (United States)

    Apps, Richard; Gardner, Lucy; Hiby, Sue E; Sharkey, Andrew M; Moffett, Ashley

    2008-07-01

    Human leucocyte antigen (HLA)-C is expressed at lower levels than other classical HLA-I molecules on somatic cells. Surface HLA-C proteins can occur as conventionally beta(2)-microglobulin (beta2m)-associated complexes or as open conformers dissociated from peptide and/or beta(2)m. We investigated the conformation of HLA-C molecules on normal human trophoblast cells, which invade the maternal decidua during placentation. A panel of monoclonal antibodies to different conformations of HLA-I molecules was used in flow cytometry and surface immunoprecipitation experiments. On the surface of trophoblast cells only beta(2)m-associated complexes of HLA-C molecules were detected. In contrast, both open conformers and beta(2)m-associated HLA-C could be detected on other cells from the decidua, HLA-C-transfectants and cell lines. The levels of HLA-C expressed on primary trophoblast cells could be detected by antibodies specific to non-beta(2)m-associated conformations because binding was seen after acid-induced denaturation of surface proteins. In contrast to HLA-G molecules on trophoblasts, we found no evidence for the presence of disulphide-linked multimers of HLA-C complexes. These results show that most HLA-C molecules present at the trophoblast cell surface are in the conventional beta(2)m-associated conformation. These findings have implications regarding the stability of trophoblast HLA-C molecules and how they interact with receptors on decidual leucocytes during placentation.

  5. Non-rigid registration of cervical spine MRI volumes.

    Science.gov (United States)

    Aktar, Mst Nargis; Alam, Md Jahangir; Pickering, Mark; Webb, Alexandra; Perriman, Diana

    2015-01-01

    Whiplash is the colloquial term for neck injuries caused by sudden extension of the cervical spine. Patients with chronic whiplash associated disorder (WAD) can experience neck pain for many years after the original injury. Researchers have found some evidence to suggest that chronic whiplash is related to the amount of intra-muscular fat in the cervical spine muscles. Hence, an important step towards developing a treatment for chronic WAD is a technique to accurately and efficiently measure the amount of intra-muscular fat in the muscles of the cervical spine. Our proposed technique for making this measurement is to automatically segment the cervical spine muscles using a fused volume created from multi-modal MRI volumes of the cervical spine. Multiple modes are required to enhance the boundaries between the different muscles to assist the following automatic segmentation process. However, before these multiple modes can be fused it is first necessary to accurately register these volumes. Hence, in this paper, we have proposed a new non-rigid multi-modal registration algorithm using the sum of conditional variance (SCV) with partial volume interpolation (PVI) similarity measure and Gauss-Newton (GN) optimization for the accurate registration of multi-modal cervical spine MRI volumes. The performance of the proposed approach is compared with the existing SCV based registration algorithm and the sum of the conditional squared deviation from the mode (SCSDM) method. The experimental results demonstrate that the proposed approach provides superior performance than the best existing approaches.

  6. Non-rigid registration for qualitiy control of printed materials

    Science.gov (United States)

    Badshah, Amir; O'Leary, Paul; Harker, Matthew; Sallinger, Christian

    2011-07-01

    This paper presents a new approach to non-rigid elastic registration. The method is applied to hyper spectral imaging data for the automatic quality control of decorative foils which are subject to deformation during lamination. A new image decimation procedure based on Savitzky-Golay smoothing is presented and applied in a multiresolution pyramid. Modified Fourier basis functions implemented by projection onto the orthogonal complement of a truncated Gram polynomial basis are presented. The modified functions are used to compute spectra whereby the Gibbs error associated with local gradients in the image are reduced. The paper also presents the first direct linear solution to weighted tensor product polynomial approximation. This method is used to regularize the patch coordinates, the solution is equivalent to a Galerkin type solution to a partial differential equations. The new solution is applied to published standard data set and to data acquired in a production environment. The speed of the new solution justifies explicit reference: the present solution implemented in MATLAB requires approximatly 1.3s to register an image of size 800 ×× 500 pixels. This is approximately a factor 10 to 100 faster than previously published results for the same data set.

  7. A Condition Number for Non-Rigid Shape Matching

    KAUST Repository

    Ovsjanikov, Maks

    2011-08-01

    © 2011 The Author(s). Despite the large amount of work devoted in recent years to the problem of non-rigid shape matching, practical methods that can successfully be used for arbitrary pairs of shapes remain elusive. In this paper, we study the hardness of the problem of shape matching, and introduce the notion of the shape condition number, which captures the intuition that some shapes are inherently more difficult to match against than others. In particular, we make a connection between the symmetry of a given shape and the stability of any method used to match it while optimizing a given distortion measure. We analyze two commonly used classes of methods in deformable shape matching, and show that the stability of both types of techniques can be captured by the appropriate notion of a condition number. We also provide a practical way to estimate the shape condition number and show how it can be used to guide the selection of landmark correspondences between shapes. Thus we shed some light on the reasons why general shape matching remains difficult and provide a way to detect and mitigate such difficulties in practice.

  8. Conformation Manipulation and Motion of a Double Paddle Molecule on an Au(111) Surface.

    Science.gov (United States)

    Soe, We-Hyo; Shirai, Yasuhiro; Durand, Corentin; Yonamine, Yusuke; Minami, Kosuke; Bouju, Xavier; Kolmer, Marek; Ariga, Katsuhiko; Joachim, Christian; Nakanishi, Waka

    2017-10-24

    The molecular conformation of a bisbinaphthyldurene (BBD) molecule is manipulated using a low-temperature ultrahigh-vacuum scanning tunneling microscope (LT-UHV STM) on an Au(111) surface. BBD has two binaphthyl groups at both ends connected to a central durene leading to anti/syn/flat conformers. In solution, dynamic nuclear magnetic resonance indicated the fast interexchange between the anti and syn conformers as confirmed by density functional theory calculations. After deposition in a submonolayer on an Au(111) surface, only the syn conformers were observed forming small islands of self-assembled syn dimers. The syn dimers can be separated into syn monomers by STM molecular manipulations. A flat conformer can also be prepared by using a peculiar mechanical unfolding of a syn monomer by STM manipulations. The experimental STM dI/dV and theoretical elastic scattering quantum chemistry maps of the low-lying tunneling resonances confirmed the flat conformer BBD molecule STM production. The key BBD electronic states for a step-by-step STM inelastic excitation lateral motion on the Au(111) are presented requiring no mechanical interactions between the STM tip apex and the BBD. On the BBD molecular board, selected STM tip apex positions for this inelastic tunneling excitation enable the flat BBD to move controllably on Au(111) by a step of 0.29 nm per bias voltage ramp.

  9. Locking the Coplanar Conformation of π-Conjugated Molecules and Macromolecules Using Dynamic Noncovalent Bonds.

    Science.gov (United States)

    Zhu, Congzhi; Fang, Lei

    2017-06-27

    Torsional conformation of the backbone of a π-conjugated molecule or macromolecule shapes its solubility, optoelectronic characteristics, rheological behaviors, and ultimately solid-state functions. In order to tailor these molecular, supramolecular, and materials properties, the desired coplanar conformation in π-conjugated systems can be locked by using dynamic noncovalent bonds. In this article, the syntheses, characterizations, and unique properties of conjugated molecules/polymers involving a variety of bridging noncovalent bonds are disussed in the context of coplanar backbone conformation. In addition, challenges in this specific field are identified and discussed for future breakthroughs in exploiting the promising potential of noncovalent-bond-bridged, π-conjugated organic materials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

    Science.gov (United States)

    Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

    2017-08-01

    We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

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

    Science.gov (United States)

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

    2012-05-08

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

  12. Survey of Non-Rigid Registration Tools in Medicine.

    Science.gov (United States)

    Keszei, András P; Berkels, Benjamin; Deserno, Thomas M

    2017-02-01

    We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.

  13. Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

    Directory of Open Access Journals (Sweden)

    Giuliano Malloci

    2016-01-01

    Full Text Available The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different charge/protonation states of ampicillin, we made available force-field parameters and static/dynamic properties derived from both Density Functional Theory and MD calculations. For the specific system investigated here, we found that: (i the conformational statistics extracted from plain MD simulations is consistent with that obtained from REMD simulations; (ii overall, our MD-based approach performs slightly better than any of the conformer generator tools if one takes into account both the diversity of the generated conformational set and the ability to reproduce experimentally-determined structures.

  14. Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers.

    Science.gov (United States)

    Kemmerich, Felix E; Swoboda, Marko; Kauert, Dominik J; Grieb, M Svea; Hahn, Steffen; Schwarz, Friedrich W; Seidel, Ralf; Schlierf, Michael

    2016-01-13

    We present a hybrid single-molecule technique combining magnetic tweezers and Förster resonance energy transfer (FRET) measurements. Through applying external forces to a paramagnetic sphere, we induce conformational changes in DNA nanostructures, which are detected in two output channels simultaneously. First, by tracking a magnetic bead with high spatial and temporal resolution, we observe overall DNA length changes along the force axis. Second, the measured FRET efficiency between two fluorescent probes monitors local conformational changes. The synchronized orthogonal readout in different observation channels will facilitate deciphering the complex mechanisms of biomolecular machines.

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

    Science.gov (United States)

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

    2011-06-28

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

  16. Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems.

    Science.gov (United States)

    Okamoto, Kenji; Hiroshima, Michio; Sako, Yasushi

    2017-12-14

    Single-molecule imaging (SMI) of proteins in operation has a history of intensive investigations over 20 years and is now widely used in various fields of biology and biotechnology. We review the recent advances in SMI of fluorescently-tagged proteins in structural biology, focusing on technical applicability of SMI to the measurements in living cells. Basic technologies and recent applications of SMI in structural biology are introduced. Distinct from other methods in structural biology, SMI directly observes single molecules and single-molecule events one-by-one, thus, explicitly analyzing the distribution of protein structures and the history of protein dynamics. It also allows one to detect single events of protein interaction. One unique feature of SMI is that it is applicable in complicated and heterogeneous environments, including living cells. The numbers, location, movements, interaction, oligomerization, and conformation of single-protein molecules have been determined using SMI in cellular systems.

  17. Quantum state selection of polar molecules: Alignment, orientation and conformational control

    Science.gov (United States)

    Stapelfeldt, Henrik

    2009-05-01

    Building on ideas that go back to Stern in the 1920s we use an inhomogeneous static electric field to deflect a cold beam of polar molecules. The deflection spatially disperses the rotational quantum states of the molecules. We show that the molecules residing in the lowest-lying rotational states can be selected and used as targets for further experiments. In particular, the quantum-state-selected molecules enable unprecedented strong alignment, induced by a moderately intense laser pulse, as well as strong orientation induced by a mixed laser and static electric field. Here, alignment refers to confinement of one or more molecule-fixed axes along laboratory-fixed axes, and orientation refers to the molecular dipole moments pointing in a specific direction. Also, it is shown that the deflection enables separation of the different conformers of a single molecule. We discuss new opportunities offered by the enhanced degree of orientational control, made possibly by quantum state selection, including time resolved studies of torsion, and eventually enantiomeric conversion, of axially chiral molecules. Collaborators: J. Küpper, G. Meijer, L. B. Madsen. [4pt] [1] Laser-Induced Alignment and Orientation of Quantum-State-Selected Large Molecules, L. Holmegaard, J. H. Nielsen, I. Nevo, H. Stapelfeldt, F. Filsinger, J. Küpper, and G. Meijer, Phys. Rev. Lett. 102. 023001 (2009).

  18. Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

    Science.gov (United States)

    Blanco, Mario R.; Martin, Joshua S.; Kahlscheuer, Matthew L.; Krishnan, Ramya; Abelson, John; Laederach, Alain; Walter, Nils G.

    2016-01-01

    The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines. PMID:26414013

  19. 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.

  20. Conformational equilibria in monomeric alpha-synuclein at the single molecule level

    CERN Document Server

    Sandal, Massimo; Tessari, Isabella; Mammi, Stefano; Bergantino, Elisabetta; Musiani, Francesco; Brucale, Marco; Bubacco, Luigi; Samori', Bruno

    2007-01-01

    Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant neurodegenerative diseases such as Alzheimer and Parkinson. A full comprehension of the formation and structure of the so-called misfolded intermediates from which the aggregated states ensue is still lacking. We characterized the folding and the conformational diversity of alpha-synuclein (aSyn), a natively unstructured protein involved in Parkinson disease, by mechanically stretching single molecules of this protein and recording their mechanical properties. These experiments permitted us to directly observe directly and quantify three main classes of conformations that, under in vitro physiological conditions, exist simultaneously in the aSyn sample, including disordered and "beta-like" structures. We found that this class of "beta-like" structures is directly related to aSyn ag...

  1. To bend or not to bend – are heteroatom interactions within conjugated molecules effective in dictating conformation and planarity?

    KAUST Repository

    Conboy, Gary

    2016-04-26

    We consider the roles of heteroatoms (mainly nitrogen, the halogens and the chalcogens) in dictating the conformation of linear conjugated molecules and polymers through non-covalent intramolecular interactions. Whilst hydrogen bonding is a competitive and sometimes more influential interaction, we provide unambiguous evidence that heteroatoms are able to determine the conformation of such materials with reasonable predictability.

  2. Subtle conformational changes induced in major histocompatibility complex class II molecules by binding peptides.

    Science.gov (United States)

    Chervonsky, A V; Medzhitov, R M; Denzin, L K; Barlow, A K; Rudensky, A Y; Janeway, C A

    1998-08-18

    Intracellular trafficking of major histocompatibility complex (MHC) class II molecules is characterized by passage through specialized endocytic compartment(s) where antigenic peptides replace invariant chain fragments in the presence of the DM protein. These changes are accompanied by structural transitions of the MHC molecules that can be visualized by formation of compact SDS-resistant dimers, by changes in binding of mAbs, and by changes in T cell responses. We have observed that a mAb (25-9-17) that is capable of staining I-Ab on the surface of normal B cells failed to interact with I-Ab complexes with a peptide derived from the Ealpha chain of the I-E molecule but bound a similar covalent complex of I-Ab with the class II binding fragment (class II-associated invariant chain peptides) of the invariant chain. Moreover, 25-9-17 blocked activation of several I-Ab-reactive T cell hybridomas but failed to block others, suggesting that numerous I-Ab-peptide complexes acquire the 25-9-17(+) or 25-9-17(-) conformation. Alloreactive T cells were also able to discriminate peptide-dependent variants of MHC class II molecules. Thus, peptides impose subtle structural transitions upon MHC class II molecules that affect T cell recognition and may thus be critical for T cell selection and autiommunity.

  3. The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET

    Directory of Open Access Journals (Sweden)

    Mengyi Yang

    2018-01-01

    Full Text Available Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox.

  4. The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET.

    Science.gov (United States)

    Yang, Mengyi; Peng, Sijia; Sun, Ruirui; Lin, Jingdi; Wang, Nan; Chen, Chunlai

    2018-01-09

    Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  5. F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements.

    Science.gov (United States)

    Sugawa, Mitsuhiro; Okazaki, Kei-Ichi; Kobayashi, Masaru; Matsui, Takashi; Hummer, Gerhard; Masaike, Tomoko; Nishizaka, Takayuki

    2016-05-24

    Despite extensive studies, the structural basis for the mechanochemical coupling in the rotary molecular motor F1-ATPase (F1) is still incomplete. We performed single-molecule FRET measurements to monitor conformational changes in the stator ring-α3β3, while simultaneously monitoring rotations of the central shaft-γ. In the ATP waiting dwell, two of three β-subunits simultaneously adopt low FRET nonclosed forms. By contrast, in the catalytic intermediate dwell, two β-subunits are simultaneously in a high FRET closed form. These differences allow us to assign crystal structures directly to both major dwell states, thus resolving a long-standing issue and establishing a firm connection between F1 structure and the rotation angle of the motor. Remarkably, a structure of F1 in an ε-inhibited state is consistent with the unique FRET signature of the ATP waiting dwell, while most crystal structures capture the structure in the catalytic dwell. Principal component analysis of the available crystal structures further clarifies the five-step conformational transitions of the αβ-dimer in the ATPase cycle, highlighting the two dominant modes: the opening/closing motions of β and the loosening/tightening motions at the αβ-interface. These results provide a new view of tripartite coupling among chemical reactions, stator conformations, and rotary angles in F1-ATPase.

  6. Bioactive conformational generation of small molecules: a comparative analysis between force-field and multiple empirical criteria based methods.

    Science.gov (United States)

    Bai, Fang; Liu, Xiaofeng; Li, Jiabo; Zhang, Haoyun; Jiang, Hualiang; Wang, Xicheng; Li, Honglin

    2010-11-04

    Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA), we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM) and multiple empirical criteria based method (MECBM) hybrided with different force fields. Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD) of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%). On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost. By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational ensemble with high accuracy but approximately the same

  7. Mouse whole-body organ mapping by non-rigid registration approach

    Science.gov (United States)

    Xiao, Di; Zahra, David; Bourgeat, Pierrick; Berghofer, Paula; Acosta Tamayo, Oscar; Green, Heather; Gregoire, Marie Claude; Salvado, Olivier

    2011-03-01

    Automatic small animal whole-body organ registration is challenging because of subject's joint structure, posture and position difference and loss of reference features. In this paper, an improved 3D shape context based non-rigid registration method is applied for mouse whole-body skeleton registration and lung registration. A geodesic path based non-rigid registration method is proposed for mouse torso skin registration. Based on the above registration methods, a novel non-rigid registration framework is proposed for mouse whole-body organ mapping from an atlas to new scanned CT data. A preliminary experiment was performed to test the method on lung and skin registration. A whole-body organ mapping was performed on three target data and the selected organs were compared with the manual outlining results. The robust of the method has been demonstrated.

  8. Level set motion assisted non-rigid 3D image registration

    Science.gov (United States)

    Yang, Deshan; Deasy, Joseph O.; Low, Daniel A.; El Naqa, Issam

    2007-03-01

    Medical imaging applications of rigid and non-rigid elastic deformable image registration are undergoing wide scale development. Our approach determines image deformation maps through a hierarchical process, from global to local scales. Vemuri (2000) reported a registration method, based on levelset evolution theory, to morph an image along the motion gradient until it deforms to the reference image. We have applied this level set motion method as basis to iteratively compute the incremental motion fields and then we approximated the field using a higher-level affine and non-rigid motion model. In such a way, we combine sequentially the global affine motion, local affine motion and local non-rigid motion. Our method is fully automated, computationally efficient, and is able to detect large deformations if used together with multi-grid approaches, potentially yielding greater registration accuracy.

  9. Dimensional Metrology of Non-rigid Parts Without Specialized Inspection Fixtures =

    Science.gov (United States)

    Sabri, Vahid

    Quality control is an important factor for manufacturing companies looking to prosper in an era of globalization, market pressures and technological advances. Functionality and product quality cannot be guaranteed without this important aspect. Manufactured parts have deviations from their nominal (CAD) shape caused by the manufacturing process. Thus, geometric inspection is a very important element in the quality control of mechanical parts. We will focus here on the geometric inspection of non-rigid (flexible) parts which are widely used in the aeronautic and automotive industries. Non-rigid parts can have different forms in a free-state condition compared with their nominal models due to residual stress and gravity loads. To solve this problem, dedicated inspection fixtures are generally used in industry to compensate for the displacement of such parts for simulating the use state in order to perform geometric inspections. These fixtures and the installation and inspection processes are expensive and time-consuming. Our aim in this thesis is therefore to develop an inspection method which eliminates the need for specialized fixtures. This is done by acquiring a point cloud from the part in a free-state condition using a contactless measuring device such as optical scanning and comparing it with the CAD model for the deviation identification. Using a non-rigid registration method and finite element analysis, we numerically inspect the profile of a non-rigid part. To do so, a simulated displacement is performed using an improved definition of displacement boundary conditions for simulating unfixed parts. In addition, we propose a numerical method for dimensional metrology of non-rigid parts in a free-state condition based on the arc length measurement by calculating the geodesic distance using the Fast Marching Method (FMM). In this thesis, we apply our developed methods on industrial non-rigid parts with free-form surfaces simulated with different types of

  10. A non-rigid map fusion-based direct SLAM method for endoscopic capsule robots.

    Science.gov (United States)

    Turan, Mehmet; Almalioglu, Yasin; Araujo, Helder; Konukoglu, Ender; Sitti, Metin

    2017-01-01

    Since the development of capsule endoscopy technology, medical device companies and research groups have made significant progress to turn passive capsule endoscopes into robotic active capsule endoscopes. However, the use of robotic capsules in endoscopy still has some challenges. One such challenge is the precise localization of the actively controlled robot in real-time. In this paper, we propose a non-rigid map fusion based direct simultaneous localization and mapping method for endoscopic capsule robots. The proposed method achieves high accuracy for extensive evaluations of pose estimation and map reconstruction performed on a non-rigid, realistic surgical EsophagoGastroDuodenoscopy Simulator and outperforms state-of-the art methods.

  11. Single-Molecule Confocal FRET Microscopy to Dissect Conformational Changes in the Catalytic Cycle of DNA Topoisomerases.

    Science.gov (United States)

    Hartmann, S; Weidlich, D; Klostermeier, D

    2016-01-01

    Molecular machines undergo large-scale conformational changes during their catalytic cycles that are linked to their biological functions. DNA topoisomerases are molecular machines that interconvert different DNA topoisomers and resolve torsional stress that is introduced during cellular processes that involve local DNA unwinding. DNA gyrase catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. During its catalytic cycle, gyrase undergoes large-scale conformational changes that drive the supercoiling reaction. These conformational changes can be followed by single-molecule Förster resonance energy transfer (FRET). Here, we use DNA gyrase from Bacillus subtilis as an illustrative example to present strategies for the investigation of conformational dynamics of multisubunit complexes. We provide a brief introduction into single-molecule FRET and confocal microscopy, with a focus on practical considerations in sample preparation and data analysis. Different strategies in the preparation of donor-acceptor-labeled molecules suitable for single-molecule FRET experiments are outlined. The insight into the mechanism of DNA supercoiling by gyrase gained from single-molecule FRET experiment is summarized. The general strategies described here can also be applied to investigate conformational changes and their link to biological function of other multisubunit molecular machines. © 2016 Elsevier Inc. All rights reserved.

  12. Learning intervention-induced deformations for non-rigid MR-CT registration and electrode localization in epilepsy patients

    Directory of Open Access Journals (Sweden)

    John A. Onofrey

    2016-01-01

    Full Text Available This paper describes a framework for learning a statistical model of non-rigid deformations induced by interventional procedures. We make use of this learned model to perform constrained non-rigid registration of pre-procedural and post-procedural imaging. We demonstrate results applying this framework to non-rigidly register post-surgical computed tomography (CT brain images to pre-surgical magnetic resonance images (MRIs of epilepsy patients who had intra-cranial electroencephalography electrodes surgically implanted. Deformations caused by this surgical procedure, imaging artifacts caused by the electrodes, and the use of multi-modal imaging data make non-rigid registration challenging. Our results show that the use of our proposed framework to constrain the non-rigid registration process results in significantly improved and more robust registration performance compared to using standard rigid and non-rigid registration methods.

  13. ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

    Science.gov (United States)

    Smith, Justin S.; Isayev, Olexandr; Roitberg, Adrian E.

    2017-01-01

    One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community. PMID:29257127

  14. ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

    Science.gov (United States)

    Smith, Justin S.; Isayev, Olexandr; Roitberg, Adrian E.

    2017-12-01

    One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

  15. 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

  16. Active zone impact on deformation state of non-rigid pavement

    Science.gov (United States)

    Mandula, Ján

    2014-06-01

    The paper deals with the design of non-rigid pavement, with emphasis on the effect of active zone on its deformation state. The concepts of determination of active zone are described. The results of numerical modelling of pavement laying on elastic subgrade are presented in the paper

  17. Active zone impact on deformation state of non-rigid pavement

    OpenAIRE

    Mandula Ján

    2014-01-01

    The paper deals with the design of non-rigid pavement, with emphasis on the effect of active zone on its deformation state. The concepts of determination of active zone are described. The results of numerical modelling of pavement laying on elastic subgrade are presented in the paper

  18. Active zone impact on deformation state of non-rigid pavement

    Directory of Open Access Journals (Sweden)

    Mandula Ján

    2014-06-01

    Full Text Available The paper deals with the design of non-rigid pavement, with emphasis on the effect of active zone on its deformation state. The concepts of determination of active zone are described. The results of numerical modelling of pavement laying on elastic subgrade are presented in the paper

  19. Non-solid non-rigid optics for high-power laser systems

    CSIR Research Space (South Africa)

    Michaelis, MM

    2006-06-14

    Full Text Available Non-solid and non-rigid optics employ gas and liquid transmission and reflection, as well as flexible membranes to influence laser beams, laser driven particle beams and harmonic generators. Some examples are acoustic gratings, phase conjugate...

  20. A field map guided approach to non-rigid registration of brain EPI to structural MRI

    Science.gov (United States)

    Gholipour, Ali; Kehtarnavaz, Nasser; Briggs, Richard W.; Gopinath, Kaundinya S.

    2007-03-01

    It is known that along the phase encoding direction the effect of magnetic field inhomogeneity causes significant spatial distortions in fast functional MRI Echo Planar Imaging (EPI). In this work, our previously developed distortion correction technique via a non-rigid registration of EPI to anatomical MRI is improved by adding information from field maps to achieve a more accurate and efficient registration. Local deformation models are used in regions of distortion artifacts instead of using a global non-rigid transformation. The use of local deformations not only enhances the efficiency of the non-rigid registration by reducing the number of deformation model parameters, but also provides constraints to avoid physically incorrect deformations in undistorted regions. The accuracy and reliability of the non-rigid registration technique is improved by using an additional high-resolution gradient echo EPI scan. In-vivo validation is performed by comparing the similarity of the low-resolution EPI to various structural MRI scans before and after applying the computed deformation models. Visual inspection of the images, as well as Mutual Information (MI) and Normalized Cross Correlation (NCC) comparisons, reveal improvements within the sub-voxel range in the moderately distorted areas but not in the signal loss regions.

  1. Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method.

    Directory of Open Access Journals (Sweden)

    Chao-Yie Yang

    Full Text Available The interleukin-1 receptor (IL-1R is the founding member of the interleukin 1 receptor family which activates innate immune response by its binding to cytokines. Reports showed dysregulation of cytokine production leads to aberrant immune cells activation which contributes to auto-inflammatory disorders and diseases. Current therapeutic strategies focus on utilizing antibodies or chimeric cytokine biologics. The large protein-protein interaction interface between cytokine receptor and cytokine poses a challenge in identifying binding sites for small molecule inhibitor development. Based on the significant conformational change of IL-1R type 1 (IL-1R1 ectodomain upon binding to different ligands observed in crystal structures, we hypothesized that transient small molecule binding sites may exist when IL-1R1 undergoes conformational transition and thus suitable for inhibitor development. Here, we employed accelerated molecular dynamics (MD simulation to efficiently sample conformational space of IL-1R1 ectodomain. Representative IL-1R1 ectodomain conformations determined from the hierarchy cluster analysis were analyzed by the SiteMap program which leads to identify small molecule binding sites at the protein-protein interaction interface and allosteric modulator locations. The cosolvent mapping analysis using phenol as the probe molecule further confirms the allosteric modulator site as a binding hotspot. Eight highest ranked fragment molecules identified from in silico screening at the modulator site were evaluated by MD simulations. Four of them restricted the IL-1R1 dynamical motion to inactive conformational space. The strategy from this study, subject to in vitro experimental validation, can be useful to identify small molecule compounds targeting the allosteric modulator sites of IL-1R and prevent IL-1R from binding to cytokine by trapping IL-1R in inactive conformations.

  2. Manipulation of Origin of Life Molecules: Recognizing Single-Molecule Conformations in β-Carotene and Chlorophyll-a/β-Carotene Clusters.

    Science.gov (United States)

    Ngo, Anh T; Skeini, Timur; Iancu, Violeta; Redfern, Paul C; Curtiss, Larry A; Hla, Saw Wai

    2018-01-11

    Carotenoids and chlorophyll are essential parts of plant leaves and are involved in photosynthesis, a vital biological process responsible for the origin of life on Earth. Here, we investigate how β-carotene and chlorophyll-a form mixed molecular phases on a Au(111) surface using low-temperature scanning tunneling microscopy and molecular manipulation at the single-molecule level supported by density functional theory calculations. By isolating individual molecules from nanoscale molecular clusters with a scanning tunneling microscope tip, we are able to identify five β-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of β-carotene/chlorophyll-a clsuters, with intimate structural details highlighting how they pair: β-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.

  3. Chemical reactions of conformationally selected 3-aminophenol molecules in a beam with Coulomb-crystallized Ca+ ions

    Science.gov (United States)

    Rösch, Daniel; Willitsch, Stefan; Chang, Yuan-Pin; Küpper, Jochen

    2014-03-01

    Many molecules exhibit multiple conformers that often easily interconvert under thermal conditions. Therefore, single conformations are difficult to isolate which renders the study of their distinct chemical reactivities challenging. We have recently reported a new experimental method for the characterization of conformer-specific effects in chemical reactions [Y.-P. Chang, K. Długołęcki, J. Küpper, D. Rösch, D. Wild, and S. Willitsch, "Specific chemical reactivities of spatially separated 3-aminophenol conformers with cold Ca+ ions," Science 342, 98-101 (2013)]. Different conformers are spatially separated using inhomogeneous electric fields and reacted with a Coulomb crystal of cold, spatially localized ions in a trap. As a first application, we studied reactions between the two conformers of 3-aminophenol and Ca+. We observed a twofold larger rate constant for the cis compared to the trans conformer which was rationalized in terms of the differences in the long-range ion-molecule interactions. The present article provides a detailed description of the new method and a full account of the experimental results as well as the accompanying theoretical calculations.

  4. Comparison of numerical results between related shapes using a non-rigid mapping with statistical quantication of uncertainty

    CSIR Research Space (South Africa)

    Jansen van Rensburg, Gerhardus J

    2011-10-01

    Full Text Available In the present study, numerical results obtained on different but related shapes are compared by using a non-rigid mapping. Non-rigid registration is employed to obtain mesh representations of different human skull geometries with the same mesh...

  5. Single molecule FRET data analysis procedures for FRET efficiency determination: probing the conformations of nucleic acid structures.

    Science.gov (United States)

    Krüger, Asger Christian; Birkedal, Victoria

    2013-11-01

    Single molecule FRET microscopy is an attractive technique for studying structural dynamics and conformational diversity of nucleic acid structures. Some of its strengths are that it can follow structural changes on a fast time scale and identify conformation distributions arising from dynamic or static population heterogeneity. Here, we give a description of the experiment and data analysis procedures of this method and detail what parameters are needed for FRET efficiency calculation. Using single molecule FRET data obtained on G-quadruplex DNA structures that exhibit large conformation diversity, we illustrate that the shape of the FRET distribution changes depending on what parameters are included in the data analysis procedure. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Non-rigid Registration by Diffusion Model with the Demons Algorithm

    Directory of Open Access Journals (Sweden)

    Shengzhou XU

    2014-03-01

    Full Text Available Non-rigid registration becomes more and more important in biomedical imaging applications. A novel non-rigid registration method based on diffusion model with demons algorithm is proposed in this paper. The moving image is considered as a deformable grid, and it is diffusing through the contours of the objects in itself, by the action of effectors, called demons, situated in these interfaces. In order to speed up the convergence of the iteration and enhance the robustness of the algorithm, the moving image is smoothed to increase the number of the ‘demons’. The deformation field has been normalized at each iteration to ensure the stability. Our algorithm is compared with the original ‘demons’ and other developed algorithms on synthetic images and real medical images, the result shows that our algorithm has obvious speed improvement and high tolerance of large deformation and noise.

  7. Blind Facial Image Quality Enhancement Using Non-Rigid Semantic Patches.

    Science.gov (United States)

    Hait, Ester; Gilboa, Guy

    2017-06-01

    We propose a new way to solve a very general blind inverse problem of multiple simultaneous degradations, such as blur, resolution reduction, noise, and contrast changes, without explicitly estimating the degradation. The proposed concept is based on combining semantic non-rigid patches, problem-specific high-quality prior data, and non-rigid registration tools. We show how a significant quality enhancement can be achieved, both visually and quantitatively, in the case of facial images. The method is demonstrated on the problem of cellular photography quality enhancement of dark facial images for different identities, expressions, and poses, and is compared with the state-of-the-art denoising, deblurring, super-resolution, and color-correction methods.

  8. Single-Molecule Analysis of Protein Large-Amplitude Conformational Transitions

    Science.gov (United States)

    Yang, Haw

    2011-03-01

    Proteins have evolved to harness thermal fluctuations, rather than frustrated by them, to carry out chemical transformations and mechanical work. What are, then, the operation and design principles of protein machines? To frame the problem in a tractable way, several basic questions have been formulated to guide the experimental design: (a) How many conformational states can a protein sample on the functionally important timescale? (b) What are the inter-conversion rates between states? (c) How do ligand binding or interactions with other proteins modulate the motions? (d) What are the structural basis of flexibility and its underlying molecular mechanics? Guided by this framework, we have studied protein tyrosine phosphatase B, PtpB, from M. tuberculosis (a virulence factor of tuberculosis and a potential drug target) and adenylate kinase, AK, from E. coli (a ubiquitous energy-balancing enzyme in cells). These domain movements have been followed in real time on their respective catalytic timescales using high-resolution single-molecule Förster resonance energy transfer (FRET) spectroscopy. It is shown quantitatively that both PtpB and AK are capable of dynamically sampling two distinct states that correlate well with those observed by x-ray crystallography. Integrating these microscopic dynamics into macroscopic kinetics allows us to place the experimentally measured free-energy landscape in the context of enzymatic turnovers.

  9. Enhanced Pose Normalization and Matching of Non-Rigid Objects based on Support Vector Machine Modelling

    OpenAIRE

    Papadakis, Panagiotis

    2013-01-01

    International audience; The estimation of 3D surface correspondence constitutes a fundamental problem in shape matching and analysis applications. In the presence of non-rigid shape deformations, the ambiguity of surface correspondence increases together with the complexity of registration algorithms. In this paper, we alleviate this problem by means of 3D pose normalization using One-Class Support Vector Machines (OCSVM). In detail, we show how OCSVM are employed in order to increase the con...

  10. A non-rigid registration algorithm for dynamic breast MR images

    OpenAIRE

    Hayton, Paul M.; Brady, Michael; Smith, Stephen M.; Moore, Niall

    1999-01-01

    Magnetic resonance image analysis is a promising technique for diagnosing breast cancer, particularly in women for whom X-ray mammography is ineffective. If breast motion is not corrected for, diagnostic accuracy is significantly reduced. In this paper, we analyse the kinds of motion that arise during image formation and we describe a model based non-rigid registration algorithm to estimate and correct for breast motion. Registration of breast MR images is complicated by the use of a contrast...

  11. Validation of a Non-Rigid Registration Error Detection Algorithm Using Clinical MRI Brain Data

    Science.gov (United States)

    Datteri, Ryan D.; Liu, Yuan; D’Haese, Pierre-François; Dawant, Benoit M.

    2014-01-01

    Identification of error in non-rigid registration is a critical problem in the medical image processing community. We recently proposed an algorithm that we call “Assessing Quality Using Image Registration Circuits” (AQUIRC) to identify non-rigid registration errors and have tested its performance using simulated cases. In this article, we extend our previous work to assess AQUIRC’s ability to detect local non-rigid registration errors and validate it quantitatively at specific clinical landmarks, namely the Anterior Commissure (AC) and the Posterior Commissure (PC). To test our approach on a representative range of error we utilize 5 different registration methods and use 100 target images and 9 atlas images. Our results show that AQUIRC’s measure of registration quality correlates with the true target registration error (TRE) at these selected landmarks with an R2 = 0.542. To compare our method to a more conventional approach, we compute Local Normalized Correlation Coefficient (LNCC) and show that AQUIRC performs similarly. However, a multi-linear regression performed with both AQUIRC’s measure and LNCC shows a higher correlation with TRE than correlations obtained with either measure alone, thus showing the complementarity of these quality measures. We conclude the article by showing that the AQUIRC algorithm can be used to reduce registration errors for all five algorithms. PMID:25095252

  12. Robust non-rigid point set registration using student's-t mixture model.

    Directory of Open Access Journals (Sweden)

    Zhiyong Zhou

    Full Text Available The Student's-t mixture model, which is heavily tailed and more robust than the Gaussian mixture model, has recently received great attention on image processing. In this paper, we propose a robust non-rigid point set registration algorithm using the Student's-t mixture model. Specifically, first, we consider the alignment of two point sets as a probability density estimation problem and treat one point set as Student's-t mixture model centroids. Then, we fit the Student's-t mixture model centroids to the other point set which is treated as data. Finally, we get the closed-form solutions of registration parameters, leading to a computationally efficient registration algorithm. The proposed algorithm is especially effective for addressing the non-rigid point set registration problem when significant amounts of noise and outliers are present. Moreover, less registration parameters have to be set manually for our algorithm compared to the popular coherent points drift (CPD algorithm. We have compared our algorithm with other state-of-the-art registration algorithms on both 2D and 3D data with noise and outliers, where our non-rigid registration algorithm showed accurate results and outperformed the other algorithms.

  13. EVolution: an edge-based variational method for non-rigid multi-modal image registration

    Science.gov (United States)

    de Senneville, B. Denis; Zachiu, C.; Ries, M.; Moonen, C.

    2016-10-01

    Image registration is part of a large variety of medical applications including diagnosis, monitoring disease progression and/or treatment effectiveness and, more recently, therapy guidance. Such applications usually involve several imaging modalities such as ultrasound, computed tomography, positron emission tomography, x-ray or magnetic resonance imaging, either separately or combined. In the current work, we propose a non-rigid multi-modal registration method (namely EVolution: an edge-based variational method for non-rigid multi-modal image registration) that aims at maximizing edge alignment between the images being registered. The proposed algorithm requires only contrasts between physiological tissues, preferably present in both image modalities, and assumes deformable/elastic tissues. Given both is shown to be well suitable for non-rigid co-registration across different image types/contrasts (T1/T2) as well as different modalities (CT/MRI). This is achieved using a variational scheme that provides a fast algorithm with a low number of control parameters. Results obtained on an annotated CT data set were comparable to the ones provided by state-of-the-art multi-modal image registration algorithms, for all tested experimental conditions (image pre-filtering, image intensity variation, noise perturbation). Moreover, we demonstrate that, compared to existing approaches, our method possesses increased robustness to transient structures (i.e. that are only present in some of the images).

  14. Conformational rearrangements in the transmembrane domain of CNGA1 channels revealed by single-molecule force spectroscopy.

    Science.gov (United States)

    Maity, Sourav; Mazzolini, Monica; Arcangeletti, Manuel; Valbuena, Alejandro; Fabris, Paolo; Lazzarino, Marco; Torre, Vincent

    2015-05-12

    Cyclic nucleotide-gated (CNG) channels are activated by binding of cyclic nucleotides. Although structural studies have identified the channel pore and selectivity filter, conformation changes associated with gating remain poorly understood. Here we combine single-molecule force spectroscopy (SMFS) with mutagenesis, bioinformatics and electrophysiology to study conformational changes associated with gating. By expressing functional channels with SMFS fingerprints in Xenopus laevis oocytes, we were able to investigate gating of CNGA1 in a physiological-like membrane. Force spectra determined that the S4 transmembrane domain is mechanically coupled to S5 in the closed state, but S3 in the open state. We also show there are multiple pathways for the unfolding of the transmembrane domains, probably caused by a different degree of α-helix folding. This approach demonstrates that CNG transmembrane domains have dynamic structure and establishes SMFS as a tool for probing conformational change in ion channels.

  15. Revealing the Conformational Dynamics in a Single-Molecule Junction by Site- and Angle-Resolved Dynamic Probe Method.

    Science.gov (United States)

    Yoshida, Shoji; Taninaka, Atsushi; Sugita, Yoshihiro; Katayama, Tomoki; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-12-27

    Single-molecule junctions have been extensively studied because of their high potential for future nanoscale device applications as well as their importance in basic studies for molecular science and technology. However, since the bonding sites at an electrode and the molecular tilt angles, for example, cannot be determined experimentally, analyses have been performed assuming the structures of such interactive key factors, with uncertainties and inconsistencies remaining in the proposed mechanisms. We have developed a methodology that enables the probing of conformational dynamics in single-molecule junctions simultaneously with the direct characterization of molecular bonding sites and tilt angles. This technique has revealed the elemental processes in single-molecule junctions, which have not been clarified using conventional methods. The mechanisms of the molecular dynamics in 1,4-benzenedithiol and 4,4'-bipyridine single-molecule junctions, which, for example, produce binary conductance switching of different types, were clearly discriminated and comprehensively explained.

  16. Constraint-Based Simulation for Non-Rigid Real-Time Registration

    OpenAIRE

    Courtecuisse, Hadrien; Peterlik, Igor; Trivisonne, Raffaella; Duriez, Christian; Cotin, Stéphane

    2014-01-01

    International audience; In this paper we propose a method to address the problem of non-rigid registration in real-time. We use Lagrange multipliers and soft sliding constraints to combine data acquired from dynamic image sequence and a biomechanical model of the structure of interest. The biomechanical model plays a role of regulariza-tion to improve the robustness and the flexibility of the registration. We apply our method to a pre-operative 3D CT scan of a porcine liver that is registered...

  17. A batch Algorithm for Implicit Non-Rigid Shape and Motion Recovery

    DEFF Research Database (Denmark)

    Bartoli, Adrien; Olsen, Søren Ingvor

    2005-01-01

    The recovery of 3D shape and camera motion for non-rigid scenes from single-camera video footage is a very important problem in computer vision. The low-rank shape model consists in regarding the deformations as linear combinations of basis shapes. Most algorithms for reconstructing the parameters...... of this model along with camera motion are based on three main steps. Given point tracks and the rank, or equivalently the number of basis shapes, they factorize a measurement matrix containing all point tracks, from which the camera motion and basis shapes are extracted and refined in a bundle adjustment...

  18. Single molecules in soft matter : a study of biomolecular conformation, heterogeneity and plasmon enhanced fluorescence

    NARCIS (Netherlands)

    Yuan, Haifeng

    2013-01-01

    We study the dynamics of single molecules and individual gold nanorods in glycerol at variable temperatures. We demonstrate temperature-cycle microscopy on FRET-labeled polyproline and double-stranded DNA molecules to access micro-second dynamics of single molecules, and reveal the influences of

  19. Nonlinear mechanics of non-rigid origami: an efficient computational approach

    Science.gov (United States)

    Liu, K.; Paulino, G. H.

    2017-10-01

    Origami-inspired designs possess attractive applications to science and engineering (e.g. deployable, self-assembling, adaptable systems). The special geometric arrangement of panels and creases gives rise to unique mechanical properties of origami, such as reconfigurability, making origami designs well suited for tunable structures. Although often being ignored, origami structures exhibit additional soft modes beyond rigid folding due to the flexibility of thin sheets that further influence their behaviour. Actual behaviour of origami structures usually involves significant geometric nonlinearity, which amplifies the influence of additional soft modes. To investigate the nonlinear mechanics of origami structures with deformable panels, we present a structural engineering approach for simulating the nonlinear response of non-rigid origami structures. In this paper, we propose a fully nonlinear, displacement-based implicit formulation for performing static/quasi-static analyses of non-rigid origami structures based on `bar-and-hinge' models. The formulation itself leads to an efficient and robust numerical implementation. Agreement between real models and numerical simulations demonstrates the ability of the proposed approach to capture key features of origami behaviour.

  20. Non-rigid Motion Correction in 3D Using Autofocusing with Localized Linear Translations

    Science.gov (United States)

    Cheng, Joseph Y.; Alley, Marcus T.; Cunningham, Charles H.; Vasanawala, Shreyas S.; Pauly, John M.; Lustig, Michael

    2012-01-01

    MR scans are sensitive to motion effects due to the scan duration. To properly suppress artifacts from non-rigid body motion, complex models with elements such as translation, rotation, shear, and scaling have been incorporated into the reconstruction pipeline. However, these techniques are computationally intensive and difficult to implement for online reconstruction. On a sufficiently small spatial scale, the different types of motion can be well-approximated as simple linear translations. This formulation allows for a practical autofocusing algorithm that locally minimizes a given motion metric – more specifically, the proposed localized gradient-entropy metric. To reduce the vast search space for an optimal solution, possible motion paths are limited to the motion measured from multi-channel navigator data. The novel navigation strategy is based on the so-called “Butterfly” navigators which are modifications to the spin-warp sequence that provide intrinsic translational motion information with negligible overhead. With a 32-channel abdominal coil, sufficient number of motion measurements were found to approximate possible linear motion paths for every image voxel. The correction scheme was applied to free-breathing abdominal patient studies. In these scans, a reduction in artifacts from complex, non-rigid motion was observed. PMID:22307933

  1. A kidney deformation model for use in non-rigid registration during image-guided surgery

    Science.gov (United States)

    Ong, Rowena E.; Herrell, S. Duke, III; Miga, Michael I.; Galloway, Robert L., Jr.

    2008-03-01

    In order to facilitate the removal of tumors during partial nephrectomies, an image-guided surgery system may be useful. This system would require a registration of the physical kidney to a pre-operative image volume; however, it is unclear whether a rigid registration would be sufficient. One possible source of non-rigid deformation is the clamping of the renal artery during surgery and the subsequent loss of pressure as the kidney is punctured and blood loss occurs. To explore this issue, a model of kidney deformation due to loss of perfusion and pressure was developed based on Biot's consolidation model. The model was tested on two resected porcine kidneys in which the renal artery and vein were clamped. CT image volumes of the kidney were obtained before and after the deformation caused unclamping, and fiducial markers embedded on the kidney surface allowed the deformation to be tracked. The accuracy of the kidney model was accessed by calculating the model error at the fiducial locations and using image similarity measures. Preliminary results indicate that the model may be useful in a non-rigid registration scheme; however, further refinements to the model may be necessary to better simulate the deformation due to loss of perfusion and pressure.

  2. Understanding geological processes: Visualization of rigid and non-rigid transformations

    Science.gov (United States)

    Shipley, T. F.; Atit, K.; Manduca, C. A.; Ormand, C. J.; Resnick, I.; Tikoff, B.

    2012-12-01

    Visualizations are used in the geological sciences to support reasoning about structures and events. Research in cognitive sciences offers insights into the range of skills of different users, and ultimately how visualizations might support different users. To understand the range of skills needed to reason about earth processes we have developed a program of research that is grounded in the geosciences' careful description of the spatial and spatiotemporal patterns associated with earth processes. In particular, we are pursuing a research program that identifies specific spatial skills and investigates whether and how they are related to each other. For this study, we focus on a specific question: Is there an important distinction in the geosciences between rigid and non-rigid deformation? To study a general spatial thinking skill we employed displays with non-geological objects that had been altered by rigid change (rotation), and two types of non-rigid change ("brittle" (or discontinuous) and "ductile" (or continuous) deformation). Disciplinary scientists (geosciences and chemistry faculty), and novices (non-science faculty and undergraduate psychology students) answered questions that required them to visualize the appearance of the object before the change. In one study, geologists and chemists were found to be superior to non-science faculty in reasoning about rigid rotations (e.g., what an object would look like from a different perspective). Geologists were superior to chemists in reasoning about brittle deformations (e.g., what an object looked like before it was broken - here the object was a word cut into many fragments displaced in different directions). This finding is consistent with two hypotheses: 1) Experts are good at visualizing the types of changes required for their domain; and 2) Visualization of rigid and non-rigid changes are not the same skill. An additional important finding is that there was a broad range of skill in both rigid and non-rigid

  3. Single molecule conformational analysis of the biologically relevant DNA G-quadruplex in the promoter of the proto-oncogene c-MYC†

    Science.gov (United States)

    Shirude, Pravin S.; Ying, Liming; Balasubramanian, Shankar

    2008-01-01

    Single molecule fluorescence spectroscopy has been employed to resolve the conformational heterogeneity, hybridization kinetics and study mutational effects on the c-MYC promoter G-quadruplex. PMID:18536803

  4. Systematic conformational bias in small-molecule crystal structures is rare and explicable

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.; Liebeschuetz, J.W.; Allen, F.H.

    2012-01-01

    Analysis of the Cambridge Structural Database, together with DFT and crystal structure prediction calculations, show that the observation of higher-energy planar conformers of biphenyl (BP) and cyclobutane (CB) is possible because of improved intermolecular interactions in their crystal structures.

  5. Using small molecule reagents to selectively modify epitopes based on their conformation

    Science.gov (United States)

    PrPSc is an infectious protein. The only experimentally verified difference between PrPSc and their normal cellular isoform (PrPC) is conformational. This work describes an approach to determining the presence of surface exposed or sequestered amino acids present in the PrPSc isoform. The N-hydroxys...

  6. Conformation-based signal transfer and processing at the single-molecule level.

    Science.gov (United States)

    Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

    2017-11-01

    Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl 2 Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

  7. Non-rigid Registration of Medical Image Data with Incomplete Information

    Directory of Open Access Journals (Sweden)

    O. V. Museyko

    2010-03-01

    Full Text Available The problem of non-rigid registration of images, where certain parts are missing, is considered in the context of pre- and intraoperative or damaged data. A variational formulation of the problem is proposed such that a counterpart of the missing data can be restored in a template image along with a corresponding registration transforma­tion between the images. The problem is a registrational variant of a free-discontinuity Mumford-Shah segmentation problem with the unknown discontinuity set representing the boundary of missing data; thus, no preliminary segmentation is needed to detect the missing information. An approximation of the free-discontinuity problem by an Ambrosio-Tortorelli-type approximation is used to compute the numerical solutions. Ex­periments with 2D examples demonstrate the efficiency of the proposed approach.

  8. Non-rigid registration of medical images based on estimation of deformation states

    Science.gov (United States)

    Marami, Bahram; Sirouspour, Shahin; Capson, David W.

    2014-11-01

    A unified framework for automatic non-rigid 3D-3D and 3D-2D registration of medical images with static and dynamic deformations is proposed in this paper. The problem of non-rigid image registration is approached as a classical state estimation problem using a generic deformation model for the soft tissue. The registration technique employs a dynamic linear elastic continuum mechanics model of the tissue deformation, which is discretized using the finite element method. In the proposed method, the registration is achieved through a Kalman-like filtering process, which incorporates information from the deformation model and a vector of observation prediction errors computed from an intensity-based similarity/distance metric between images. With this formulation, single and multiple-modality, 3D-3D and 3D-2D image registration problems can all be treated within the same framework. The performance of the proposed registration technique was evaluated in a number of different registration scenarios. First, 3D magnetic resonance (MR) images of uncompressed and compressed breast tissue were co-registered. 3D MR images of the uncompressed breast tissue were also registered to a sequence of simulated 2D interventional MR images of the compressed breast. Finally, the registration algorithm was employed to dynamically track a target sub-volume inside the breast tissue during the process of the biopsy needle insertion based on registering pre-insertion 3D MR images to a sequence of real-time simulated 2D interventional MR images. Registration results indicate that the proposed method can be effectively employed for the registration of medical images in image-guided procedures, such as breast biopsy in which the tissue undergoes static and dynamic deformations.

  9. Experiment and numerical simulation on the characteristics of fluid–structure interactions of non-rigid airships

    Directory of Open Access Journals (Sweden)

    Xiaocui Wu

    2015-11-01

    Full Text Available Fluid–structure interaction is an important issue for non-rigid airships with inflated envelopes. In this study, a wind tunnel test is conducted, and a loosely coupled procedure is correspondingly established for numerical simulation based on computational fluid dynamics and nonlinear finite element analysis methods. The typical results of the numerical simulation and wind tunnel experiment, including the overall lift and deformation, are in good agreement with each other. The results obtained indicate that the effect of fluid–structure interaction is noticeable and should be considered for non-rigid airships. Flow-induced deformation can further intensify the upward lift force and pitching moment, which can lead to a large deformation. Under a wind speed of 15 m/s, the lift force of the non-rigid model is increased to approximately 60% compared with that of the rigid model under a high angle of attack.

  10. Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

    Science.gov (United States)

    Zhang, Ce; Zhang, Fang; van Kan, Jeroen A.; van der Maarel, Johan R. C.

    2008-06-01

    Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

  11. Numerical calculation of the stress-strain state of non-rigid pavements, renovated by cold recycling technology

    Directory of Open Access Journals (Sweden)

    Світлана Михайлівна Талах

    2017-01-01

    Full Text Available The problem of improving the scientific basis to determine the stress-strain state of non-rigid pavements, renovated by cold recycling technology, is considered. The results of numerical calculation of stress-strain state of non-rigid pavements in the section of road Kyv-Kovel (297 + 700 km - 302 + 400 km are given using automated calculation software complex of thin-walled spatial structures (KARTPK. The real state of the road section through 8.5 years after the renovation is analyzed

  12. Conformational parameters of poly(N-methyl-N-vinylacetamide) molecules through the hydrodynamic characteristics studies.

    Science.gov (United States)

    Pavlov, George M; Okatova, Olga V; Mikhailova, Anastasia V; Ulyanova, Natalia N; Gavrilova, Irina I; Panarin, Evgenii F

    2010-07-07

    Water-soluble PMVA was synthesized by radical polymerization methods. A number of polymer samples were fractionated in the chloroform-diethyl ether system. Fractions were studied by molecular hydrodynamics methods (sedimentation velocity, translational isothermal diffusion and viscosity) in H(2)O and DMF. The molecular masses of fractions were determined and the Kuhn-Mark-Houwink-Sakurada relationships were obtained in the molecular mass range of 3.5 < M x 10(-3) g x mol(-1) <540. A negative temperature coefficient of the characteristic viscosity was obtained in both solvents. The Kuhn statistic segment length and the hydrodynamic diameter of the molecule were estimated for PMVA. The hydrodynamic volumes, occupied by the molecules of PMVA, poly(1-vinyl-2-pyrrolidone), poly(vinylformamide), and pullulan were compared.

  13. Sensitivity of photoelectron diffraction to conformational changes of adsorbed molecules: Tetra-tert-butyl-azobenzene/Au(111).

    Science.gov (United States)

    Schuler, A; Greif, M; Seitsonen, A P; Mette, G; Castiglioni, L; Osterwalder, J; Hengsberger, M

    2017-01-01

    Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate. 3,3',5,5'-tetra-tert-butyl-azobenzene served as test case. This molecule can be switched between two isomers, trans and cis, by absorption of ultraviolet light. X-ray photoelectron diffraction patterns were recorded from tetra-tert-butyl-azobenzene/Au(111) in thermal equilibrium at room temperature and compared to patterns taken in the photostationary state obtained by exposing the surface to radiation from a high-intensity helium discharge lamp. Difference patterns were simulated by means of multiple-scattering calculations, which allowed us to determine the fraction of molecules that underwent isomerization.

  14. Sensitivity of photoelectron diffraction to conformational changes of adsorbed molecules: Tetra-tert-butyl-azobenzene/Au(111

    Directory of Open Access Journals (Sweden)

    A. Schuler

    2017-01-01

    Full Text Available Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate. 3,3′,5,5′-tetra-tert-butyl-azobenzene served as test case. This molecule can be switched between two isomers, trans and cis, by absorption of ultraviolet light. X-ray photoelectron diffraction patterns were recorded from tetra-tert-butyl-azobenzene/Au(111 in thermal equilibrium at room temperature and compared to patterns taken in the photostationary state obtained by exposing the surface to radiation from a high-intensity helium discharge lamp. Difference patterns were simulated by means of multiple-scattering calculations, which allowed us to determine the fraction of molecules that underwent isomerization.

  15. Non-rigid registration using free-form deformations for recognition of facial actions and their temporal dynamics

    NARCIS (Netherlands)

    Koelstra, Sander; Pantic, Maja

    In this paper we propose an appearance-based approach to recognition of facial Action Units (AUs) and their temporal segments in frontal-view face videos. Non-rigid registration using free-form deformations is used to determine motion in the face region of an input video. The extracted motion fields

  16. Validation of Osteoarthritis synthetic defect database via non-rigid registration.

    Science.gov (United States)

    Paniagua, Beatriz; Pera, Juliette; Budin, Francois; Gomes, Liliane; Styner, Martin; Lucia, Cevidanes; Nguyen, Tung

    2015-03-17

    Temporomandibular joint (TMJ) disorders are a group of conditions that cause pain and dysfunction in the jaw joint and the muscles controlling jaw movement. However, diagnosis and treatment of these conditions remain controversial. To date, there is no single sign, symptom, or test that can clearly diagnose early stages of osteoarthritis (OA). Instead, the diagnosis is based on a consideration of several factors, including radiological evaluation. The current radiological diagnosis scores of TMJ pathology are subject to misdiagnosis. We believe these scores are limited by the acquisition procedures, such as oblique cuts of the CT and head positioning errors, and can lead to incorrect diagnoses of flattening of the head of the condyle, formation of osteophytes, or condylar pitting. This study consists of creating and validating a methodological framework to simulate defects in CBCT scans of known location and size, in order to create synthetic TMJ OA database. User-generated defects were created using a non-rigid deformation protocol in CBCT. All segmentation evaluation, surface distances and linear distances from the user-generated to the simulated defects showed our methodological framework to be very precise and within a voxel (0.5 mm) of magnitude. A TMJ OA synthetic database will be created next, and evaluated by expert radiologists, and this will serve to evaluate how sensitive the current radiological diagnosis tools are.

  17. Validation of TMJ osteoarthritis synthetic defect database via non-rigid registration

    Science.gov (United States)

    Paniagua, Beatriz; Pera, Juliette; Budin, Francois; Gomes, Liliane; Styner, Martin; Lucia, Cevidanes; Nguyen, Tung

    2015-03-01

    Temporomandibular joint (TMJ) disorders are a group of conditions that cause pain and dysfunction in the jaw joint and the muscles controlling jaw movement. However, diagnosis and treatment of these conditions remain controversial. To date, there is no single sign, symptom, or test that can clearly diagnose early stages of osteoarthritis (OA). Instead, the diagnosis is based on a consideration of several factors, including radiological evaluation. The current radiological diagnosis scores of TMJ pathology are subject to misdiagnosis. We believe these scores are limited by the acquisition procedures, such as oblique cuts of the CT and head positioning errors, and can lead to incorrect diagnoses of flattening of the head of the condyle, formation of osteophytes, or condylar pitting. This study consists of creating and validating a methodological framework to simulate defects in CBCT scans of known location and size, in order to create synthetic TMJ OA database. User-generated defects were created using a non-rigid deformation protocol in CBCT. All segmentation evaluation, surface distances and linear distances from the user-generated to the simulated defects showed our methodological framework to be very precise and within a voxel (0.5 mm) of magnitude. A TMJ OA synthetic database will be created next, and evaluated by expert radiologists, and this will serve to evaluate how sensitive the current radiological diagnosis tools are.

  18. Efficient convex optimization approach to 3D non-rigid MR-TRUS registration.

    Science.gov (United States)

    Sun, Yue; Yuan, Jing; Rajchl, Martin; Qiu, Wu; Romagnoli, Cesare; Fenster, Aaron

    2013-01-01

    In this study, we propose an efficient non-rigid MR-TRUS deformable registration method to improve the accuracy of targeting suspicious locations during a 3D ultrasound (US) guided prostate biopsy. The proposed deformable registration approach employs the multi-channel modality independent neighbourhood descriptor (MIND) as the local similarity feature across the two modalities of MR and TRUS, and a novel and efficient duality-based convex optimization based algorithmic scheme is introduced to extract the deformations which align the two MIND descriptors. The registration accuracy was evaluated using 10 patient images by measuring the TRE of manually identified corresponding intrinsic fiducials in the whole gland and peripheral zone, and performance metrics (DSC, MAD and MAXD) for the apex, mid-gland and base of the prostate were also calculated by comparing two manually segmented prostate surfaces in the registered 3D MR and TRUS images. Experimental results show that the proposed method yielded an overall mean TRE of 1.74 mm, which is favorably comparable to a clinical requirement for an error of less than 2.5 mm.

  19. Bayesian Characterization of Uncertainty in Intra-Subject Non-Rigid Registration

    Science.gov (United States)

    Risholm, Petter; Janoos, Firdaus; Norton, Isaiah; Golby, Alex J.; Wells, William M.

    2013-01-01

    In settings where high-level inferences are made based on registered image data, the registration uncertainty can contain important information. In this article, we propose a Bayesian non-rigid registration framework where conventional dissimilarity and regularization energies can be included in the likelihood and the prior distribution on deformations respectively through the use of Boltzmann’s distribution. The posterior distribution is characterized using Markov Chain Monte Carlo (MCMC) methods with the effect of the Boltzmann temperature hyper-parameters marginalized under broad uninformative hyper-prior distributions. The MCMC chain permits estimation of the most likely deformation as well as the associated uncertainty. On synthetic examples, we demonstrate the ability of the method to identify the maximum a posteriori estimate and the associated posterior uncertainty, and demonstrate that the posterior distribution can be non-Gaussian. Additionally, results from registering clinical data acquired during neurosurgery for resection of brain tumor are provided; we compare the method to single transformation results from a deterministic optimizer and introduce methods that summarize the high-dimensional uncertainty. At the site of resection, the registration uncertainty increases and the marginal distribution on deformations is shown to be multi-modal. PMID:23602919

  20. Robust feature estimation by non-rigid hierarchical image registration and its application in disparity measurement

    Science.gov (United States)

    Badshah, Amir; Choudhry, Aadil Jaleel; Ullah, Shan

    2017-03-01

    Industries are moving towards automation in order to increase productivity and ensure quality. Variety of electronic and electromagnetic systems are being employed to assist human operator in fast and accurate quality inspection of products. Majority of these systems are equipped with cameras and rely on diverse image processing algorithms. Information is lost in 2D image, therefore acquiring accurate 3D data from 2D images is an open issue. FAST, SURF and SIFT are well-known spatial domain techniques for features extraction and henceforth image registration to find correspondence between images. The efficiency of these methods is measured in terms of the number of perfect matches found. A novel fast and robust technique for stereo-image processing is proposed. It is based on non-rigid registration using modified normalized phase correlation. The proposed method registers two images in hierarchical fashion using quad-tree structure. The registration process works through global to local level resulting in robust matches even in presence of blur and noise. The computed matches can further be utilized to determine disparity and depth for industrial product inspection. The same can be used in driver assistance systems. The preliminary tests on Middlebury dataset produced satisfactory results. The execution time for a 413 x 370 stereo-pair is 500ms approximately on a low cost DSP.

  1. High-throughput mouse phenotyping using non-rigid registration and robust principal component analysis

    Science.gov (United States)

    Xie, Zhongliu; Kitamoto, Asanobu; Tamura, Masaru; Shiroishi, Toshihiko; Gillies, Duncan

    2016-03-01

    Intensive international efforts are underway towards phenotyping the mouse genome, by knocking out each of its ≍25,000 genes one-by-one for comparative study. With vast amounts of data to analyze, the traditional method using time-consuming histological examination is clearly impractical, leading to an overwhelming demand for some high-throughput phenotyping framework, especially with the employment of biomedical image informatics to efficiently identify phenotypes concerning morphological abnormality. Existing work has either excessively relied on volumetric analytics which is insensitive to phenotypes associated with no severe volume variations, or tailored for specific defects and thus fails to serve a general phenotyping purpose. Furthermore, the prevailing requirement of an atlas for image segmentation in contrast to its limited availability further complicates the issue in practice. In this paper we propose a high-throughput general-purpose phenotyping framework that is able to efficiently perform batch-wise anomaly detection without prior knowledge of the phenotype and the need for atlas-based segmentation. Anomaly detection is centered on the combined use of group-wise non-rigid image registration and robust principal component analysis (RPCA) for feature extraction and decomposition.

  2. Harmonic Auto-Regularization for Non Rigid Groupwise Registration in Cardiac Magnetic Resonance Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Sanz-Estebanez, S.; Royuela-del-Val, J.; Sevilla, T.; Revilla-Orodea, A.; Aja-Fernandez, S.; Alberola-Lopez, C.

    2016-07-01

    In this paper we present a new approach for non rigid groupwise registration of cardiac magnetic resonance images by means of free-form deformations, imposing a prior harmonic deformation assumption. The procedure proposes a primal-dual framework for solving an equality constrained minimization problem, which allows an automatic estimate of the trade-off between image fidelity and the Laplacian smoothness terms for each iteration. The method has been applied to both a 4D extended cardio-torso phantom and to a set of voluntary patients. The accuracy of the method has been measured for the synthetic experiment as the difference in modulus between the estimated displacement field and the ground truth; as for the real data, we have calculated the Dice coefficient between the contour manual delineations provided by two cardiologists at end systolic phase and those provided by them at end diastolic phase and, consequently propagated by the registration algorithm to the systolic instant. The automatic procedure turns out to be competitive in motion compensation with other methods even though their parameters have been previously set for optimal performance in different scenarios. (Author)

  3. A Group Theoretical and Quantum Chemical Study of Electronic Absorption and Fluorescence, Vibrational Spectra, and Conformations of Trimethine Cyanine Dye Molecules

    Directory of Open Access Journals (Sweden)

    Vita Solomko

    2016-01-01

    Full Text Available The energetic structures and conformations of trimethine cyanine dye molecules were investigated. For research, group theoretical and quantum chemical calculation methods were used. The theoretical group analysis of electronic and vibrational structure of molecules was carried out. Also, the energetic structures and conformations of the molecule of this dye were studied. Research shows that the investigated molecule may reside in three different conformational states, one of which is highly symmetric (symmetry C2v and the other two with low symmetry. The third conformer is characterized by lowering of binding energy of the electronic system by 0.23 eV, and the long-wavelength absorption band is shifted to lower energies. Also the group theoretical analysis of the trimethine cyanine molecule had allowed systematizing the vibrational and electronic quantum transitions and identifying the bands in the absorption spectra. It is shown that the excitation of the molecule in S1-state causes trans-cis-isomerization. The presence of the barrier of ~0.1 eV allows the fluorescence process to compete with isomerization process, but isomerization causes a decrease in the fluorescence quantum yield of the dye.

  4. Mechanism of Mcl-1 Conformational Regulation Upon Small Molecule Binding Revealed by Molecular Dynamic Simulation.

    Science.gov (United States)

    Wang, Anhui; Song, Ting; Wang, Ziqian; Liu, Yubo; Fan, Yudan; Zhang, Yahui; Zhang, Zhichao

    2016-04-01

    Inhibition of interactions between Mcl-1 and proapoptotic proteins is considered to be a therapeutic strategy to induce apoptosis in cancer cells. Here, we adopted molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to study the inhibition mechanism of three Mcl-1 inhibitors, compounds 1, 2 and 3. Analysis of energy components shows that the better binding free energy of compound 3 than compounds 1 and 2 is attributable to the van der Waals energy (ΔEvdw ) and non-polar solvation energy (ΔGnp ) upon binding. In addition to the excellent agreement with previous experimentally determined affinities, our simulation results further show a bend of helix 4 on Mcl-1 upon compound 3 binding, which is driven by hydrophobic interaction with residue Val(253) , leading to a narrowed BH3-binding groove to impede Puma(BH) (3) binding. The computational result is consistent with our competitive isothermal titration calorimetry (ITC) assays, which shows that the competitive ability of compound 3 toward Mcl-1/Puma(BH) (3) complex is improved beyond its direct binding affinity toward Mcl-1 itself, and compound 3 exhibits much more efficiency to compete with Puma(BH) (3) than compound 2. Our study provides a new strategy to improve inhibitory activity on Mcl-1 based on the conformational dynamic change. © 2015 John Wiley & Sons A/S.

  5. Visual Tracking of Deformation and Classification of Non-Rigid Objects with Robot Hand Probing

    Directory of Open Access Journals (Sweden)

    Fei Hui

    2017-03-01

    Full Text Available Performing tasks with a robot hand often requires a complete knowledge of the manipulated object, including its properties (shape, rigidity, surface texture and its location in the environment, in order to ensure safe and efficient manipulation. While well-established procedures exist for the manipulation of rigid objects, as well as several approaches for the manipulation of linear or planar deformable objects such as ropes or fabric, research addressing the characterization of deformable objects occupying a volume remains relatively limited. The paper proposes an approach for tracking the deformation of non-rigid objects under robot hand manipulation using RGB-D data. The purpose is to automatically classify deformable objects as rigid, elastic, plastic, or elasto-plastic, based on the material they are made of, and to support recognition of the category of such objects through a robotic probing process in order to enhance manipulation capabilities. The proposed approach combines advantageously classical color and depth image processing techniques and proposes a novel combination of the fast level set method with a log-polar mapping of the visual data to robustly detect and track the contour of a deformable object in a RGB-D data stream. Dynamic time warping is employed to characterize the object properties independently from the varying length of the tracked contour as the object deforms. The proposed solution achieves a classification rate over all categories of material of up to 98.3%. When integrated in the control loop of a robot hand, it can contribute to ensure stable grasp, and safe manipulation capability that will preserve the physical integrity of the object.

  6. Near real-time robust non-rigid registration of volumetric ultrasound images for neurosurgery.

    Science.gov (United States)

    Rivaz, Hassan; Collins, D Louis

    2015-02-01

    Ultrasound images are acquired before and after the resection of brain tumors to help the surgeon to localize the tumor and its extent and to minimize the amount of residual tumor after the resection. Because the brain undergoes large deformation between these two acquisitions, deformable image-based registration of these data sets is of substantial clinical importance. In this work, we present an algorithm for non-rigid registration of ultrasound images (RESOUND) that models the deformation with free-form cubic B-splines. We formulate a regularized cost function that uses normalized cross-correlation as the similarity metric. To optimize the cost function, we calculate its analytic derivative and use the stochastic gradient descent technique to achieve near real-time performance. We further propose a robust technique to minimize the effect of non-corresponding regions such as the resected tumor and possible hemorrhage in the post-resection image. Using manually labeled corresponding landmarks in the pre- and post-resection ultrasound volumes, we illustrate that our registration algorithm reduces the mean target registration error from an initial value of 3.7 to 1.5 mm. We also compare RESOUND with the previous work of Mercier et al. (2013) and illustrate that it has three important advantages: (i) it is fully automatic and does not require a manual segmentation of the tumor, (ii) it produces smaller registration errors and (iii) it is about 30 times faster. The clinical data set is available online on the BITE database website. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  7. Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data.

    Science.gov (United States)

    Tektonidis, Marco; Kim, Il-Han; Chen, Yi-Chun M; Eils, Roland; Spector, David L; Rohr, Karl

    2015-01-01

    The analysis of the motion of subcellular particles in live cell microscopy images is essential for understanding biological processes within cells. For accurate quantification of the particle motion, compensation of the motion and deformation of the cell nucleus is required. We introduce a non-rigid multi-frame registration approach for live cell fluorescence microscopy image data. Compared to existing approaches using pairwise registration, our approach exploits information from multiple consecutive images simultaneously to improve the registration accuracy. We present three intensity-based variants of the multi-frame registration approach and we investigate two different temporal weighting schemes. The approach has been successfully applied to synthetic and live cell microscopy image sequences, and an experimental comparison with non-rigid pairwise registration has been carried out. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Operative Line of Resection Determination Method for Emphysema Surgery using High-Speed Laser Scanner and Non-Rigid Registration

    Directory of Open Access Journals (Sweden)

    Jong-Ha Lee

    2016-02-01

    Full Text Available A successful image-to-physical space overlay method is necessary to provide reliable guidance information to surgeons and accurate surface displacement data for use in compensation algorithm of soft tissue deformation. In this paper we outline a novel approach to relate preoperative images to intraoperative space in a lung volume reduction surgery. The protocol requires intraoperative geometric data to measure and compensate for tissue deformation in the organ. We use 3D laser scanner to accomplish these tasks intraoperatively. A laser scanner based on the optical principle of triangulation acquires a dense set of three-dimensional point data in a very short time. The non-rigid registration is then performed via robust point matching algorithm between control points identifiable in both the preoperative tomograms and the intraoperatively acquired point cloud data provided by a laser scanner. Using the obtained warping field, preoperative region of interest is determined in a physical space. Phantom studies using commercial pig’s lung were performed to test the ability to link 3D laser scanner with preoperative modality data through non-rigid registration. The experiments demonstrate that the proposed protocol is capable of achieving non-overlapping ratio of less than 1.41 %. Surface deformation studies were performed in order to determine if the non-rigid registration is capable of compensate soft tissue deformation. In the deformation studies, the laser scanner with non-rigid registration method was able to track changes in preoperative region of interest less than 3.13 % non-overlapping ratio. The experiments were also performed different field of vision data: the non-overlapping error was below 4.14 % with 84 % of the organ visible and below 1.66 % with 96 % of the organ visible.

  9. A Robust and Accurate Non-rigid Medical Image Registration Algorithm Based on Multi-level Deformable Model.

    Science.gov (United States)

    Wan, Yanli; Hu, Hongpu; Xu, Yanli; Chen, Quan; Wang, Yan; Gao, Dongping

    2017-12-01

    Compared to the rigid image registration task, the non-rigid image registration task faces much more challenges due to its high degree of freedom and inherent requirement of smoothness in the deformation field. The purpose was to propose an efficient coarse-to-fine non-rigid medical image registration algorithm based on a multilevel deformable model. In this paper, a robust and efficient coarse-to-fine non-rigid medical image registration algorithm is proposed. It contains three level deformation models, i.e., the global homography model, the local mesh-level homography model, and the local B-spline FFD (Free-Form Deformation) model. The coarse registration is achieved by the first two level models. In the global homography model, a robust algorithm for simultaneous outliers (error matched feature points) removal and model estimation is applied. In the local mesh-level homography model, a new similarity measure is proposed to improve the robustness and accuracy of local mesh based registration. In the fine registration, a local B-spline FFD model with normalized mutual information gradient is employed. We verified the effectiveness of each stage of the proposed registration algorithm with many non-rigid transformation image pairs, and quantitatively compared our proposed registration algorithm with the HBFFD method which is based on the control points of multi-resolution. The experimental results show that our algorithm is more accurate than the hierarchical local B-spline FFD method. Our algorithm can achieve high precision registration by coarse-to-fine process based on multi-level deformable model, which ourperforms the state-of-the-art methods.

  10. Non-rigid, but not rigid, motion interferes with the processing of structural face information in developmental prosopagnosia.

    Science.gov (United States)

    Maguinness, Corrina; Newell, Fiona N

    2015-04-01

    There is growing evidence to suggest that facial motion is an important cue for face recognition. However, it is poorly understood whether motion is integrated with facial form information or whether it provides an independent cue to identity. To provide further insight into this issue, we compared the effect of motion on face perception in two developmental prosopagnosics and age-matched controls. Participants first learned faces presented dynamically (video), or in a sequence of static images, in which rigid (viewpoint) or non-rigid (expression) changes occurred. Immediately following learning, participants were required to match a static face image to the learned face. Test face images varied by viewpoint (Experiment 1) or expression (Experiment 2) and were learned or novel face images. We found similar performance across prosopagnosics and controls in matching facial identity across changes in viewpoint when the learned face was shown moving in a rigid manner. However, non-rigid motion interfered with face matching across changes in expression in both individuals with prosopagnosia compared to the performance of control participants. In contrast, non-rigid motion did not differentially affect the matching of facial expressions across changes in identity for either prosopagnosics (Experiment 3). Our results suggest that whilst the processing of rigid motion information of a face may be preserved in developmental prosopagnosia, non-rigid motion can specifically interfere with the representation of structural face information. Taken together, these results suggest that both form and motion cues are important in face perception and that these cues are likely integrated in the representation of facial identity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. A GPU-based symmetric non-rigid image registration method in human lung.

    Science.gov (United States)

    Haghighi, Babak; D Ellingwood, Nathan; Yin, Youbing; Hoffman, Eric A; Lin, Ching-Long

    2017-08-01

    Quantitative computed tomography (QCT) of the lungs plays an increasing role in identifying sub-phenotypes of pathologies previously lumped into broad categories such as chronic obstructive pulmonary disease and asthma. Methods for image matching and linking multiple lung volumes have proven useful in linking structure to function and in the identification of regional longitudinal changes. Here, we seek to improve the accuracy of image matching via the use of a symmetric multi-level non-rigid registration employing an inverse consistent (IC) transformation whereby images are registered both in the forward and reverse directions. To develop the symmetric method, two similarity measures, the sum of squared intensity difference (SSD) and the sum of squared tissue volume difference (SSTVD), were used. The method is based on a novel generic mathematical framework to include forward and backward transformations, simultaneously, eliminating the need to compute the inverse transformation. Two implementations were used to assess the proposed method: a two-dimensional (2-D) implementation using synthetic examples with SSD, and a multi-core CPU and graphics processing unit (GPU) implementation with SSTVD for three-dimensional (3-D) human lung datasets (six normal adults studied at total lung capacity (TLC) and functional residual capacity (FRC)). Success was evaluated in terms of the IC transformation consistency serving to link TLC to FRC. 2-D registration on synthetic images, using both symmetric and non-symmetric SSD methods, and comparison of displacement fields showed that the symmetric method gave a symmetrical grid shape and reduced IC errors, with the mean values of IC errors decreased by 37%. Results for both symmetric and non-symmetric transformations of human datasets showed that the symmetric method gave better results for IC errors in all cases, with mean values of IC errors for the symmetric method lower than the non-symmetric methods using both SSD and SSTVD

  12. Conformational preferences of ethyl propionate molecule: Raman, temperature dependent FTIR spectroscopic study aided by ab initio quantum chemical and Car-Parrinello molecular dynamics simulation studies.

    Science.gov (United States)

    Dutta, Bipan; Tanaka, Takeyuki; Banerjee, Arup; Chowdhury, Joydeep

    2013-06-13

    The conformational preferences of the industrially significant ethyl propionate (EP) molecule have been investigated from the Raman and FTIR spectra, aided by ab initio and Car-Parrinello molecular dynamics (CPMD) simulation studies. The vibrational signatures of various rotameric forms of the EP molecule have been assigned for the first time from the potential energy distributions (PEDs). The critical analyses of the vibrational signatures reveal the coexistences of the Trans-Trans (TT), Trans-Antigauche (TG(-)) [Trans-Gauche (TG(+))], Antigauche-Trans (G(-)T) [Gauche-Trans (G(+)T)], Antigauche-Antigauche (G(-)G(-)) [Gauche-Gauche (G(+)G(+))], and Gauche-Antigauche (G(+)G(-)) [Antigauche-Gauche (G(-)G(+))] forms of the EP molecule at room and at high temperatures. However, at low temperature (ca. 70 °C), the TT and TG(-) forms of the EP molecule is estimated to be preponderant. The Car-Parrinello molecular dynamics simulation studies of the EP molecule estimated at high, room, and low temperatures are also in harmony with our conjecture as suggested from the vibrational analyses. The ab intio molecular dynamics simulations are observed to be a useful tool for the conformational analyses of the molecule.

  13. Digital anthropomorphic phantoms of non-rigid human respiratory and voluntary body motion for investigating motion correction in emission imaging

    Science.gov (United States)

    Könik, Arda; Connolly, Caitlin M.; Johnson, Karen L.; Dasari, Paul; Segars, Paul W.; Pretorius, P. H.; Lindsay, Clifford; Dey, Joyoni; King, Michael A.

    2014-07-01

    The development of methods for correcting patient motion in emission tomography has been receiving increased attention. Often the performance of these methods is evaluated through simulations using digital anthropomorphic phantoms, such as the commonly used extended cardiac torso (XCAT) phantom, which models both respiratory and cardiac motion based on human studies. However, non-rigid body motion, which is frequently seen in clinical studies, is not present in the standard XCAT phantom. In addition, respiratory motion in the standard phantom is limited to a single generic trend. In this work, to obtain a more realistic representation of motion, we developed a series of individual-specific XCAT phantoms, modeling non-rigid respiratory and non-rigid body motions derived from the magnetic resonance imaging (MRI) acquisitions of volunteers. Acquisitions were performed in the sagittal orientation using the Navigator methodology. Baseline (no motion) acquisitions at end-expiration were obtained at the beginning of each imaging session for each volunteer. For the body motion studies, MRI was again acquired only at end-expiration for five body motion poses (shoulder stretch, shoulder twist, lateral bend, side roll, and axial slide). For the respiratory motion studies, an MRI was acquired during free/regular breathing. The magnetic resonance slices were then retrospectively sorted into 14 amplitude-binned respiratory states, end-expiration, end-inspiration, six intermediary states during inspiration, and six during expiration using the recorded Navigator signal. XCAT phantoms were then generated based on these MRI data by interactive alignment of the organ contours of the XCAT with the MRI slices using a graphical user interface. Thus far we have created five body motion and five respiratory motion XCAT phantoms from the MRI acquisitions of six healthy volunteers (three males and three females). Non-rigid motion exhibited by the volunteers was reflected in both respiratory

  14. Digital anthropomorphic phantoms of non-rigid human respiratory and voluntary body motion for investigating motion correction in emission imaging.

    Science.gov (United States)

    Könik, Arda; Connolly, Caitlin M; Johnson, Karen L; Dasari, Paul; Segars, Paul W; Pretorius, P H; Lindsay, Clifford; Dey, Joyoni; King, Michael A

    2014-07-21

    The development of methods for correcting patient motion in emission tomography has been receiving increased attention. Often the performance of these methods is evaluated through simulations using digital anthropomorphic phantoms, such as the commonly used extended cardiac torso (XCAT) phantom, which models both respiratory and cardiac motion based on human studies. However, non-rigid body motion, which is frequently seen in clinical studies, is not present in the standard XCAT phantom. In addition, respiratory motion in the standard phantom is limited to a single generic trend. In this work, to obtain a more realistic representation of motion, we developed a series of individual-specific XCAT phantoms, modeling non-rigid respiratory and non-rigid body motions derived from the magnetic resonance imaging (MRI) acquisitions of volunteers. Acquisitions were performed in the sagittal orientation using the Navigator methodology. Baseline (no motion) acquisitions at end-expiration were obtained at the beginning of each imaging session for each volunteer. For the body motion studies, MRI was again acquired only at end-expiration for five body motion poses (shoulder stretch, shoulder twist, lateral bend, side roll, and axial slide). For the respiratory motion studies, an MRI was acquired during free/regular breathing. The magnetic resonance slices were then retrospectively sorted into 14 amplitude-binned respiratory states, end-expiration, end-inspiration, six intermediary states during inspiration, and six during expiration using the recorded Navigator signal. XCAT phantoms were then generated based on these MRI data by interactive alignment of the organ contours of the XCAT with the MRI slices using a graphical user interface. Thus far we have created five body motion and five respiratory motion XCAT phantoms from the MRI acquisitions of six healthy volunteers (three males and three females). Non-rigid motion exhibited by the volunteers was reflected in both respiratory

  15. An apparatus for the measurement of tensile creep and contraction ratios in small non-rigid specimens

    OpenAIRE

    Darlington, M. W.; Saunders, D W

    2015-01-01

    An apparatus is described for precise measurement of creep properties in specimens with gauge lengths down to 1.2 cm. An extensometer has been developed which is supported independently of the specimen and exerts a load on the specimen of less than 5 grams. It can thus be used with small non-rigid specimens. The extensometer will detect strains down to 2 x 10-6. The stability is excellent. An adaptation of the system which allows simultaneous measurement of tensile strain...

  16. Using mass spectrometry and small molecule reagents to detect distinctive structural features of different prion conformations (strains)

    Science.gov (United States)

    A prion (PrPSc) is a conformer of a normal cellular prion protein (PrPC). Although they are isosequential, PrPSc is an infectious protein able to convert PrPC into the prion conformation and thereby propagate an infection. PrPC is monomeric while PrPSc is a multimer. PrPSc can adopt more than one co...

  17. Restricted Conformation Dynamics of Single Functionalized Perylene Bisimide Molecules on SiO2 Surfaces and in Thin Polymer Films

    OpenAIRE

    Kowerko, Danny; Schuster, Jörg; von Borczyskowski, Christian

    2009-01-01

    Abstract Intramolecular conformational dynamics caused by the bay groups of perylene bisimide (PBI) molecules have been investigated by single molecule spectroscopy in thin PMMA polymer films and on SiO2 surfaces. All dynamic processes occur in a jump-like fashion on SiO2 but in a likewise continuous way in PMMA. Surface attachment on SiO2 is accomplished by pyridyl functionalisation of PBI demonstrating a nearly perpendicular orientation of the long axis of perylene as has been co...

  18. A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

    Science.gov (United States)

    2015-01-01

    Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

  19. Topology preserving non-rigid image registration using time-varying elasticity model for MRI brain volumes.

    Science.gov (United States)

    Ahmad, Sahar; Khan, Muhammad Faisal

    2015-12-01

    In this paper, we present a new non-rigid image registration method that imposes a topology preservation constraint on the deformation. We propose to incorporate the time varying elasticity model into the deformable image matching procedure and constrain the Jacobian determinant of the transformation over the entire image domain. The motion of elastic bodies is governed by a hyperbolic partial differential equation, generally termed as elastodynamics wave equation, which we propose to use as a deformation model. We carried out clinical image registration experiments on 3D magnetic resonance brain scans from IBSR database. The results of the proposed registration approach in terms of Kappa index and relative overlap computed over the subcortical structures were compared against the existing topology preserving non-rigid image registration methods and non topology preserving variant of our proposed registration scheme. The Jacobian determinant maps obtained with our proposed registration method were qualitatively and quantitatively analyzed. The results demonstrated that the proposed scheme provides good registration accuracy with smooth transformations, thereby guaranteeing the preservation of topology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. An accurate 3D shape context based non-rigid registration method for mouse whole-body skeleton registration

    Science.gov (United States)

    Xiao, Di; Zahra, David; Bourgeat, Pierrick; Berghofer, Paula; Acosta Tamayo, Oscar; Wimberley, Catriona; Gregoire, Marie C.; Salvado, Olivier

    2011-03-01

    Small animal image registration is challenging because of its joint structure, and posture and position difference in each acquisition without a standard scan protocol. In this paper, we face the issue of mouse whole-body skeleton registration from CT images. A novel method is developed for analyzing mouse hind-limb and fore-limb postures based on geodesic path descriptor and then registering the major skeletons and fore limb skeletons initially by thin-plate spline (TPS) transform based on the obtained geodesic paths and their enhanced correspondence fields. A target landmark correction method is proposed for improving the registration accuracy of the improved 3D shape context non-rigid registration method we previously proposed. A novel non-rigid registration framework, combining the skeleton posture analysis, geodesic path based initial alignment and 3D shape context model, is proposed for mouse whole-body skeleton registration. The performance of the proposed methods and framework was tested on 12 pairs of mouse whole-body skeletons. The experimental results demonstrated the flexibility, stability and accuracy of the proposed framework for automatic mouse whole body skeleton registration.

  1. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    Directory of Open Access Journals (Sweden)

    Villoutreix Bruno O

    2009-11-01

    Full Text Available Abstract Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

  2. Forbidden transitions in the microwave spectrum of the trans conformer of the (CD3)2CDOH molecule

    Science.gov (United States)

    Kazimova, S. B.

    2013-07-01

    We searched for forbidden transitions in the microwave rotational spectrum of the (CD3)2CDOH molecule in the frequency range 17030-79050 MHz. The (CD3)2CDOH molecule has a symmetry plane containing the dipole moment components μ b and μ c , while μ a = 0. As a result of centrifugal distortion, in this type of molecule an induced dipole moment component μ a may appear perpendicular to the symmetry plane. We have observed forbidden "centrifugal" transitions in the (CD3)2CDOH molecule arising as a result of the induced component of the dipole moment. We have identified 92 μ a -transitions.

  3. Conformational Transformations of Hemoglobin Molecules During in vivo Blood Irradiation by Low-Intensity Laser Radiation in the Red and Near IR Ranges

    Science.gov (United States)

    Zalesskaya, G. A.

    2014-07-01

    The effect of in vivo blood irradiation by low-intensity laser radiation on electronic-conformational interactions in hemoglobin molecules has been studied experimentally. The changes in the electronic and IR absorption spectra were followed for blood samples drawn at specific times during intravenous and supravascular irradiation, and also after dark reactions have occurred. The nature of the spectral changes observed is discussed. It is shown that the reversible photodissociation of hemoglobin-ligand complexes, initiated by blood irradiation, changes the oxyhemoglobin and deoxyhemoglobin levels, which leads to changes in the electronic absorption spectra of the blood and erythrocytes, and all the conformational transitions in the hemoglobin macromolecules accompanying ligand detachment and addition are responsible for the changes in their IR spectra.

  4. Continuum-based 4D Plate Reconstructions: Linking Non-rigid Lithospheric Kinematics to Rigid Plate Motion

    Science.gov (United States)

    Kneller, E. A.; Johnson, C. A.; Queffelec, T. A.; Nachtegaele, L.

    2010-12-01

    Non-rigid deformation in regions of continental extension and compression can lead to large lateral strain and changes in the shape and surface area of continental plates. This large lateral strain in turn leads to vertical strain in the lithosphere, which is a fundamental control on mechanical and thermal subsidence. Traditional plate reconstruction approaches only describe 2D changes in the shape of tectonic plates and do not include lateral strain gradients and vertical strain. Incorporating lateral and vertical strain into kinematic plate tectonic models is necessary for quantifying the past configuration of tectonic plates, modeling paleogeography and for linking subsidence and heat flow to lateral plate motion. Furthermore, traditional approaches are limited to describing processes at the surface of the Earth and cannot be used to investigate 3D slab kinematics. We build on previous work and overcome the limitations of traditional methods by developing an inverse non-rigid continuum-based plate reconstruction approach that links lateral plate tectonic motion to large-scale 4D deformation of continental plates and subducting slabs. We also describe how this approach can be implemented in open source 3D animation software that can be used to create extendable and easily maintained interactive tools. These tools allow the modeler to rapidly reconstruct deformation and map data and constrain plate models with 3D information. The methods presented in this work can improve paleogeographic reconstructions, help visualize complicated 4D deformation processes in a reconstructed framework, and constrain subsidence and lithospheric stretching, all of which are important for understanding thermal history and estimating heat flow in sedimentary basins.

  5. Exploiting a single intramolecular conformational switching Ni-TPP molecule to probe charge transfer dynamics at the nanoscale on bare Si(100)-2 × 1.

    Science.gov (United States)

    Labidi, Hatem; Pinto, Henry P; Leszczynski, Jerzy; Riedel, Damien

    2017-11-01

    Acquiring quantitative information on charge transfer (CT) dynamics at the nanoscale remains an important scientific challenge. In particular, CT processes in single molecules at surfaces need to be investigated to be properly controlled in various devices. To address this issue, the dynamics of switching molecules can be exploited. Here, nickel-tetraphenylporphyrin adsorbed on the Si(100) surface is used to study the CT process ruling the reversible activation of two chiral molecular conformations. Via the electrons of a scanning tunneling microscope (STM), a statistical study of molecular switching reveals two specific locations of the molecule for which their efficiency is optimized. The CT mechanism is shown to propagate from two lateral aryl groups towards the porphyrin macrocycle inducing an intramolecular movement of two symmetric pyrroles. The measured switching efficiencies can thus be related to a Markus-Jordner model to estimate relevant parameters that describe the dynamics of the CT process. Numerical simulations provide a precise description of the molecular conformations and unveil the molecular energy levels that are involved in the CT process. This quantitative method opens a completely original approach to study CT at the nanoscale.

  6. Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods

    Science.gov (United States)

    Li, Lanlan; Wei, Wei; Jia, Wen-Juan; Zhu, Yongchang; Zhang, Yan; Chen, Jiang-Huai; Tian, Jiaqi; Liu, Huanxiang; He, Yong-Xing; Yao, Xiaojun

    2017-12-01

    Conformational conversion of the normal cellular prion protein, PrPC, into the misfolded isoform, PrPSc, is considered to be a central event in the development of fatal neurodegenerative diseases. Stabilization of prion protein at the normal cellular form (PrPC) with small molecules is a rational and efficient strategy for treatment of prion related diseases. However, few compounds have been identified as potent prion inhibitors by binding to the normal conformation of prion. In this work, to rational screening of inhibitors capable of stabilizing cellular form of prion protein, multiple approaches combining docking-based virtual screening, steady-state fluorescence quenching, surface plasmon resonance and thioflavin T fluorescence assay were used to discover new compounds interrupting PrPC to PrPSc conversion. Compound 3253-0207 that can bind to PrPC with micromolar affinity and inhibit prion fibrillation was identified from small molecule databases. Molecular dynamics simulation indicated that compound 3253-0207 can bind to the hotspot residues in the binding pocket composed by β1, β2 and α2, which are significant structure moieties in conversion from PrPC to PrPSc.

  7. Calculation of the temperature of asphalt concrete at making the joints of multilane road pavement of non-rigid type

    Directory of Open Access Journals (Sweden)

    Giyasov Botir Iminzhonovich

    2015-03-01

    Full Text Available The construction quality of road surface of non-rigid type essentially depend on providing the temperature regimes in the process of laying and packing of hot asphalt concrete mixtures. In order to provide the required characteristics of asphalt concrete due to the surface width it is necessary to provide the temperature regimes of hot asphalt concrete mixture in the zones of lane connection. The hot mixture is promptly cooling right after laying within several minutes, which results, according to the construction technology and the specific conditions of work production, in temperature abuse of the mixture at joints of the lanes at packing. The authors present the analysis of the technology of arranging multilane road surface by one paver with the possibility of heating the surface lane edge with the temperature of the adjacent lane. The results of the studies of the production conditions effect on the temperature of edge heating of the previously laid lanes, and the time required to achieve the maximum heating temperature depending on the relative thickness of coating layers.

  8. Experiences in determination of non-rigid body motion in industrial environment using low-cost photogrammetry

    Science.gov (United States)

    Rupnik, Ewelina; Jansa, Josef

    2013-04-01

    Central to our investigation is determination of dynamic behaviour of a highly reflective platform floating on water, as well as derivation of parameters defining instantaneous water state. The employed imaging setup consists of three off-the-shelf dSLR cameras capable of video recording at a 30Hz frame rate. In order to observe a change, the non-rigid and non-diffuse bodies impose the adoption of artificial targetting and custom measurement algorithms. Attention will be given to an in-house software tool implemented to carry out point measurement, correspondence search, tracking and outlier detection methods in the presence of specular reflections and a multimedia scene. A methodology for retrieval of wave parameters in regular wave conditions is also automatically handled by the software and will be discussed. In the context of performed measurements and achieved results, we will point out the extent to which consumer grade camera can fulfil automation and accuracy demands of industrial applications and the pitfalls entailed. Lastly, we will elaborate on visual representation of computed motion and deformations.

  9. Non-rigid contour-to-pixel registration of photographic and quantitative light-induced fluorescence imaging of decalcified teeth

    Science.gov (United States)

    Berkels, Benjamin; Deserno, Thomas; Ehrlich, Eva E.; Fritz, Ulrike B.; Sirazitdinova, Ekaterina; Tatano, Rosalia

    2016-03-01

    Quantitative light-induced fluorescence (QLF) is widely used to assess the damage of a tooth due to decalcification. In digital photographs, decalcification appears as white spot lesions, i.e. white spots on the tooth surface. We propose a novel multimodal registration approach for the matching of digital photographs and QLF images of decalcified teeth. The registration is based on the idea of contour-to-pixel matching. Here, the curve, which represents the shape of the tooth, is extracted from the QLF image using a contour segmentation by binarization and morphological processing. This curve is aligned to the photo with a non-rigid variational registration approach. Thus, the registration problem is formulated as minimization problem with an objective function that consists of a data term and a regularizer for the deformation. To construct the data term, the photo is pointwise classified into tooth and non-tooth regions. Then, the signed distance function of the tooth region allows to measure the mismatch between curve and photo. As regularizer a higher order, linear elastic prior is used. The resulting minimization problem is solved numerically using bilinear Finite Elements for the spatial discretization and the Gauss-Newton algorithm. The evaluation is based on 150 image pairs, where an average of 5 teeth have been captured from 32 subjects. All registrations have been confirmed correctly by a dental expert. The contour-to-pixel methods can directly be used in 3D for surface-to-voxel tasks.

  10. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.

    Science.gov (United States)

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M; Lin, Jung-Hsin

    2009-07-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design.

  11. Susceptibility to HLA-DM Protein Is Determined by a Dynamic Conformation of Major Histocompatibility Complex Class II Molecule Bound with Peptide*

    Science.gov (United States)

    Yin, Liusong; Trenh, Peter; Guce, Abigail; Wieczorek, Marek; Lange, Sascha; Sticht, Jana; Jiang, Wei; Bylsma, Marissa; Mellins, Elizabeth D.; Freund, Christian; Stern, Lawrence J.

    2014-01-01

    HLA-DM mediates the exchange of peptides loaded onto MHCII molecules during antigen presentation by a mechanism that remains unclear and controversial. Here, we investigated the sequence and structural determinants of HLA-DM interaction. Peptides interacting nonoptimally in the P1 pocket exhibited low MHCII binding affinity and kinetic instability and were highly susceptible to HLA-DM-mediated peptide exchange. These changes were accompanied by conformational alterations detected by surface plasmon resonance, SDS resistance assay, antibody binding assay, gel filtration, dynamic light scattering, small angle x-ray scattering, and NMR spectroscopy. Surprisingly, all of those changes could be reversed by substitution of the P9 pocket anchor residue. Moreover, MHCII mutations outside the P1 pocket and the HLA-DM interaction site increased HLA-DM susceptibility. These results indicate that a dynamic MHCII conformational determinant rather than P1 pocket occupancy is the key factor determining susceptibility to HLA-DM-mediated peptide exchange and provide a molecular mechanism for HLA-DM to efficiently target unstable MHCII-peptide complexes for editing and exchange those for more stable ones. PMID:25002586

  12. Susceptibility to HLA-DM protein is determined by a dynamic conformation of major histocompatibility complex class II molecule bound with peptide.

    Science.gov (United States)

    Yin, Liusong; Trenh, Peter; Guce, Abigail; Wieczorek, Marek; Lange, Sascha; Sticht, Jana; Jiang, Wei; Bylsma, Marissa; Mellins, Elizabeth D; Freund, Christian; Stern, Lawrence J

    2014-08-22

    HLA-DM mediates the exchange of peptides loaded onto MHCII molecules during antigen presentation by a mechanism that remains unclear and controversial. Here, we investigated the sequence and structural determinants of HLA-DM interaction. Peptides interacting nonoptimally in the P1 pocket exhibited low MHCII binding affinity and kinetic instability and were highly susceptible to HLA-DM-mediated peptide exchange. These changes were accompanied by conformational alterations detected by surface plasmon resonance, SDS resistance assay, antibody binding assay, gel filtration, dynamic light scattering, small angle x-ray scattering, and NMR spectroscopy. Surprisingly, all of those changes could be reversed by substitution of the P9 pocket anchor residue. Moreover, MHCII mutations outside the P1 pocket and the HLA-DM interaction site increased HLA-DM susceptibility. These results indicate that a dynamic MHCII conformational determinant rather than P1 pocket occupancy is the key factor determining susceptibility to HLA-DM-mediated peptide exchange and provide a molecular mechanism for HLA-DM to efficiently target unstable MHCII-peptide complexes for editing and exchange those for more stable ones. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Thermally-induced phase transition of pseudorotaxane crystals: changes in conformation and interaction of the molecules and optical properties of the crystals.

    Science.gov (United States)

    Horie, Masaki; Suzaki, Yuji; Hashizume, Daisuke; Abe, Tomoko; Wu, Tiendi; Sassa, Takafumi; Hosokai, Takuya; Osakada, Kohtaro

    2012-10-31

    This paper presents a pseudorotaxane that acts as a thermally driven molecular switch in the single-crystal state. Crystals of the cationic pseudorotaxane consisting of dibenzo[24]crown-8 (DB24C8) and N-(xylylammonium)-methylferrocene as the cyclic and axle component molecules, respectively, undergo crystalline-phase transition at 128 °C with heating and 116 °C with cooling, according to differential-scanning-calorimetry measurements. X-ray crystallographic analyses revealed that the phase transition was accompanied by rotation of the 4-methylphenyl group of the axle component molecule and a simultaneous shift in the position of the PF(6)(-) counteranion. Crystalline phase transition changes the conformation and position of the DB24C8 molecule relative to the ammonium cation partially; the interaction between the cyclic component and the PF(6)(-) anion in the crystal changes to a greater extent. Moreover, there are changes in the vibration angle (θ) and birefringence (Δn) on the (001) face of the crystal transitionally; θ is rotated by +12°, and Δn is decreased from 0.070 to 0.059 upon heating across the phase transition temperature. The phase transition and accompanying change in the optical properties of the crystal occur reversibly and repeatedly upon heating and cooling processes. The switching rotation of the aromatic plane of the molecule induces a change in the optical anisotropy of the crystal, which is regarded as a demonstration of a new type of optical crystal. Partial replacement of the PF(6)(-) anion with the bulkier AsF(6)(-) anion forms crystals with similar crystallographic parameters. An increase in the AsF(6)(-) content decreases the reversible-phase-transition temperature gradually down to 99 °C (T(end)) and 68 °C (T(exo)) ([AsF(6)(-)]:[PF(6)(-)] = 0.4:0.6).

  14. 3D Visual Data-Driven Spatiotemporal Deformations for Non-Rigid Object Grasping Using Robot Hands

    Directory of Open Access Journals (Sweden)

    Carlos M. Mateo

    2016-05-01

    Full Text Available Sensing techniques are important for solving problems of uncertainty inherent to intelligent grasping tasks. The main goal here is to present a visual sensing system based on range imaging technology for robot manipulation of non-rigid objects. Our proposal provides a suitable visual perception system of complex grasping tasks to support a robot controller when other sensor systems, such as tactile and force, are not able to obtain useful data relevant to the grasping manipulation task. In particular, a new visual approach based on RGBD data was implemented to help a robot controller carry out intelligent manipulation tasks with flexible objects. The proposed method supervises the interaction between the grasped object and the robot hand in order to avoid poor contact between the fingertips and an object when there is neither force nor pressure data. This new approach is also used to measure changes to the shape of an object’s surfaces and so allows us to find deformations caused by inappropriate pressure being applied by the hand’s fingers. Test was carried out for grasping tasks involving several flexible household objects with a multi-fingered robot hand working in real time. Our approach generates pulses from the deformation detection method and sends an event message to the robot controller when surface deformation is detected. In comparison with other methods, the obtained results reveal that our visual pipeline does not use deformations models of objects and materials, as well as the approach works well both planar and 3D household objects in real time. In addition, our method does not depend on the pose of the robot hand because the location of the reference system is computed from a recognition process of a pattern located place at the robot forearm. The presented experiments demonstrate that the proposed method accomplishes a good monitoring of grasping task with several objects and different grasping configurations in indoor

  15. Evaluation of non-rigid registration parameters for atlas-based segmentation of CT images of human cochlea

    Science.gov (United States)

    Elfarnawany, Mai; Alam, S. Riyahi; Agrawal, Sumit K.; Ladak, Hanif M.

    2017-02-01

    Cochlear implant surgery is a hearing restoration procedure for patients with profound hearing loss. In this surgery, an electrode is inserted into the cochlea to stimulate the auditory nerve and restore the patient's hearing. Clinical computed tomography (CT) images are used for planning and evaluation of electrode placement, but their low resolution limits the visualization of internal cochlear structures. Therefore, high resolution micro-CT images are used to develop atlas-based segmentation methods to extract these nonvisible anatomical features in clinical CT images. Accurate registration of the high and low resolution CT images is a prerequisite for reliable atlas-based segmentation. In this study, we evaluate and compare different non-rigid B-spline registration parameters using micro-CT and clinical CT images of five cadaveric human cochleae. The varying registration parameters are cost function (normalized correlation (NC), mutual information and mean square error), interpolation method (linear, windowed-sinc and B-spline) and sampling percentage (1%, 10% and 100%). We compare the registration results visually and quantitatively using the Dice similarity coefficient (DSC), Hausdorff distance (HD) and absolute percentage error in cochlear volume. Using MI or MSE cost functions and linear or windowed-sinc interpolation resulted in visually undesirable deformation of internal cochlear structures. Quantitatively, the transforms using 100% sampling percentage yielded the highest DSC and smallest HD (0.828+/-0.021 and 0.25+/-0.09mm respectively). Therefore, B-spline registration with cost function: NC, interpolation: B-spline and sampling percentage: moments 100% can be the foundation of developing an optimized atlas-based segmentation algorithm of intracochlear structures in clinical CT images.

  16. List-mode-based reconstruction for respiratory motion correction in PET using non-rigid body transformations

    Energy Technology Data Exchange (ETDEWEB)

    Lamare, F [INSERM, U650, Laboratoire du Traitement de l' Information Medicale (LaTIM), Brest, F-29200 (France); Carbayo, M J Ledesma [ETSI Telecomunicacion Universidad Politecnica de Madrid, Ciudad Universitaria s/n 28040, Madrid (Spain); Cresson, T [INSERM, U650, Laboratoire du Traitement de l' Information Medicale (LaTIM), Brest, F-29200 (France); Kontaxakis, G [ETSI Telecomunicacion Universidad Politecnica de Madrid, Ciudad Universitaria s/n 28040, Madrid (Spain); Santos, A [ETSI Telecomunicacion Universidad Politecnica de Madrid, Ciudad Universitaria s/n 28040, Madrid (Spain); Rest, C Cheze Le [INSERM, U650, Laboratoire du Traitement de l' Information Medicale (LaTIM), Brest, F-29200 (France); Reader, A J [School of Chemical Engineering and Analytical Science, University of Manchester, Manchester (United Kingdom); Visvikis, D [INSERM, U650, Laboratoire du Traitement de l' Information Medicale (LaTIM), Brest, F-29200 (France)

    2007-09-07

    Respiratory motion in emission tomography leads to reduced image quality. Developed correction methodology has been concentrating on the use of respiratory synchronized acquisitions leading to gated frames. Such frames, however, are of low signal-to-noise ratio as a result of containing reduced statistics. In this work, we describe the implementation of an elastic transformation within a list-mode-based reconstruction for the correction of respiratory motion over the thorax, allowing the use of all data available throughout a respiratory motion average acquisition. The developed algorithm was evaluated using datasets of the NCAT phantom generated at different points throughout the respiratory cycle. List-mode-data-based PET-simulated frames were subsequently produced by combining the NCAT datasets with Monte Carlo simulation. A non-rigid registration algorithm based on B-spline basis functions was employed to derive transformation parameters accounting for the respiratory motion using the NCAT dynamic CT images. The displacement matrices derived were subsequently applied during the image reconstruction of the original emission list mode data. Two different implementations for the incorporation of the elastic transformations within the one-pass list mode EM (OPL-EM) algorithm were developed and evaluated. The corrected images were compared with those produced using an affine transformation of list mode data prior to reconstruction, as well as with uncorrected respiratory motion average images. Results demonstrate that although both correction techniques considered lead to significant improvements in accounting for respiratory motion artefacts in the lung fields, the elastic-transformation-based correction leads to a more uniform improvement across the lungs for different lesion sizes and locations.

  17. Conformational dynamics of DNA hairpins at millisecond resolution obtained from analysis of single-molecule FRET histograms.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Berger, Yaron; Liber, Miran; Nir, Eyal

    2013-12-19

    Here we provide high resolution study of DNA hairpin dynamics achieved by probability distribution analysis (PDA) of diffusion-based single-molecule Förster resonance energy transfer (sm-FRET) histograms. The opening and closing rates of three hairpins both free and attached to DNA origami were determined. The agreement with rates previously obtained using the total internal reflection (TIRF) technique and between free hairpins and hairpins attached to origami validated the PDA and demonstrated that the origami had no influence on the hairpin dynamics. From comparison of rates of four DNA hairpins, differing only in stem sequence, and from comparison with rates calculated using nearest-neighbor method and standard transition state theory, we conclude that the unfolding reaction resembles that of melting of DNA duplex with a corresponding sequence and that the folding reaction depends on counterion concentration and not on stem sequence. Our validation and demonstration of the PDA method will encourage its implementation in future high-resolution dynamic studies of freely diffusing biomolecules.

  18. Fully automated targeting using non-rigid image registration matches accuracy and exceeds precision of best manual approaches to Subthalamic Deep Brain Stimulation targeting in Parkinson's disease

    Science.gov (United States)

    Pallavaram, Srivatsan; D'Haese, Pierre-François; Lake, Wendell; Konrad, Peter E.; Dawant, Benoit M.; Neimat, Joseph S.

    2015-01-01

    Background Finding the optimal location for the implantation of the electrode in Deep Brain Stimulation (DBS) surgery is crucial for maximizing therapeutic benefit to the patient. Such targeting is challenging for several reasons including anatomical variability between patients as well as lack of consensus about the location of the optimal target. Objective To compare the performance of popular manual targeting methods against a fully automatic non-rigid image registration based approach. Methods In 71 Parkinson's disease STN-DBS implantations, an experienced functional neurosurgeon selected the target manually using three different approaches; indirect targeting using standard stereotactic coordinates, direct targeting based on the patient MRI, and indirect targeting relative to the red nucleus. Targets were also automatically predicted using a leave-one-out approach to populate the CranialVault atlas using non-rigid image registration. The different targeting methods were compared against the location of the final active contact, determined through iterative clinical programming in each individual patient. Results Targeting using standard stereotactic coordinates corresponding to the center of the motor territory of the STN had the largest targeting error (3.69 mm), followed by direct targeting (3.44 mm), average stereotactic coordinates of active contacts from this study (3.02 mm), red nucleus based targeting (2.75 mm), and non-rigid image registration based automatic predictions using the CranialVault atlas (2.70 mm). The CranialVault atlas method had statistically smaller variance than all manual approaches. Conclusions Fully automatic targeting based on non-rigid image registration using the CranialVault atlas is as accurate and more precise than popular manual methods for STN-DBS. PMID:25988929

  19. Contour propagation in MRI-guided radiotherapy treatment of cervical cancer: the accuracy of rigid, non-rigid and semi-automatic registrations

    Science.gov (United States)

    van der Put, R. W.; Kerkhof, E. M.; Raaymakers, B. W.; Jürgenliemk-Schulz, I. M.; Lagendijk, J. J. W.

    2009-12-01

    External beam radiation treatment for patients with cervical cancer is hindered by the relatively large motion of the target volume. A hybrid MRI-accelerator system makes it possible to acquire online MR images during treatment in order to correct for motion and deformation. To fully benefit from such a system, online delineation of the target volumes is necessary. The aim of this study is to investigate the accuracy of rigid, non-rigid and semi-automatic registrations of MR images for interfractional contour propagation in patients with cervical cancer. Registration using mutual information was performed on both bony anatomy and soft tissue. A B-spline transform was used for the non-rigid method. Semi-automatic registration was implemented with a point set registration algorithm on a small set of manual landmarks. Online registration was simulated by application of each method to four weekly MRI scans for each of 33 cervical cancer patients. Evaluation was performed by distance analysis with respect to manual delineations. The results show that soft-tissue registration significantly (P cervical cancer, online MRI imaging will allow target localization based on soft tissue visualization, which provides a significantly higher accuracy than localization based on bony anatomy. The use of limited user input to guide the registration increases overall accuracy. Additional non-rigid registration further reduces the propagation error and negates errors caused by small observer variations.

  20. Influence of CH center dot center dot center dot N Interaction in the Self-Assembly of an Oligo(isoquinolyne-ethynylyne) Molecule with Distinct Conformational States

    DEFF Research Database (Denmark)

    Nuermaimaiti, Ajiguli; Ning, Yanxiao; Cramer, Jacob L.

    2017-01-01

    Molecular conformational flexibility can play an important role in supramolecular self-assembly on surfaces, affecting not least chiral molecular assemblies. To explicitly and systematically investigate the role of molecular conformational flexibility in surface self-assembly, we synthesized...

  1. The effect of rigid and non-rigid connections between implants and teeth on biological and technical complications: a systematic review and a meta-analysis.

    Science.gov (United States)

    Tsaousoglou, Phoebus; Michalakis, Konstantinos; Kang, Kiho; Weber, Hans-Peter; Sculean, Anton

    2017-07-01

    To assess survival, as well as technical and biological complication rates of partial fixed dental prostheses (FDPs) supported by implants and teeth. An electronic Medline search was conducted to identify articles, published in dental journals from January 1980 to August 2015, reporting on partial FDPs supported by implants and teeth. The search terms were categorized into four groups comprising the PICO question. Manual searches of published full-text articles and related reviews were also performed. The initial database search produced 3587 relevant titles. Three hundred and eighty-six articles were retrieved for abstract review, while 39 articles were selected for full-text review. A total of 10 studies were selected for inclusion. Overall survival rate for implants ranged between 90% and 100%, after follow-up periods with a mean range of 18-120 months. The survival of the abutment teeth was 94.1-100%, while the prostheses survival was 85-100% for the same time period. The most frequent complications were "periapical lesions" (11.53%). The most frequent technical complication was "porcelain occlusal fracture" (16.6%), followed by "screw loosening" (15%). According to the meta-analysis, no intrusion was noted on the rigid connection group, while five teeth (8.19%) were intruded in the non-rigid connection group [95% CI (0.013-0.151)]. The tooth-implant FDP seems to be a possible alternative to an implant-supported FDP. There is limited evidence that rigid connection between teeth and implants presents better results when compared with the non-rigid one. The major drawback of non-rigidly connected FDPs is tooth intrusion. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Learning Non-rigid Deformations for Robust, Constrained Point-based Registration in Image-Guided MR-TRUS Prostate Intervention.

    Science.gov (United States)

    Onofrey, John A; Staib, Lawrence H; Sarkar, Saradwata; Venkataraman, Rajesh; Nawaf, Cayce B; Sprenkle, Preston C; Papademetris, Xenophon

    2017-07-01

    Accurate and robust non-rigid registration of pre-procedure magnetic resonance (MR) imaging to intra-procedure trans-rectal ultrasound (TRUS) is critical for image-guided biopsies of prostate cancer. Prostate cancer is one of the most prevalent forms of cancer and the second leading cause of cancer-related death in men in the United States. TRUS-guided biopsy is the current clinical standard for prostate cancer diagnosis and assessment. State-of-the-art, clinical MR-TRUS image fusion relies upon semi-automated segmentations of the prostate in both the MR and the TRUS images to perform non-rigid surface-based registration of the gland. Segmentation of the prostate in TRUS imaging is itself a challenging task and prone to high variability. These segmentation errors can lead to poor registration and subsequently poor localization of biopsy targets, which may result in false-negative cancer detection. In this paper, we present a non-rigid surface registration approach to MR-TRUS fusion based on a statistical deformation model (SDM) of intra-procedural deformations derived from clinical training data. Synthetic validation experiments quantifying registration volume of interest overlaps of the PI-RADS parcellation standard and tests using clinical landmark data demonstrate that our use of an SDM for registration, with median target registration error of 2.98 mm, is significantly more accurate than the current clinical method. Furthermore, we show that the low-dimensional SDM registration results are robust to segmentation errors that are not uncommon in clinical TRUS data. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A new technique for noise reduction at coronary CT angiography with multi-phase data-averaging and non-rigid image registration.

    Science.gov (United States)

    Tatsugami, Fuminari; Higaki, Toru; Nakamura, Yuko; Yamagami, Takuji; Date, Shuji; Fujioka, Chikako; Kiguchi, Masao; Kihara, Yasuki; Awai, Kazuo

    2015-01-01

    To investigate the feasibility of a newly developed noise reduction technique at coronary CT angiography (CTA) that uses multi-phase data-averaging and non-rigid image registration. Sixty-five patients underwent coronary CTA with prospective ECG-triggering. The range of the phase window was set at 70-80% of the R-R interval. First, three sets of consecutive volume data at 70%, 75% and 80% of the R-R interval were prepared. Second, we applied non-rigid registration to align the 70% and 80% images to the 75% image. Finally, we performed weighted averaging of the three images and generated a de-noised image. The image noise and contrast-to-noise ratio (CNR) in the proximal coronary arteries between the conventional 75% and the de-noised images were compared. Two radiologists evaluated the image quality using a 5-point scale (1, poor; 5, excellent). On de-noised images, mean image noise was significantly lower than on conventional 75% images (18.3 HU ± 2.6 vs. 23.0 HU ± 3.3, P < 0.01) and the CNR was significantly higher (P < 0.01). The mean image quality score for conventional 75% and de-noised images was 3.9 and 4.4, respectively (P < 0.01). Our method reduces image noise and improves image quality at coronary CTA. • We introduce a new method for image noise reduction at cardiac CT. • Multiple data acquisitions of an object and their averaging yield lower noise. • Our method uses multi-phase images reconstructed from unused redundant imaging data. • It reduces image noise by averaging multi-phase images transformed by non-rigid registration. • This method achieves a 20% image noise reduction at cardiac CT.

  4. Non-rigid registration of a 3D ultrasound and a MR image data set of the female pelvic floor using a biomechanical model

    Directory of Open Access Journals (Sweden)

    Rexilius Jan

    2005-03-01

    Full Text Available Abstract Background The visual combination of different modalities is essential for many medical imaging applications in the field of Computer-Assisted medical Diagnosis (CAD to enhance the clinical information content. Clinically, incontinence is a diagnosis with high clinical prevalence and morbidity rate. The search for a method to identify risk patients and to control the success of operations is still a challenging task. The conjunction of magnetic resonance (MR and 3D ultrasound (US image data sets could lead to a new clinical visual representation of the morphology as we show with corresponding data sets of the female anal canal with this paper. Methods We present a feasibility study for a non-rigid registration technique based on a biomechanical model for MR and US image data sets of the female anal canal as a base for a new innovative clinical visual representation. Results It is shown in this case study that the internal and external sphincter region could be registered elastically and the registration partially corrects the compression induced by the ultrasound transducer, so the MR data set showing the native anatomy is used as a frame for the US data set showing the same region with higher resolution but distorted by the transducer Conclusion The morphology is of special interest in the assessment of anal incontinence and the non-rigid registration of normal clinical MR and US image data sets is a new field of the adaptation of this method incorporating the advantages of both technologies.

  5. Evaluation of non-rigid constrained CT/CBCT registration algorithms for delineation propagation in the context of prostate cancer radiotherapy

    Science.gov (United States)

    Rubeaux, Mathieu; Simon, Antoine; Gnep, Khemara; Colliaux, Jérémy; Acosta, Oscar; de Crevoisier, Renaud; Haigron, Pascal

    2013-03-01

    Image-Guided Radiation Therapy (IGRT) aims at increasing the precision of radiation dose delivery. In the context of prostate cancer, a planning Computed Tomography (CT) image with manually defined prostate and organs at risk (OAR) delineations is usually associated with daily Cone Beam Computed Tomography (CBCT) follow-up images. The CBCT images allow to visualize the prostate position and to reposition the patient accordingly. They also should be used to evaluate the dose received by the organs at each fraction of the treatment. To do so, the first step is a prostate and OAR segmentation on the daily CBCTs, which is very timeconsuming. To simplify this task, CT to CBCT non-rigid registration could be used in order to propagate the original CT delineations in the CBCT images. For this aim, we compared several non-rigid registration methods. They are all based on the Mutual Information (MI) similarity measure, and use a BSpline transformation model. But we add different constraints to this global scheme in order to evaluate their impact on the final results. These algorithms are investigated on two real datasets, representing a total of 70 CBCT on which a reference delineation has been realized. The evaluation is led using the Dice Similarity Coefficient (DSC) as a quality criteria. The experiments show that a rigid penalty term on the bones improves the final registration result, providing high quality propagated delineations.

  6. A new technique for noise reduction at coronary CT angiography with multi-phase data-averaging and non-rigid image registration

    Energy Technology Data Exchange (ETDEWEB)

    Tatsugami, Fuminari; Higaki, Toru; Nakamura, Yuko; Yamagami, Takuji; Date, Shuji; Awai, Kazuo [Hiroshima University, Department of Diagnostic Radiology, Minami-ku, Hiroshima (Japan); Fujioka, Chikako; Kiguchi, Masao [Hiroshima University, Department of Radiology, Minami-ku, Hiroshima (Japan); Kihara, Yasuki [Hiroshima University, Department of Cardiovascular Medicine, Minami-ku, Hiroshima (Japan)

    2015-01-15

    To investigate the feasibility of a newly developed noise reduction technique at coronary CT angiography (CTA) that uses multi-phase data-averaging and non-rigid image registration. Sixty-five patients underwent coronary CTA with prospective ECG-triggering. The range of the phase window was set at 70-80 % of the R-R interval. First, three sets of consecutive volume data at 70 %, 75 % and 80 % of the R-R interval were prepared. Second, we applied non-rigid registration to align the 70 % and 80 % images to the 75 % image. Finally, we performed weighted averaging of the three images and generated a de-noised image. The image noise and contrast-to-noise ratio (CNR) in the proximal coronary arteries between the conventional 75 % and the de-noised images were compared. Two radiologists evaluated the image quality using a 5-point scale (1, poor; 5, excellent). On de-noised images, mean image noise was significantly lower than on conventional 75 % images (18.3 HU ± 2.6 vs. 23.0 HU ± 3.3, P < 0.01) and the CNR was significantly higher (P < 0.01). The mean image quality score for conventional 75 % and de-noised images was 3.9 and 4.4, respectively (P < 0.01). Our method reduces image noise and improves image quality at coronary CTA. (orig.)

  7. How to use a very simple microcomputing system for a dynamical conformational analysis of versatile molecules. The case of some anticancer inorganic ring systems

    Science.gov (United States)

    Lahana, Roger; Labarre, Jean-Francois

    A very simple use of a suitable microcomputing system allows discrimination of a set of X-ray structures of anticancer drugs which (i) are the "natural" preferred conformations and (ii) are the direct relationships logically linking these conformations together. Such an approach appears the main interest for a deep understanding of the relative antitumour activities of drugs, whatever the target may be.

  8. Solvent Induced Conformational Kinetics (SICK)

    NARCIS (Netherlands)

    Jonkman, Leffert; Kommandeur, Jan

    1970-01-01

    Specific conformations of molecules may be induced by the solvent when a large free volume is associated with the oonformational change. The conformational energy barrier is then a property of the solvent, rather than of the molecule. Such effects are reported for several substituted

  9. 3D shape reconstruction of bone from two x-ray images using 2D/3D non-rigid registration based on moving least-squares deformation

    Science.gov (United States)

    Cresson, T.; Branchaud, D.; Chav, R.; Godbout, B.; de Guise, J. A.

    2010-03-01

    Several studies based on biplanar radiography technologies are foreseen as great systems for 3D-reconstruction applications for medical diagnoses. This paper proposes a non-rigid registration method to estimate a 3D personalized shape of bone models from two planar x-ray images using an as-rigid-as-possible deformation approach based on a moving least-squares optimization method. Based on interactive deformation methods, the proposed technique has the ability to let a user improve readily and with simplicity a 3D reconstruction which is an important step in clinical applications. Experimental evaluations of six anatomical femur specimens demonstrate good performances of the proposed approach in terms of accuracy and robustness when compared to CT-scan.

  10. Non-rigid MR-TRUS image registration for image-guided prostate biopsy using correlation ratio-based mutual information.

    Science.gov (United States)

    Gong, Lun; Wang, Haifeng; Peng, Chengtao; Dai, Yakang; Ding, Min; Sun, Yinghao; Yang, Xiaodong; Zheng, Jian

    2017-01-10

    To improve the accuracy of ultrasound-guided biopsy of the prostate, the non-rigid registration of magnetic resonance (MR) images onto transrectal ultrasound (TRUS) images has gained increasing attention. Mutual information (MI) is a widely used similarity criterion in MR-TRUS image registration. However, the use of MI has been challenged because of intensity distortion, noise and down-sampling. Hence, we need to improve the MI measure to get better registration effect. We present a novel two-dimensional non-rigid MR-TRUS registration algorithm that uses correlation ratio-based mutual information (CRMI) as the similarity criterion. CRMI includes a functional mapping of intensity values on the basis of a generalized version of intensity class correspondence. We also analytically acquire the derivative of CRMI with respect to deformation parameters. Furthermore, we propose an improved stochastic gradient descent (ISGD) optimization method based on the Metropolis acceptance criteria to improve the global optimization ability and decrease the registration time. The performance of the proposed method is tested on synthetic images and 12 pairs of clinical prostate TRUS and MR images. By comparing label map registration frame (LMRF) and conditional mutual information (CMI), the proposed algorithm has a significant improvement in the average values of Hausdorff distance and target registration error. Although the average Dice Similarity coefficient is not significantly better than CMI, it still has a crucial increase over LMRF. The average computation time consumed by the proposed method is similar to LMRF, which is 16 times less than CMI. With more accurate matching performance and lower sensitivity to noise and down-sampling, the proposed algorithm of minimizing CRMI by ISGD is more robust and has the potential for use in aligning TRUS and MR images for needle biopsy.

  11. General Theory of the Rotation of the Non-rigid Earth at the Second Order. I. The Rigid Model in Andoyer Variables

    Science.gov (United States)

    Getino, J.; Escapa, A.; Miguel, D.

    2010-05-01

    This paper is the first part of an investigation where we will present an analytical general theory of the rotation of the non-rigid Earth at the second order, which considers the effects of the interaction of the rotation of the Earth with itself, also named as the spin-spin coupling. Here, and as a necessary step in the development of that theory, we derive complete, explicit, analytical formulae of the rigid Earth rotation that account for the second-order rotation-rotation interaction. These expressions are not provided in this form by any current rigid Earth model. Working within the Hamiltonian framework established by Kinoshita, we study the second-order effects arising from the interaction of the main term in the Earth geopotential expansion with itself, and with the complementary term arising when referring the rotational motion to the moving ecliptic. To this aim, we apply a canonical perturbation method to solve analytically the canonical equations at the second order, determining the expressions that provide the nutation-precession, the polar motion, and the length of day. In the case of the motion of the equatorial plane, nutation-precession, we compare our general approach with the particular study for this motion developed by Souchay et al., showing the existence of new terms whose numerical values are within the truncation level of 0.1 μas adopted by those authors. These terms emerge as a consequence of not assuming in this work the same restrictive simplifications taken by Souchay et al. The importance of these additional contributions is that, as the analytical formulae show, they depend on the Earth model considered, in such a way that the fluid core resonance could amplify them significatively when extending this theory to the non-rigid Earth models.

  12. Client Proteins and Small Molecule Inhibitors Display Distinct Binding Preferences for Constitutive and Stress-Induced HSP90 Isoforms and Their Conformationally Restricted Mutants.

    Directory of Open Access Journals (Sweden)

    Thomas L Prince

    Full Text Available The two cytosolic/nuclear isoforms of the molecular chaperone HSP90, stress-inducible HSP90α and constitutively expressed HSP90β, fold, assemble and maintain the three-dimensional structure of numerous client proteins. Because many HSP90 clients are important in cancer, several HSP90 inhibitors have been evaluated in the clinic. However, little is known concerning possible unique isoform or conformational preferences of either individual HSP90 clients or inhibitors. In this report, we compare the relative interaction strength of both HSP90α and HSP90β with the transcription factors HSF1 and HIF1α, the kinases ERBB2 and MET, the E3-ubiquitin ligases KEAP1 and RHOBTB2, and the HSP90 inhibitors geldanamycin and ganetespib. We observed unexpected differences in relative client and drug preferences for the two HSP90 isoforms, with HSP90α binding each client protein with greater apparent affinity compared to HSP90β, while HSP90β bound each inhibitor with greater relative interaction strength compared to HSP90α. Stable HSP90 interaction was associated with reduced client activity. Using a defined set of HSP90 conformational mutants, we found that some clients interact strongly with a single, ATP-stabilized HSP90 conformation, only transiently populated during the dynamic HSP90 chaperone cycle, while other clients interact equally with multiple HSP90 conformations. These data suggest different functional requirements among HSP90 clientele that, for some clients, are likely to be ATP-independent. Lastly, the two inhibitors examined, although sharing the same binding site, were differentially able to access distinct HSP90 conformational states.

  13. 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.

  14. The influence of non-rigid anatomy and patient positioning on endoscopy-CT image registration in the head and neck.

    Science.gov (United States)

    Ingram, W Scott; Yang, Jinzhong; Wendt, Richard; Beadle, Beth M; Rao, Arvind; Wang, Xin A; Court, Laurence E

    2017-08-01

    To assess the influence of non-rigid anatomy and differences in patient positioning between CT acquisition and endoscopic examination on endoscopy-CT image registration in the head and neck. Radiotherapy planning CTs and 31-35 daily treatment-room CTs were acquired for nineteen patients. Diagnostic CTs were acquired for thirteen of the patients. The surfaces of the airways were segmented on all scans and triangular meshes were created to render virtual endoscopic images with a calibrated pinhole model of an endoscope. The virtual images were used to take projective measurements throughout the meshes, with reference measurements defined as those taken on the planning CTs and test measurements defined as those taken on the daily or diagnostic CTs. The influence of non-rigid anatomy was quantified by 3D distance errors between reference and test measurements on the daily CTs, and the influence of patient positioning was quantified by 3D distance errors between reference and test measurements on the diagnostic CTs. The daily CT measurements were also used to investigate the influences of camera-to-surface distance, surface angle, and the interval of time between scans. Average errors in the daily CTs were 0.36 ± 0.61 cm in the nasal cavity, 0.58 ± 0.83 cm in the naso- and oropharynx, and 0.47 ± 0.73 cm in the hypopharynx and larynx. Average errors in the diagnostic CTs in those regions were 0.52 ± 0.69 cm, 0.65 ± 0.84 cm, and 0.69 ± 0.90 cm, respectively. All CTs had errors heavily skewed towards 0, albeit with large outliers. Large camera-to-surface distances were found to increase the errors, but the angle at which the camera viewed the surface had no effect. The errors in the Day 1 and Day 15 CTs were found to be significantly smaller than those in the Day 30 CTs (P muscle motion. The errors are larger when the interval of time between CT acquisitions is longer, which suggests that the interval of time between the CT acquisition and the

  15. Acute high-grade acromioclavicular joint injuries treatment: Arthroscopic non-rigid coracoclavicular fixation provides better quality of life outcomes than hook plate ORIF.

    Science.gov (United States)

    Natera-Cisneros, L; Sarasquete-Reiriz, J; Escolà-Benet, A; Rodriguez-Miralles, J

    2016-02-01

    Treatment of acute high-grade acromioclavicular joint (ACJ) injuries with metal hardware alters the biomechanics of the ACJ, implying a second surgery for hardware removal. The period during which the plate is present involves functional limitations, pain and a risk factor for the development of hardware-related-injuries. Arthroscopy-assisted procedures compared to open-metal hardware techniques offer: less morbidity, the possibility to treat associated lesions and no need for a second operation. The aim was to compare the Quality of life (QoL) of patients with acute high-grade ACJ injuries (Rockwood grade III-V), managed arthroscopically with a non-rigid coracoclavicular (CC) fixation versus the QoL of patients managed with a hook plate, 24 months or more after their shoulder injury. A retrospective revision of high-grade ACJ injuries managed in three institutions was performed. Patients treated by means of an arthroscopy-assisted CC fixation or by means of a hook plate were included. The inclusion period was between 2008 and 2012. The QoL was evaluated at the last follow-up visit by means of the SF36, the visual analog scale (VAS), the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire, the Constant score and the global satisfaction (scale from 0 to 10). The presence of scapular dyskinesis and remaining vertical instability were evaluated. Comparison between groups was performed. Thirty-one patients were included: 20 arthroscopy-group (ARTH group: 3 Rockwood III, 3 IV and 14 V) and 11 hook plate-group (HOOK group: 5 Rockwood III and 6 V). The mean age was 36 [25-52] year-old for the ARTH group and 41 [19-55] for the HOOK group (P=0.185). The mean results of the questionnaires were: (1) physical SF36 score (ARTH group 58.24±2.16 and HOOK group 53.70±4.33, Pgrade ACJ injuries managed arthroscopically with a non-rigid CC fixation seem to have a better QoL than patients managed with a hook plate. Level IV therapeutic; retrospective comparative study

  16. Cardiovascular magnetic resonance myocardial feature tracking using a non-rigid, elastic image registration algorithm: assessment of variability in a real-life clinical setting.

    Science.gov (United States)

    Morais, Pedro; Marchi, Alberto; Bogaert, Julie A; Dresselaers, Tom; Heyde, Brecht; D'hooge, Jan; Bogaert, Jan

    2017-02-17

    Cardiovascular magnetic resonance myocardial feature tracking (CMR-FT) is a promising technique for quantification of myocardial strain from steady-state free precession (SSFP) cine images. We sought to determine the variability of CMR-FT using a non-rigid elastic registration algorithm recently available in a commercial software package (Segment, Medviso) in a real-life clinical setting. Firstly, we studied the variability in a healthy volunteer who underwent 10 CMR studies over five consecutive days. Secondly, 10 patients were selected from our CMR database yielding normal findings (normal group). Finally, we prospectively studied 10 patients with known or suspected myocardial pathology referred for further investigation to CMR (patient group). In the patient group a second study was performed respecting an interval of 30 min between studies. All studies were manually segmented at the end-diastolic phase by three observers. In all subjects left ventricular (LV) circumferential and radial strain were calculated in the short-axis direction (EccSAX and ErrSAX, respectively) and longitudinal strain in the long-axis direction (EllLAX). The level of CMR experience of the observers was 2 weeks, 6 months and >20 years. Mean contouring time was 7 ± 1 min, mean FT calculation time 13 ± 2 min. Intra- and inter-observer variability was good to excellent with an coefficient of reproducibility (CR) ranging 1.6% to 11.5%, and 1.7% to 16.0%, respectively and an intraclass correlation coefficient (ICC) ranging 0.89 to 1.00 and 0.74 to 0.99, respectively. Variability considerably increased in the test-retest setting with a CR ranging 4.2% to 29.1% and an ICC ranging 0.66 to 0.95 in the patient group. Variability was not influenced by level of expertise of the observers. Neither did the presence of myocardial pathology at CMR negatively impact variability. However, compared to global myocardial strain, segmental myocardial strain variability increased with a factor

  17. Structure of the HIV-1 Full-Length Capsid Protein in a Conformationally Trapped Unassembled State Induced by Small-Molecule Binding

    Energy Technology Data Exchange (ETDEWEB)

    Du, Shoucheng; Betts, Laurie; Yang, Ruifeng; Shi, Haibin; Concel, Jason; Ahn, Jinwoo; Aiken, Christopher; Zhang, Peijun; Yeh, Joanne I. (Pitt); (Vanderbilt); (UNC)

    2012-11-26

    The capsid (CA) protein plays crucial roles in HIV infection and replication, essential to viral maturation. The absence of high-resolution structural data on unassembled CA hinders the development of antivirals effective in inhibiting assembly. Unlike enzymes that have targetable, functional substrate-binding sites, the CA does not have a known site that affects catalytic or other innate activity, which can be more readily targeted in drug development efforts. We report the crystal structure of the HIV-1 CA, revealing the domain organization in the context of the wild-type full-length (FL) unassembled CA. The FL CA adopts an antiparallel dimer configuration, exhibiting a domain organization sterically incompatible with capsid assembly. A small compound, generated in situ during crystallization, is bound tightly at a hinge site ('H site'), indicating that binding at this interdomain region stabilizes the ADP conformation. Electron microscopy studies on nascent crystals reveal both dimeric and hexameric lattices coexisting within a single condition, in agreement with the interconvertibility of oligomeric forms and supporting the feasibility of promoting assembly-incompetent dimeric states. Solution characterization in the presence of the H-site ligand shows predominantly unassembled dimeric CA, even under conditions that promote assembly. Our structure elucidation of the HIV-1 FL CA and characterization of a potential allosteric binding site provides three-dimensional views of an assembly-defective conformation, a state targeted in, and thus directly relevant to, inhibitor development. Based on our findings, we propose an unprecedented means of preventing CA assembly, by 'conformationally trapping' CA in assembly-incompetent conformational states induced by H-site binding.

  18. Combined use of a priori data for fast system self-calibration of a non-rigid multi-camera fringe projection system

    Science.gov (United States)

    Stavroulakis, Petros I.; Chen, Shuxiao; Sims-Waterhouse, Danny; Piano, Samanta; Southon, Nicholas; Bointon, Patrick; Leach, Richard

    2017-06-01

    In non-rigid fringe projection 3D measurement systems, where either the camera or projector setup can change significantly between measurements or the object needs to be tracked, self-calibration has to be carried out frequently to keep the measurements accurate1. In fringe projection systems, it is common to use methods developed initially for photogrammetry for the calibration of the camera(s) in the system in terms of extrinsic and intrinsic parameters. To calibrate the projector(s) an extra correspondence between a pre-calibrated camera and an image created by the projector is performed. These recalibration steps are usually time consuming and involve the measurement of calibrated patterns on planes, before the actual object can continue to be measured after a motion of a camera or projector has been introduced in the setup and hence do not facilitate fast 3D measurement of objects when frequent experimental setup changes are necessary. By employing and combining a priori information via inverse rendering, on-board sensors, deep learning and leveraging a graphics processor unit (GPU), we assess a fine camera pose estimation method which is based on optimising the rendering of a model of a scene and the object to match the view from the camera. We find that the success of this calibration pipeline can be greatly improved by using adequate a priori information from the aforementioned sources.

  19. 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...

  20. Effect of conformational propensity of peptide antigens in their interaction with MHC class II molecules. Failure to document the importance of regular secondary structures

    DEFF Research Database (Denmark)

    Sette, A; Lamont, A; Buus, S

    1989-01-01

    for its IAd binding capacity was analyzed. In most instances these substitutions had little or no effect, suggesting that neither alpha-helical nor beta-sheet regular structures may be strictly required for productive interaction with MHC molecules. Some of the same substitutions were also found to have...

  1. Management of seating posture of children with cerebral palsy by using thoracic-lumbar-sacral orthosis with non-rigid SIDO frame.

    Science.gov (United States)

    Vekerdy, Zsuzsanna

    2007-09-30

    To investigate the effects of a special seating device: Thoracic-lumbar-sacral orthosis with non-rigid SIDO frame (TLSO-SIDO) in non-ambulant children with cerebral palsy. A prospective study with matched pairs (the same subject pre- and post-intervention) was carried out. A comparison of the lateral view of thoracic-lumbar spine X-ray before and after TLSO-SIDO application was made. The assessment of changes in daily activities, posture was recorded by questionnaires. A total of 47 children with cerebral palsy at a mean age of 53.2 months +/- 30.1 SD were involved in the study; 15 (35.71%) of the 42 children showed significant problems in feeding at the beginning of the study period, they were identified as a special subgroup with feeding difficulties. The mean pre-TLSO-SIDO thoracic kyphosis was 53.7 +/- 16.2 in Cobb angle, while the post-TLSO-SIDO thoracic kyphosis was 47.2 +/- 12.1. The lumbar lordosis was 21.3 +/- 13 and in the TLSO-SIDO 17.8 +/- 11.9. The majority of the children have shown improvement in the feeding items and in posture (trunk, head and extremities). The overall satisfaction of the parents with the TLSO-SIDO was very good, namely 3.972 +/- 0.796 on the 5-point analogue scale. We did not find a direct correlation with the improvement in the separate items and the overall satisfaction. It is extremely difficult to measure the effect of the postural management on the development of children with cerebral palsy. According to the results of the study, regular application of the TLSO-SIDO in children with spastic cerebral palsy had a beneficial effect on feeding problems and on posture.

  2. Creation of 3D digital anthropomorphic phantoms which model actual patient non-rigid body motion as determined from MRI and position tracking studies of volunteers

    Science.gov (United States)

    Connolly, C. M.; Konik, A.; Dasari, P. K. R.; Segars, P.; Zheng, S.; Johnson, K. L.; Dey, J.; King, M. A.

    2011-03-01

    Patient motion can cause artifacts, which can lead to difficulty in interpretation. The purpose of this study is to create 3D digital anthropomorphic phantoms which model the location of the structures of the chest and upper abdomen of human volunteers undergoing a series of clinically relevant motions. The 3D anatomy is modeled using the XCAT phantom and based on MRI studies. The NURBS surfaces of the XCAT are interactively adapted to fit the MRI studies. A detailed XCAT phantom is first developed from an EKG triggered Navigator acquisition composed of sagittal slices with a 3 x 3 x 3 mm voxel dimension. Rigid body motion states are then acquired at breath-hold as sagittal slices partially covering the thorax, centered on the heart, with 9 mm gaps between them. For non-rigid body motion requiring greater sampling, modified Navigator sequences covering the entire thorax with 3 mm gaps between slices are obtained. The structures of the initial XCAT are then adapted to fit these different motion states. Simultaneous to MRI imaging the positions of multiple reflective markers on stretchy bands about the volunteer's chest and abdomen are optically tracked in 3D via stereo imaging. These phantoms with combined position tracking will be used to investigate both imaging-data-driven and motion-tracking strategies to estimate and correct for patient motion. Our initial application will be to cardiacperfusion SPECT imaging where the XCAT phantoms will be used to create patient activity and attenuation distributions for each volunteer with corresponding motion tracking data from the markers on the body-surface. Monte Carlo methods will then be used to simulate SPECT acquisitions, which will be used to evaluate various motion estimation and correction strategies.

  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. Potential mesogens based on pyridine derivatives: The geometric structure, conformational properties and characteristics of intermolecular hydrogen bonds

    Science.gov (United States)

    Fedorov, Mikhail S.; Giricheva, Nina I.; Shpilevaya, Kseniya E.; Lapykina, Elena A.; Syrbu, Svetlana A.

    2017-03-01

    Conformational properties of the main part (excluding sbnd OC3H7 radicals) of the p-n-propyloxybenzoic (A1) and p-n-propyloxycinnamic (A2) acids molecules (relating to mesomorphic compounds) as well as p-n-propyloxybenzoic acid pyridine ester (B1) and p-n-propyloxyphenylazopyridine (B2) molecules (relating to non-mesomorphic compounds) were studied by DFT(B3LYP)/cc-pVTZ method. It was shown that the main parts of A1 and A2 acids are rigid. The barrier to internal rotation of pyridine fragment in the B1 and B2 molecules depends on the nature of the bridging group. It was determined that all studied A1⋯B1, A2⋯B1 and A2⋯B2 complexes are characterized by a strong hydrogen bond. The binding energy of complexes (≈14 kcal/mol, with BSSE corrections, DFT(B97D)/6-311++G**) exceeds the energy per hydrogen bond in the corresponding acid dimers (≈10 kcal/mol). The structural non-rigidity of A⋯B complexes is mainly caused by possibility of sbnd OC3H7 radicals internal rotation and A and B molecules rotation about the (H)O⋯N line. The characteristics of intermolecular hydrogen bonds were determined by NBO-analysis. The obtained results indicate that examined complexes correspond to the basic requirements to mesogen molecular forms. The thermodynamic functions of the gas-phase complexation reactions (idealized model of the complexes formation in the condensed state) were calculated. Preliminary studies of mesogen-non-mesogen A1⋯B2 system by differential scanning calorimetry and polarizing optical microscopy, showed that it has mesomorphic properties.

  5. 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.

  6. Diffuse Oceanic Plate Boundaries, Plate Non-Rigidity, True Polar Wander, and Motion Between Hotspots: Results From Investigations of Marine Magnetic Anomalies

    Science.gov (United States)

    Gordon, R. G.

    2009-05-01

    Marine magnetic anomalies due to seafloor spreading record reversals of Earth's magnetic field and the orientation of the paleomagnetic field. They can be used to make precise estimates of relative plate motion and of the apparent polar wander of oceanic plates. In this talk I will present the results of several studies that include analyses of marine magnetic anomalies. A new set of geologically current relative plate angular velocities, termed MORVEL, has been determined in part from 1696 rates of seafloor spreading estimated from marine magnetic anomalies (DeMets, Gordon, & Argus 2009). The MORVEL set of angular velocities supersede those of NUVEL-1A (DeMets et al. 1994). A new feature of MORVEL is the assumed existence of many diffuse oceanic plate boundaries, such as that between the Indian and Capricorn plates. An important result from MORVEL is that several plate circuits fail closure, that is, the relative plate angular velocities summed around the circuit differ significantly from zero as would be expected if all the plates are rigid. Thus, it appears that at least some plates are not rigid. The most dramatic example of plate circuit non-closure is for the Pacific-Nazca-Cocos plate circuit, which encloses the Galapagos triple junction and fails to close by a stunning 14 ± 5 mm/yr (95% confidence limits). Part of the observed non-rigidity is likely due to predictable horizontal thermal contraction as oceanic lithosphere cools and subsides (Kumar & Gordon 2009). I will present simple illustrations of the velocity field within a plate expected from horizontal thermal contraction and speculate on how it may relate to observed plate circuit non-closures. The shapes of magnetic anomalies due to seafloor spreading contain valuable information about the location of the paleomagnetic pole, especially for the Pacific plate for which oriented rock samples are scarce. Particularly useful are Pacific-Farallon magnetic anomaly crossings near the paleo-equator. I use

  7. 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.

  8. 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.

  9. 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.

  10. An explicit-solvent conformation search method using open software

    Directory of Open Access Journals (Sweden)

    Kari Gaalswyk

    2016-05-01

    Full Text Available Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules α-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different.

  11. Application of Conformational Space Search in Drug Action | Adikwu ...

    African Journals Online (AJOL)

    The role of conformational space in drug action is presented. Two examples of molecules in different therapeutic groups are presented. Conformational space search will lead to isolating the exact conformation with the desired medicinal properties. Many conformations of a plant isolate may exist which are active, weakly ...

  12. Dose reconstruction technique using non-rigid registration to evaluate spatial correspondence between high-dose region and late radiation toxicity: a case of tracheobronchial stenosis after external beam radiotherapy combined with endotracheal brachytherapy for tracheal cancer

    Directory of Open Access Journals (Sweden)

    Kazuma Kobayashi

    2016-04-01

    Full Text Available Purpose : Small organ subvolume irradiated by a high-dose has been emphasized to be associated with late complication after radiotherapy. Here, we demonstrate a potential use of surface-based, non-rigid registration to investigate how high-dose volume topographically correlates with the location of late radiation morbidity in a case of tracheobronchial radiation stenosis. Material and methods: An algorithm of point set registration was implemented to handle non-rigid registration between contour points on the organ surfaces. The framework estimated the global correspondence between the dose distribution and the varying anatomical structure. We applied it to an 80-year-old man who developed tracheobronchial stenosis 2 years after high-dose-rate endobronchial brachytherapy (HDR-EBT (24 Gy in 6 Gy fractions and external beam radiotherapy (EBRT (40 Gy in 2 Gy fractions for early-stage tracheal cancer. Results and conclusions : Based on the transformation function computed by the non-rigid registration, irradiated dose distribution was reconstructed on the surface of post-treatment tracheobronchial stenosis. For expressing the equivalent dose in a fractional dose of 2 Gy in HDR-EBT, α/β of linear quadratic model was assumed as 3 Gy for the tracheal bronchus. The tracheobronchial surface irradiated by more than 100 Gy3 tended to develop severe stenosis, which attributed to a more than 50% decrease in the luminal area. The proposed dose reconstruction technique can be a powerful tool to predict late radiation toxicity with spatial consideration.

  13. Structural selection by microsolvation: Conformational locking of tryptamine

    NARCIS (Netherlands)

    Schmitt, M.; Bohm, M.; Ratzer, C.; Vu, C.; Kalkman, L.; Meerts, W.L.

    2005-01-01

    The conformational space of tryptamine has been thoroughly investigated using rotationally resolved laser-induced fluorescence spectroscopy. Six conformers could be identified on the basis of the inertial parameters of several deuterated isotopomers. Upon attaching a single water molecule, the

  14. Passing Current through Touching Molecules

    DEFF Research Database (Denmark)

    Schull, G.; Frederiksen, Thomas; Brandbyge, Mads

    2009-01-01

    The charge flow from a single C-60 molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two...

  15. Imaging of conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Michl, Josef [Univ. of Colorado, Boulder, CO (United States)

    2016-03-13

    Control of intramolecular conformational change in a small number of molecules or even a single one by an application of an outside electric field defined by potentials on nearby metal or dielectric surfaces has potential applications in both 3-D and 2-D nanotechnology. Specifically, the synthesis, characterization, and understanding of designed solids with controlled built-in internal rotational motion of a dipole promises a new class of materials with intrinsic dielectric, ferroelectric, optical and optoelectronic properties not found in nature. Controlled rotational motion is of great interest due to its expected utility in phenomena as diverse as transport, current flow in molecular junctions, diffusion in microfluidic channels, and rotary motion in molecular machines. A direct time-resolved observation of the dynamics of motion on ps or ns time scale in a single molecule would be highly interesting but is also very difficult and has yet to be accomplished. Much can be learned from an easier but still challenging comparison of directly observed initial and final orientational states of a single molecule, which is the basis of this project. The project also impacts the understanding of surface-enhanced Raman spectroscopy (SERS) and single-molecule spectroscopic detection, as well as the synthesis of solid-state materials with tailored properties from designed precursors.

  16. Electrons in Molecules

    Indian Academy of Sciences (India)

    etc.) as well as explain the variations in bond lengths, bond angles, conformational angles, barriers to internal rotation! inversion, stretching!bending force constants, etc. However, when a molecule is quite large, with many occupied MOs, it is not advisable to bypass the actual computation of forces. As another application of ...

  17. Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition.

    Directory of Open Access Journals (Sweden)

    Yonatan Savir

    Full Text Available To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.

  18. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

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

  19. Free fructose is conformationally locked.

    Science.gov (United States)

    Cocinero, Emilio J; Lesarri, Alberto; Écija, Patricia; Cimas, Álvaro; Davis, Benjamin G; Basterretxea, Francisco J; Fernández, José A; Castaño, Fernando

    2013-02-20

    Fructose has been examined under isolation conditions using a combination of UV ultrafast laser vaporization and Fourier-transform microwave (FT-MW) spectroscopy. The rotational spectra for the parent, all (six) monosubstituted (13)C species, and two single D species reveal unambiguously that the free hexoketose is conformationally locked in a single dominant β-pyranose structure. This six-membered-chair skeleton adopts a (2)C(5) configuration (equivalent to (1)C(4) in aldoses). The free-molecule structure sharply contrasts with the furanose form observed in biochemically relevant polysaccharides, like sucrose. The structure of free fructose has been determined experimentally using substitution and effective structures. The enhanced stability of the observed conformation is primarily attributed to a cooperative network of five intramolecular O-H···O hydrogen bonds and stabilization of both endo and exo anomeric effects. Breaking a single intramolecular hydrogen bond destabilizes the free molecule by more than 10 kJ mol(-1). The structural results are compared to ribose, recently examined with rotational resolution, where six different conformations coexist with similar conformational energies. In addition, several DFT and ab initio methods and basis sets are benchmarked with the experimental data.

  20. Probing RNA native conformational ensembles with structural constraints

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; van den Bedem, Henry; Bernauer, Julie

    2016-01-01

    substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined...... by distance constraints in the tertiary structure. The dimensionality reduction enables efficient exploration of conformational space. We show that the conformational distributions obtained with our method broadly sample the conformational landscape observed in NMR experiments. Compared to normal mode...

  1. Reporter molecules as probes of DNA conformation: structure of a crystalline complex containing 2-methyl-4-nitro-aniline ethylene dimethylammonium hydrobromide - 5-iodocytidylyl(3'-5')guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Vyas, N.K.; Nyas, M.N.; Jain, S.C.; Sobell, H.M.

    1984-05-31

    2-Methyl-4-nitroaniline ethylene dimethylammonium hydrobromide forms a crystalline complex with the self-complementary dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine. The crystals are tetragonal, with a = b = 32.192 A and c = 23.964 A, space group P4/sub 3/2/sub 1/2. The structure has been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least squares. 5-Iodocytidylyl(3'-5')guanosine molecules are held together in pairs through Watson-Crick base-pairing, forming an antiparallel duplex structure. Nitroaniline molecules stack above and below guanine-cytosine pairs in this duplex structure. In addition, a third nitroaniline molecule stacks on one of the other two nitroaniline molecules. The asymmetric unit contains two 5-iodocytidylyl(3'-5')guanosine molecules, three nitroaniline molecules, one bromide ion and thirty-one water molecules, at total of 160 atoms. Details of the structure are described. 15 references, 4 figures, 2 tables.

  2. On conformally related -waves

    Indian Academy of Sciences (India)

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

  3. Augmented reality for non-rigid surfaces

    OpenAIRE

    Pilet, Julien

    2008-01-01

    Augmented Reality (AR) is the process of integrating virtual elements in reality, often by mixing computer graphics into a live video stream of a real scene. It requires registration of the target object with respect to the cameras. To this end, some approaches rely on dedicated hardware, such as magnetic trackers or infra-red cameras, but they are too expensive and cumbersome to reach a large public. Others are based on specifically designed markers which usually look like bar-codes. However...

  4. Brownian Warps for Non-Rigid Registration

    DEFF Research Database (Denmark)

    Nielsen, Mads; Johansen, Peter; Jackson, Andrew D.

    2008-01-01

    A Brownian motion model in the group of diffeomorphisms has been introduced as inducing a least committed prior on warps. This prior is source-destination symmetric, fulfills a natural semi-group property for warps, and with probability 1 creates invertible warps. Using this as a least committed...

  5. Single molecule logical devices.

    Science.gov (United States)

    Renaud, Nicolas; Hliwa, Mohamed; Joachim, Christian

    2012-01-01

    After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit.

  6. 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....

  7. PubChem3D: Similar conformers

    Directory of Open Access Journals (Sweden)

    Bolton Evan E

    2011-05-01

    Full Text Available Abstract Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features. Results The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST of 0.8 or greater and a color Tanimoto (CT of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds" for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs, despite limited PubChem 2-D similarity. In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average

  8. 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.

  9. Molecule nanoweaver

    Science.gov (United States)

    Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  10. Molecule Matters

    Indian Academy of Sciences (India)

    Fluorescence usually originates from the lowest excited electronic state (singlet) irrespective of the excitation and hence, the fluorescence spectrum of a molecule is characterized by a single band. However, what makes DMABN a very special molecule is that it exhibits dual fluorescence (i.e. emission of. Molecule Matters.

  11. Patterns and conformations in molecularly thin films

    Science.gov (United States)

    Basnet, Prem B.

    Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn

  12. Oligomerization-induced conformational change in the C-terminal region of Nel-like molecule 1 (NELL1) protein is necessary for the efficient mediation of murine MC3T3-E1 cell adhesion and spreading.

    Science.gov (United States)

    Nakamura, Yoko; Hasebe, Ai; Takahashi, Kaneyoshi; Iijima, Masumi; Yoshimoto, Nobuo; Maturana, Andrés D; Ting, Kang; Kuroda, Shun'ichi; Niimi, Tomoaki

    2014-04-04

    NELL1 is a large oligomeric secretory glycoprotein that functions as an osteoinductive factor. NELL1 contains several conserved domains, has structural similarities to thrombospondin 1, and supports osteoblastic cell adhesion through integrins. To define the structural requirements for NELL1-mediated cell adhesion, we prepared a series of recombinant NELL1 proteins (intact, deleted, and cysteine-mutant) from a mammalian expression system and tested their activities. A deletion analysis demonstrated that the C-terminal cysteine-rich region of NELL1 is critical for the cell adhesion activity of NELL1. Reducing agent treatment decreased the cell adhesion activity of full-length NELL1 but not of its C-terminal fragments, suggesting that the intramolecular disulfide bonds within this region are not functionally necessary but that other disulfide linkages in the N-terminal region of NELL1 may be involved in cell adhesion activity. By replacing cysteine residues with serines around the coiled-coil domain of NELL1, which is responsible for oligomerization, we created a mutant NELL1 protein that was unable to form homo-oligomers, and this monomeric mutant showed substantially lower cell adhesion activity than intact NELL1. These results suggest that an oligomerization-induced conformational change in the C-terminal region of NELL1 is important for the efficient mediation of cell adhesion and spreading by NELL1.

  13. Oligomerization-induced Conformational Change in the C-terminal Region of Nel-like Molecule 1 (NELL1) Protein Is Necessary for the Efficient Mediation of Murine MC3T3-E1 Cell Adhesion and Spreading*

    Science.gov (United States)

    Nakamura, Yoko; Hasebe, Ai; Takahashi, Kaneyoshi; Iijima, Masumi; Yoshimoto, Nobuo; Maturana, Andrés D.; Ting, Kang; Kuroda, Shun'ichi; Niimi, Tomoaki

    2014-01-01

    NELL1 is a large oligomeric secretory glycoprotein that functions as an osteoinductive factor. NELL1 contains several conserved domains, has structural similarities to thrombospondin 1, and supports osteoblastic cell adhesion through integrins. To define the structural requirements for NELL1-mediated cell adhesion, we prepared a series of recombinant NELL1 proteins (intact, deleted, and cysteine-mutant) from a mammalian expression system and tested their activities. A deletion analysis demonstrated that the C-terminal cysteine-rich region of NELL1 is critical for the cell adhesion activity of NELL1. Reducing agent treatment decreased the cell adhesion activity of full-length NELL1 but not of its C-terminal fragments, suggesting that the intramolecular disulfide bonds within this region are not functionally necessary but that other disulfide linkages in the N-terminal region of NELL1 may be involved in cell adhesion activity. By replacing cysteine residues with serines around the coiled-coil domain of NELL1, which is responsible for oligomerization, we created a mutant NELL1 protein that was unable to form homo-oligomers, and this monomeric mutant showed substantially lower cell adhesion activity than intact NELL1. These results suggest that an oligomerization-induced conformational change in the C-terminal region of NELL1 is important for the efficient mediation of cell adhesion and spreading by NELL1. PMID:24563467

  14. Conformational Study of Dibenzyl Ether

    Science.gov (United States)

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

    2017-06-01

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

  15. Conformal Carroll groups

    OpenAIRE

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

    2014-01-01

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

  16. Molecule Matters

    Indian Academy of Sciences (India)

    is such an innocuous molecule that you might not think it worthy of special attention. We take this molecule for granted because it is abundantly available on earth. About 80 % of the earth's atmosphere, which means a total of 4×1018 kg, is dinitrogen![1] Secondly, it is ignored because it is quite un- reactive. Nitrogen is such ...

  17. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

  18. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Trandum, Christa; Larsen, Nanna Brink

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (Tm) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal alpha-helix was of major importance to the conformational stability of calreticulin....

  19. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C.S.; Trandum, C.; Larsen, N.

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

  20. Single molecule detection, thermal fluctuation and life

    Science.gov (United States)

    YANAGIDA, Toshio; ISHII, Yoshiharu

    2017-01-01

    Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines. PMID:28190869

  1. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

    Directory of Open Access Journals (Sweden)

    Li Honglin

    2009-03-01

    Full Text Available Abstract Background Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. Results The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105–112. Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 Å to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 ± 0.18 seconds per molecule renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. Conclusion On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms

  2. Atkins' molecules

    CERN Document Server

    Atkins, Peters

    2003-01-01

    Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

  3. Interstellar Molecules

    Science.gov (United States)

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  4. Enumerating molecules.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  5. Single Molecule Studies on Dynamics in Liquid Crystals

    OpenAIRE

    Daniela Täuber; Christian von Borczyskowski

    2013-01-01

    Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization...

  6. Focused conformational sampling in proteins

    Science.gov (United States)

    Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

    2017-11-01

    A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

  7. Effects of conformational distributions on sigma profiles in COSMO theories.

    Science.gov (United States)

    Wang, Shu; Stubbs, John M; Siepmann, J Ilja; Sandler, Stanley I

    2005-12-15

    The charge density or sigma profile of a solute molecule is an essential component in COSMO (conductor-like screen model) based solvation theories, and its generation depends on the molecular conformation used. The usual procedure is to determine the conformation of an isolated molecule, and assume that this is unchanged when the molecule is placed in solution. In this paper, the conformations of 1-hexanol and 2-methoxy-ethanol in both the liquid and vapor phases obtained from Gibbs ensemble simulation and from an isolated-molecule quantum DFT optimization are used to determine the effect of realistic conformation differences on COSMO-based properties predictions. In particular, the vapor pressure at the normal boiling temperature and the binary mixture VLE (vapor-liquid equilibrium) predictions obtained using different conformations are investigated. The results show that the sigma profile for 1-hexanol varies only slightly using the different conformations, while the sigma profile of 2-methoxy-ethanol shows a significant difference between the liquid and vapor phases. Consequently, the vapor pressure predictions for 1-hexanol are similar regardless of the manner in which the conformation population was obtained, while there is a larger difference for 2-methoxy-ethanol depending on whether the liquid or vapor conformations from simulation or the DFT-optimized structure is used. These differences in predictions are seen to be largely due to differences in the ideal solvation energy term. In mixture VLE calculations involving 1-hexanol, we again see that there is little difference in the phase equilibrium predictions among the different conformations, while for the mixture with 2-methoxy-ethanol, the differences in the sigma profiles lead to a more noticeable, though not significant, difference in the phase equilibrium predictions.

  8. Conformal expansions and renormalons

    CERN Document Server

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

    2001-01-01

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

  9. Conformal expansions and renormalons

    CERN Document Server

    Gardi, E; Gardi, Einan; Grunberg, Georges

    2001-01-01

    The large-order behaviour of QCD is dominated by renormalons. On the other hand renormalons do not occur in conformal theories, such as the one describing the infrared fixed-point of QCD at small beta_0 (the Banks--Zaks limit). Since the fixed-point has a perturbative realization, all-order perturbative relations exist between the conformal coefficients, which are renormalon-free, and the standard perturbative coefficients, which contain renormalons. Therefore, an explicit cancellation of renormalons should occur in these relations. The absence of renormalons in the conformal limit can thus be seen as a constraint on the structure of the QCD perturbative expansion. We show that the conformal constraint is non-trivial: a generic model for the large-order behaviour violates it. We also analyse a specific example, based on a renormalon-type integral over the two-loop running-coupling, where the required cancellation does occur.

  10. Redox-Dependent Conformational Switching of Diphenylacetylenes

    Directory of Open Access Journals (Sweden)

    Ian M. Jones

    2014-07-01

    Full Text Available Herein we describe the design and synthesis of a redox-dependent single-molecule switch. Appending a ferrocene unit to a diphenylacetylene scaffold gives a redox-sensitive handle, which undergoes reversible one-electron oxidation, as demonstrated by cyclic voltammetry analysis. 1H-NMR spectroscopy of the partially oxidized switch and control compounds suggests that oxidation to the ferrocenium cation induces a change in hydrogen bonding interactions that results in a conformational switch.

  11. Group Size and Conformity

    OpenAIRE

    Bond, Rod

    2005-01-01

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

  12. 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.

  13. Quantum massive conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    Faria, F.F. [Universidade Estadual do Piaui, Centro de Ciencias da Natureza, Teresina, PI (Brazil)

    2016-04-15

    We first find the linear approximation of the second plus fourth order derivative massive conformal gravity action. Then we reduce the linearized action to separated second order derivative terms, which allows us to quantize the theory by using the standard first order canonical quantization method. It is shown that quantum massive conformal gravity is renormalizable but has ghost states. A possible decoupling of these ghost states at high energies is discussed. (orig.)

  14. Delineating the conformal window

    DEFF Research Database (Denmark)

    Frandsen, Mads Toudal; Pickup, Thomas; Teper, Michael

    2011-01-01

    We identify and characterise the conformal window in gauge theories relevant for beyond the standard model building, e.g. Technicolour, using the criteria of metric confinement and causal analytic couplings, which are known to be consistent with the phase diagram of supersymmetric QCD from Seiberg...... duality. Using these criteria we find perturbation theory to be consistent throughout the predicted conformal window for several of these gauge theories and we discuss recent lattice results in the light of our findings....

  15. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 9. Molecule Matters - A Chromium Compound with a Quintuple Bond. K C Kumara Swamy. Feature Article Volume 11 Issue 9 September 2006 pp 72-75. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 5. Molecule Matters - N-Heterocyclic Carbenes - The Stable Form of R2 C: Anil J Elias. Feature Article Volume 13 Issue 5 May 2008 pp 456-467. Fulltext. Click here to view fulltext PDF. Permanent link:

  17. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 11. Molecule Matters - Carbon Dioxide: Molecular States and Beyond. T P Radhakrishnan. Feature Article Volume 11 Issue 11 November 2006 pp 88-92. Fulltext. Click here to view fulltext PDF. Permanent link:

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

    Science.gov (United States)

    Ishioka, Tsutomu; Kiritani, Atsushi; Kojima, Takuya

    2007-04-01

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

  19. Conformal invariance of curvature perturbation

    CERN Document Server

    Gong, Jinn-Ouk; Park, Wan Il; Sasaki, Misao; Song, Yong-Seon

    2011-01-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the delta N formalism, and show its conformal invariance.

  20. Conformal invariance of curvature perturbation

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Jinn-Ouk [Theory Division, CERN, CH-1211 Genève 23 (Switzerland); Hwang, Jai-chan [Department of Astronomy and Atmospheric Sciences, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Park, Wan Il; Sasaki, Misao; Song, Yong-Seon, E-mail: jinn-ouk.gong@cern.ch, E-mail: jchan@knu.ac.kr, E-mail: wipark@kias.re.kr, E-mail: misao@yukawa.kyoto-u.ac.jp, E-mail: ysong@kias.re.kr [Korea Institute for Advanced Study, Seoul 130-722 (Korea, Republic of)

    2011-09-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the δN formalism, and show its conformal invariance.

  1. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We...... show that the reduced free energy changes sign, at the second, fifth and sixth order in the coupling, when decreasing the number of flavors from the upper end of the conformal window. If the change in sign is interpreted as signal of an instability of the system then we infer a critical number...... of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i...

  2. 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.

  3. Dynamics of DNA conformations and DNA-protein interaction

    DEFF Research Database (Denmark)

    Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

    2005-01-01

    Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturat......Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...

  4. Galilean conformal and superconformal symmetries

    Energy Technology Data Exchange (ETDEWEB)

    Lukierski, J., E-mail: lukier@ift.uni.wroc.pl [University of Wroclaw, Institute for Theoretical Physics (Poland)

    2012-10-15

    Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

  5. NMR studies of dynamic biomolecular conformational ensembles.

    Science.gov (United States)

    Torchia, Dennis A

    2015-02-01

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

  6. Fast, clash-free RNA conformational morphing using molecular junctions.

    Science.gov (United States)

    Héliou, Amélie; Budday, Dominik; Fonseca, Rasmus; van den Bedem, Henry

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online.

  7. The conformational musings of a medicinal chemist.

    Science.gov (United States)

    Finch, Harry

    2014-03-01

    Structure-based drug design strategies based on X-ray crystallographic data of ligands bound to biological targets or computationally derived pharmacophore models have been introduced over the past 25 years or so. These have now matured and are deeply embedded in the drug discovery process in most pharmaceutical and biotechnology companies where they continue to play a major part in the discovery of new medicines and drug candidates. Newly developed NMR methods can now provide a full description of the conformations in which ligands exist in free solution, crucially allowing those that are dominant to be identified. Integrating experimentally determined conformational information on active and inactive molecules in drug discovery programmes, alongside the existing techniques, should have a major impact on the success of drug discovery. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Conformational biosensor for diagnosis of prion diseases.

    Science.gov (United States)

    Tcherkasskaya, Olga; Davidson, Eugene A; Schmerr, Mary Jo; Orser, Cindy S

    2005-05-01

    A fluorescence technology to monitor the proliferation of amyloidogenic neurological disorders is proposed. A crude brain homogenate (0.01%) from animals infected with a transmissible spongiform encephalopathy is employed as a catalytic medium initiating conformational changes in 520 nM polypeptide biosensors (Tris/trifluoroethanol 50% mixture at pH 7). The fluorescence methods utilize pyrene residues covalently attached to the peptide ends. The coil-to-beta-strand transitions in biosensor molecules cause elevation of a distinct fluorescence band of the pyrene aggregates (i.e. excimers). This approach enables the detection of infectious prion proteins at fmol, does not require antibody binding or protease treatment. Technology might be adopted for diagnosing a large variety of conformational disorders as well as for generic high-throughput screening of the amyloidogenic potential in plasma.

  9. Transportation Conformity Training and Presentations

    Science.gov (United States)

    EPA's OTAQ has provided multiple conformity training sessions in the past to assist state and local governments in implementing conformity requirements. As training information is prepared for other venues, it will be posted on this page.

  10. Dynamical spacetimes in conformal gravity

    National Research Council Canada - National Science Library

    Hongsheng Zhang; Yi Zhang; Xin-Zhou Li

    2017-01-01

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

  11. Multiscale conformal pattern transfer

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  12. Multiscale conformal pattern transfer.

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-22

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  13. Conformal boundaries of warped products

    DEFF Research Database (Denmark)

    Kokkendorff, Simon Lyngby

    2006-01-01

    In this note we prove a result on how to determine the conformal boundary of a type of warped product of two length spaces in terms of the individual conformal boundaries. In the situation, that we treat, the warping and conformal distortion functions are functions of distance to a base point....... The result is applied to produce examples of CAT(0)-spaces, where the conformal and ideal boundaries differ in interesting ways....

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

    CERN Document Server

    Yvernay, Pierre

    2015-01-01

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

  15. Polymer Conformation under Confinement

    Directory of Open Access Journals (Sweden)

    Stavros Bollas

    2017-02-01

    Full Text Available The conformation of polymer chains under confinement is investigated in intercalated polymer/layered silicate nanocomposites. Hydrophilic poly(ethylene oxide/sodium montmorillonite, PEO/Na+-MMT, hybrids were prepared utilizing melt intercalation with compositions where the polymer chains are mostly within the ~1 nm galleries of the inorganic material. The polymer chains are completely amorphous in all compositions even at temperatures where the bulk polymer is highly crystalline. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR is utilized to investigate the conformation of the polymer chains over a broad range of temperatures from below to much higher than the bulk polymer melting temperature. A systematic increase of the gauche conformation relatively to the trans is found with decreasing polymer content both for the C–C and the C–O bonds that exist along the PEO backbone indicating that the severe confinement and the proximity to the inorganic surfaces results in a more disordered state of the polymer.

  16. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

  17. Experimental determination of rotational constants of low-lying vibrational levels in the 0g- pure long-range state of ultracold Cs2 molecule

    Science.gov (United States)

    Wu, Jizhou; Liu, Wenliang; Li, Yuqing; Ma, Jie; Xiao, Liantuan; Jia, Suotang

    2017-04-01

    We report an accurate experimental determination of rotational constants of the lowest vibrational levels in the purely long-range state of ultracold cesium molecules (Cs2). We engineer a precise reference of the frequency difference through double photoassociation spectroscopy (PAS). The PAS for the lowest vibrational levels, v=0-3, has been obtained with an enhanced sensitivity and accuracy, according to which the binding energies have been corrected. As deduced from the reference, the frequency intervals between neighboring rotational levels are fitted to a non-rigid rotor model, thus the rotational constants are precisely obtained. The experimental results show good agreement with theoretical expectations.

  18. Single Molecule Studies on Dynamics in Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Daniela Täuber

    2013-09-01

    Full Text Available Single molecule (SM methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC. Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC.

  19. Specific chemical reactivities of spatially separated 3-aminophenol conformers with cold Ca+ ions.

    Science.gov (United States)

    Chang, Yuan-Pin; Długołęcki, Karol; Küpper, Jochen; Rösch, Daniel; Wild, Dieter; Willitsch, Stefan

    2013-10-04

    Many molecules exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chemical reactions has proven challenging. We have probed the reactivity of specific conformers by using an experimental technique based on their spatial separation in a molecular beam by electrostatic deflection. The separated conformers react with a target of Coulomb-crystallized ions in a trap. In the reaction of Ca(+) with 3-aminophenol, we find a twofold larger rate constant for the cis compared with the trans conformer (differentiated by the O-H bond orientation). This result is explained by conformer-specific differences in the long-range ion-molecule interaction potentials. Our approach demonstrates the possibility of controlling reactivity through selection of conformational states.

  20. Conformal Janus on Euclidean sphere

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-07

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

  1. Factor Va alternative conformation reconstruction using atomic force microscopy.

    Science.gov (United States)

    Chaves, R C; Dahmane, S; Odorico, M; Nicolaes, G A F; Pellequer, J-L

    2014-12-01

    Protein conformational variability (or dynamics) for large macromolecules and its implication for their biological function attracts more and more attention. Collective motions of domains increase the ability of a protein to bind to partner molecules. Using atomic force microscopy (AFM) topographic images, it is possible to take snapshots of large multi-component macromolecules at the single molecule level and to reconstruct complete molecular conformations. Here, we report the application of a reconstruction protocol, named AFM-assembly, to characterise the conformational variability of the two C domains of human coagulation factor Va (FVa). Using AFM topographic surfaces obtained in liquid environment, it is shown that the angle between C1 and C2 domains of FVa can vary between 40° and 166°. Such dynamical variation in C1 and C2 domain arrangement may have important implications regarding the binding of FVa to phospholipid membranes.

  2. Is DNA a nonlinear dynamical system where solitary conformational ...

    Indian Academy of Sciences (India)

    Unknown

    In recent years, many investigators dealing with large- amplitude internal motions in DNA have come to the con- clusion that the molecule can be considered as a nonlinear dynamical system where solitary conformational waves can be excited. Do these waves really exist in DNA? Or is this only an example of an incorrect ...

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

    Science.gov (United States)

    Yi, Taeil; Wang, Qian; Lichter, Seth

    2012-10-30

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

  4. Observations on the Influence of Precursor Conformations on Macrocyclization Reactions

    DEFF Research Database (Denmark)

    Hammershøj, Peter; Beldring, Klavs; Nielsen, Anders R.

    2016-01-01

    macrocyclization to afford a mixture of diastereomeric sulfites, subjection of the other precursor to identical reaction conditions resulted in the isolation of the linear dichloride. We hypothesize that there is a difference in the ability of the two molecules to adopt a conformation that is germane...

  5. Second-order nonlinear optical properties of the four tetranitrotetrapropoxycalix[4]arene conformers

    NARCIS (Netherlands)

    Kenis, Paul J.A.; Kenis, P.J.A.; Noordman, Oscar F.J.; Noordman, O.F.J.; Houbrechts, Stephan; van Hummel, G.J.; Harkema, Sybolt; van Veggel, F.C.J.M.; Clays, Koen; Engbersen, Johannes F.J.; Persoons, Andre; van Hulst, N.F.; Reinhoudt, David

    1998-01-01

    This paper reports a systematic experimental and theoretical study of the second-order nonlinear optical properties of multichromophoric molecules that range from dipolar symmetry to three-dimensional octupolar symmetry. The four possible conformers of tetranitrotetrapropoxycalix[4]arene (cone,

  6. Cosmological Perturbations in Conformal Gravity

    CERN Document Server

    Mannheim, Philip D

    2011-01-01

    We present the first steps needed for an analysis of the perturbations that occur in the cosmology associated with the conformal gravity theory. We discuss the implications of conformal invariance for perturbative coordinate gauge choices, and show that in the conformal theory the trace of the metric fluctuation kinematically decouples from the first-order gravitational fluctuation equations. We determine the equations that describe first-order metric fluctuations around the illustrative conformally flat de Sitter background. Via a conformal transformation we show that such fluctuations can be constructed from fluctuations around a flat background, even though the fluctuations themselves are associated with a perturbative geometry that is not itself conformal to flat. We extend the analysis to fluctuations around other cosmologically relevant backgrounds, such as the conformally-flat Robertson-Walker background, and find tensor fluctuations that grow far more rapidly than those that occur in the analogous sta...

  7. WIZARD: AI in conformational analysis

    Science.gov (United States)

    Dolata, Daniel P.; Leach, Andrew R.; Prout, Keith

    1987-04-01

    A program which utilizes the techniques of Artificial Intelligence and Expert Systems to solve problems in the area of Conformational Analysis is described. The program searches conformational space in a systematic fashion, based on the technique known as heuristic state-space search. The program proceeds by recognizing conformational units, assigning one or more conformational templates to each unit, and joining them to form conformational suggestions. These suggestions are criticized to discover logical inconsistencies, and any resulting stresses are resolved. The resulting conformational suggestions are sometimes accurate enough for immediate use, or may be further refined by a numerical program. The latter combination is shown to be quite efficient compared to purely numerical conformational search techniques.

  8. In silico Exploration of the Conformational Universe of GPCRs.

    Science.gov (United States)

    Rodríguez-Espigares, Ismael; Kaczor, Agnieszka A; Selent, Jana

    2016-07-01

    The structural plasticity of G protein coupled receptors (GPCRs) leads to a conformational universe going from inactive to active receptor states with several intermediate states. Many of them have not been captured yet and their role for GPCR activation is not well understood. The study of this conformational space and the transition dynamics between different receptor populations is a major challenge in molecular biophysics. The rational design of effector molecules that target such receptor populations allows fine-tuning receptor signalling with higher specificity to produce drugs with safer therapeutic profiles. In this minireview, we outline highly conserved receptor regions which are considered determinant for the establishment of distinct receptor states. We then discuss in-silico approaches such as dimensionality reduction methods and Markov State Models to explore the GPCR conformational universe and exploit the obtained conformations through structure-based drug design. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    NARCIS (Netherlands)

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

    2013-01-01

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

  10. Conformance and Deviance

    DEFF Research Database (Denmark)

    Gjerdrum Pedersen, Esben Rahbek; Neergaard, Peter; Thusgaard Pedersen, Janni

    2013-01-01

    This paper analyses how large Danish companies are responding to new governmental regulation which requires them to report on corporate social responsibility (CSR). The paper is based on an analysis of 142 company annual reports required by the new Danish regulation regarding CSR reporting, plus ...... in CSR reporting practices. Finally, it is argued that non-conformance with the new regulatory requirements is not solely about conscious resistance but may also be caused by, for example, lack of awareness, resource limitations, misinterpretations, and practical difficulties....

  11. Reversible switching of ultrastrong light-molecule coupling

    DEFF Research Database (Denmark)

    Schwartz, T; Hutchison, J A; Genet, C

    2011-01-01

    We demonstrate that photochromic molecules enable switching from the weak- to ultrastrong-coupling regime reversibly, by using all-optical control. This switch is achieved by photochemically inducing conformational changes in the molecule. Remarkably, a Rabi splitting of 700 meV is measured at room...

  12. Periodic systems of N-atom molecules

    Science.gov (United States)

    Hefferlin, R. A.; Zhuvikin, G. V.; Caviness, K. E.; Duerksen, P. J.

    1984-10-01

    The atoms have long been classified into a periodic system, which is now based on quantum mechanics and group theory. A classification of molecules containing any number (N) of atoms is proposed. It is an extension of the periodic system of the atoms. The approach in this paper is that of group theory, although the proposed system has been subjected to exhaustive comparison with experimental and ab initio computational results for diatomic molecules, and conforms to the commonly known behaviors of molecules with larger N. Orthonormal transformations are performed so that the molecules can be arranged according to their numbers of electrons and to the differences of atomic numbers of the constituent atoms. These arrangements parallel the physical reality of atomic bonding and permit partial three-dimensional models of the systems to be constructed for molecules with as many as four atoms.

  13. Supergravitational conformal Galileons

    Science.gov (United States)

    Deen, Rehan; Ovrut, Burt

    2017-08-01

    The worldvolume actions of 3+1 dimensional bosonic branes embedded in a five-dimensional bulk space can lead to important effective field theories, such as the DBI conformal Galileons, and may, when the Null Energy Condition is violated, play an essential role in cosmological theories of the early universe. These include Galileon Genesis and "bouncing" cosmology, where a pre-Big Bang contracting phase bounces smoothly to the presently observed expanding universe. Perhaps the most natural arena for such branes to arise is within the context of superstring and M -theory vacua. Here, not only are branes required for the consistency of the theory, but, in many cases, the exact spectrum of particle physics occurs at low energy. However, such theories have the additional constraint that they must be N = 1 supersymmetric. This motivates us to compute the worldvolume actions of N = 1 supersymmetric three-branes, first in flat superspace and then to generalize them to N = 1 supergravitation. In this paper, for simplicity, we begin the process, not within the context of a superstring vacuum but, rather, for the conformal Galileons arising on a co-dimension one brane embedded in a maximally symmetric AdS 5 bulk space. We proceed to N = 1 supersymmetrize the associated worldvolume theory and then generalize the results to N = 1 supergravity, opening the door to possible new cosmological scenarios

  14. Conformal Methods in General Relativity

    Science.gov (United States)

    Valiente Kroon, Juan A.

    2016-07-01

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

  15. Tracing conformational changes in proteins

    OpenAIRE

    Haspel, Nurit; Moll, Mark; Baker, Matthew L; Chiu, Wah; Kavraki, Lydia E.

    2010-01-01

    Background Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions. Results In this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grain...

  16. Conformal Fermi Coordinates

    CERN Document Server

    Dai, Liang; Schmidt, Fabian

    2015-01-01

    Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable ef...

  17. Reflections on conformal spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyungrok; Kravchuk, Petr [Walter Burke Institute for Theoretical Physics, Caltech,Pasadena, California 91125 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, New Jersey 08540 (United States); Ooguri, Hirosi [Walter Burke Institute for Theoretical Physics, Caltech,Pasadena, California 91125 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, New Jersey 08540 (United States); Kavli Institute for the Physics and Mathematics of the Universe (WPI),University of Tokyo,Kashiwa 277-8583 (Japan)

    2016-04-29

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ{sub 0} of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ{sub 0} as well as for large Δ{sub 0}. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function.

  18. Conformal (In)Equality

    Science.gov (United States)

    Hyun, Young-Hwan; Kim, Yoonbai; Lee, Seokcheon

    2018-01-01

    The current accelerating expansion of the Universe is explained either by dark energy or by modified gravity theories. Both of them can explain exactly the same background evolution of the Universe, however this degeneracy may be broken when the observation of large scale structure formation is taken into account. Two observables are parameterized by the so-called dark energy equation of state, ω and the growth index parameter, γ. From these observed parameters, one may reconstruct the model parameters of the so-called scalar-tensor gravity theory, one of the modified gravity theories. Especially, the scalar-tensor gravity theory is described both in Jordan frame and in Einstein frame. If cosmological observations are interpreted in one frame, then all of the observables should also be interpreted in that frame. This explicitly shows conformal inequality of cosmological observables.

  19. Conformal (InEquality

    Directory of Open Access Journals (Sweden)

    Hyun Young-Hwan

    2018-01-01

    Full Text Available The current accelerating expansion of the Universe is explained either by dark energy or by modified gravity theories. Both of them can explain exactly the same background evolution of the Universe, however this degeneracy may be broken when the observation of large scale structure formation is taken into account. Two observables are parameterized by the so-called dark energy equation of state, ω and the growth index parameter, γ. From these observed parameters, one may reconstruct the model parameters of the so-called scalar-tensor gravity theory, one of the modified gravity theories. Especially, the scalar-tensor gravity theory is described both in Jordan frame and in Einstein frame. If cosmological observations are interpreted in one frame, then all of the observables should also be interpreted in that frame. This explicitly shows conformal inequality of cosmological observables.

  20. Reflections on Conformal Spectra

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ0 of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ0 as well as for large Δ0. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function. (based on 1510.08772 with Kim & Ooguri). This seminar will be given via videolink

  1. Conformational behavior of insect pheromones and analogues. Part II

    Science.gov (United States)

    Koča, Jaroslav; Carlsen, Per H. J.

    1992-04-01

    The conformational potential energy surface paths of the sex pheromone, Ipsenol, to the Bark Beetle, Ips typographus, and of a series of analogues have been elucidated using the program DAISY. The following structures were calculated: 2-methyl-6-methylene-7-octen-4-ol (Ipsenol, ( II)), 2-methyl-6-methylene-2,7-octadiene-4-ol acetate ( III), 2-methyl-6-methylene-3,7-octadien-2-ol ( IV), 2-methyl-6-methylene-1,7-octadien-3-ol ( V), 5-(3-furanyl)-2-methyl-1-penten-3-ol ( VI) and 1-(3-furanyl)-4-methyl-3-penten-2-ol ( VII). As a measure of the conformational flexibility of the molecules the flexibility coefficients, f, were determined. The f values for the molecules were determined to be: II, 0.145; III, 0.144; IV, 1.240; V, 0.133; VI, 0.825; and VII, 0.451. The molecular mechanics method was used for energy calculations in conjunction with DAISY. Low-energy conformations (conformational channels) together with energy barriers for conformational changes are presented.

  2. Conformational flexibility of a rotaxane thread probed by electronic spectroscopy in helium nanodroplets.

    Science.gov (United States)

    Smolarek, Szymon; Rijs, Anouk M; Hannam, Jeffrey S; Leigh, David A; Drabbels, Marcel; Buma, Wybren J

    2009-09-16

    Ultrahigh-resolution spectroscopic studies have been performed to elucidate the conformational landscape of the succinamide-based thread 1 that is frequently employed in mechanically interlocked molecular assemblies. We show how dissolving single molecules into a helium nanodroplet enables us to resolve the broad absorption spectrum--which is normally observed--into the separate contributions of individual conformers that are populated under the employed experimental conditions. Excellent agreement is obtained with the results of molecular dynamics calculations. The absorption spectrum of each conformer reveals a splitting of the zero-phonon resonance that is different for each conformer and could thus serve as a spectral signature.

  3. 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.

  4. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast.

    Science.gov (United States)

    Belton, Jon-Matthew; Dekker, Job

    2015-06-01

    Chromosome conformation capture carbon copy (5C) is a high-throughput method for detecting ligation products of interest in a chromosome conformation capture (3C) library. 5C uses ligation-mediated amplification (LMA) to generate carbon copies of 3C ligation product junctions using single-stranded oligonucleotide probes. This procedure produces a 5C library of short DNA molecules which represent the interactions between the corresponding restriction fragments. The 5C library can be amplified using universal primers containing the Illumina paired-end adaptor sequences for subsequent high-throughput sequencing. © 2015 Cold Spring Harbor Laboratory Press.

  5. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

  6. t-SNARE protein conformations patterned by the lipid microenvironment.

    Science.gov (United States)

    Rickman, Colin; Medine, Claire N; Dun, Alison R; Moulton, David J; Mandula, Ondrej; Halemani, Nagaraj D; Rizzoli, Silvio O; Chamberlain, Luke H; Duncan, Rory R

    2010-04-30

    The spatial distribution of the target (t-)SNARE proteins (syntaxin and SNAP-25) on the plasma membrane has been extensively characterized. However, the protein conformations and interactions of the two t-SNAREs in situ remain poorly defined. By using super-resolution optical techniques and fluorescence lifetime imaging microscopy, we observed that within the t-SNARE clusters syntaxin and SNAP-25 molecules interact, forming two distinct conformations of the t-SNARE binary intermediate. These are spatially segregated on the plasma membrane with each cluster exhibiting predominantly one of the two conformations, representing the two- and three-helical forms previously observed in vitro. We sought to explain why these two t-SNARE intermediate conformations exist in spatially distinct clusters on the plasma membrane. By disrupting plasma membrane lipid order, we found that all of the t-SNARE clusters now adopted a single conformational state corresponding to the three helical t-SNARE intermediates. Together, our results define spatially distinct t-SNARE intermediate states on the plasma membrane and how the conformation adopted can be patterned by the underlying lipid environment.

  7. t-SNARE Protein Conformations Patterned by the Lipid Microenvironment*

    Science.gov (United States)

    Rickman, Colin; Medine, Claire N.; Dun, Alison R.; Moulton, David J.; Mandula, Ondřej; Halemani, Nagaraj D.; Rizzoli, Silvio O.; Chamberlain, Luke H.; Duncan, Rory R.

    2010-01-01

    The spatial distribution of the target (t-)SNARE proteins (syntaxin and SNAP-25) on the plasma membrane has been extensively characterized. However, the protein conformations and interactions of the two t-SNAREs in situ remain poorly defined. By using super-resolution optical techniques and fluorescence lifetime imaging microscopy, we observed that within the t-SNARE clusters syntaxin and SNAP-25 molecules interact, forming two distinct conformations of the t-SNARE binary intermediate. These are spatially segregated on the plasma membrane with each cluster exhibiting predominantly one of the two conformations, representing the two- and three-helical forms previously observed in vitro. We sought to explain why these two t-SNARE intermediate conformations exist in spatially distinct clusters on the plasma membrane. By disrupting plasma membrane lipid order, we found that all of the t-SNARE clusters now adopted a single conformational state corresponding to the three helical t-SNARE intermediates. Together, our results define spatially distinct t-SNARE intermediate states on the plasma membrane and how the conformation adopted can be patterned by the underlying lipid environment. PMID:20093362

  8. Movement of elongation factor G between compact and extended conformations.

    Science.gov (United States)

    Salsi, Enea; Farah, Elie; Netter, Zoe; Dann, Jillian; Ermolenko, Dmitri N

    2015-01-30

    Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer. Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pretranslocation ribosomes or with posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to but likely precedes both GTP hydrolysis and mRNA/tRNA translocation. Copyright © 2014. Published by Elsevier Ltd.

  9. Movement of Elongation Factor G between Compact and Extended Conformations

    Science.gov (United States)

    Salsi, Enea; Farah, Elie; Netter, Zoe; Dann, Jillian; Ermolenko, Dmitri N.

    2014-01-01

    Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer (smFRET). Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pre- or posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to, but likely precedes both GTP hydrolysis and mRNA/tRNA translocation. PMID:25463439

  10. Recent advancements in conformal gravity

    Science.gov (United States)

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

    2017-05-01

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

  11. Counselor Identity: Conformity or Distinction?

    Science.gov (United States)

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  12. Microtubule's conformational cap

    DEFF Research Database (Denmark)

    Chretien, D.; Janosi, I.; Taveau, J.C.

    1999-01-01

    The molecular mechanisms that allow elongation of the unstable microtubule lattice remain unclear. It is usually thought that the GDP-liganded tubulin lattice is capped by a small layer of GTP- or GDP-P(i)-liganded molecules, the so called "GTP-cap". Here, we point-out that the elastic properties...... of the microtubule lattice cause a difference in stability between the elongating tubulin sheet and the completed microtubule wall. The implications of our observations for microtubule structure and dynamics are discussed....

  13. Recursion Relations for Conformal Blocks

    CERN Document Server

    Penedones, João; Yamazaki, Masahito

    2016-09-12

    In the context of conformal field theories in general space-time dimension, we find all the possible singularities of the conformal blocks as functions of the scaling dimension $\\Delta$ of the exchanged operator. In particular, we argue, using representation theory of parabolic Verma modules, that in odd spacetime dimension the singularities are only simple poles. We discuss how to use this information to write recursion relations that determine the conformal blocks. We first recover the recursion relation introduced in 1307.6856 for conformal blocks of external scalar operators. We then generalize this recursion relation for the conformal blocks associated to the four point function of three scalar and one vector operator. Finally we specialize to the case in which the vector operator is a conserved current.

  14. Conformal solids and holography

    Science.gov (United States)

    Esposito, A.; Garcia-Saenz, S.; Nicolis, A.; Penco, R.

    2017-12-01

    We argue that a SO( d) magnetic monopole in an asymptotically AdS space-time is dual to a d-dimensional strongly coupled system in a solid state. In light of this, it would be remiss of us not to dub such a field configuration solidon. In the presence of mixed boundary conditions, a solidon spontaneously breaks translations (among many other symmetries) and gives rise to Goldstone excitations on the boundary — the phonons of the solid. We derive the quadratic action for the boundary phonons in the probe limit and show that, when the mixed boundary conditions preserve conformal symmetry, the longitudinal and transverse sound speeds are related to each other as expected from effective field theory arguments. We then include backreaction and calculate the free energy of the solidon for a particular choice of mixed boundary conditions, corresponding to a relevant multi-trace deformation of the boundary theory. We find such free energy to be lower than that of thermal AdS. This suggests that our solidon undergoes a solid-to-liquid first order phase transition by melting into a Schwarzschild-AdS black hole as the temperature is raised.

  15. Non-rigid consistent registration of 2D image sequences

    Energy Technology Data Exchange (ETDEWEB)

    Arganda-Carreras, I; Sorzano, C O S; Marabini, R; Carazo, J M [Biocomputing Unit, National Centre for Biotechnology, CSIC, Darwin 3, Universidad Autonoma de Madrid, 28049 Madrid (Spain); Thevenaz, P [Biomedical Imaging Group, Ecole polytechnique federale de Lausanne (EPFL) (Switzerland); Munoz-Barrutia, A; Ortiz-de Solorzano, C [Cancer Imaging Laboratory, Centre for Applied Medical Research, University of Navarra, Pamplona (Spain); Kybic, J, E-mail: iarganda@cnb.csic.e [Center for Machine Perception, Czech Technical University, Prague (Czech Republic)

    2010-10-21

    We present a novel algorithm for the registration of 2D image sequences that combines the principles of multiresolution B-spline-based elastic registration and those of bidirectional consistent registration. In our method, consecutive triples of images are iteratively registered to gradually extend the information through the set of images of the entire sequence. The intermediate results are reused for the registration of the following triple. We choose to interpolate the images and model the deformation fields using B-spline multiresolution pyramids. Novel boundary conditions are introduced to better characterize the deformations at the boundaries. In the experimental section, we quantitatively show that our method recovers from barrel/pincushion and fish-eye deformations with subpixel error. Moreover, it is more robust against outliers-occasional strong noise and large rotations-than the state-of-the-art methods. Finally, we show that our method can be used to realign series of histological serial sections, which are often heavily distorted due to folding and tearing of the tissues.

  16. Non-rigid consistent registration of 2D image sequences

    Science.gov (United States)

    Arganda-Carreras, I.; Sorzano, C. O. S.; Thévenaz, P.; Muñoz-Barrutia, A.; Kybic, J.; Marabini, R.; Carazo, J. M.; Ortiz-de Solorzano, C.

    2010-10-01

    We present a novel algorithm for the registration of 2D image sequences that combines the principles of multiresolution B-spline-based elastic registration and those of bidirectional consistent registration. In our method, consecutive triples of images are iteratively registered to gradually extend the information through the set of images of the entire sequence. The intermediate results are reused for the registration of the following triple. We choose to interpolate the images and model the deformation fields using B-spline multiresolution pyramids. Novel boundary conditions are introduced to better characterize the deformations at the boundaries. In the experimental section, we quantitatively show that our method recovers from barrel/pincushion and fish-eye deformations with subpixel error. Moreover, it is more robust against outliers—occasional strong noise and large rotations—than the state-of-the-art methods. Finally, we show that our method can be used to realign series of histological serial sections, which are often heavily distorted due to folding and tearing of the tissues.

  17. Coherent control of the motion of complex molecules and the coupling to internal state dynamics.

    Science.gov (United States)

    Venn, Paul; Ulbricht, Hendrik

    2011-01-01

    We discuss coherent control of the centre of mass motion of complex molecules by de Broglie interferometry. We describe an experiment to couple the dynamics of internal state population of complex molecules to their centre of mass motion. We discuss how this can be used to probe state population and transition, especially the photo-switching of flourinated di-azobenzene molecules between their cis- and trans-configuration. We propose an experiment to photo-isomerise complex di-azobenzene molecules in the gas-phase, including the selective detection of molecules in different conformations. In addition we discuss possible ways of optimising the conformation detection through cooling, and optical techiques.

  18. Locally conformal symplectic manifolds

    Directory of Open Access Journals (Sweden)

    Izu Vaisman

    1985-01-01

    Full Text Available A locally conformal symplectic (l. c. s. manifold is a pair (M2n,Ω where M2n(n>1 is a connected differentiable manifold, and Ω a nondegenerate 2-form on M such that M=⋃αUα (Uα- open subsets. Ω/Uα=eσαΩα, σα:Uα→ℝ, dΩα=0. Equivalently, dΩ=ω∧Ω for some closed 1-form ω. L. c. s. manifolds can be seen as generalized phase spaces of Hamiltonian dynamical systems since the form of the Hamilton equations is, in fact, preserved by homothetic canonical transformations. The paper discusses first Hamiltonian vector fields, and infinitesimal automorphisms (i. a. on l. c. s. manifolds. If (M,Ω has an i. a. X such that ω(X≠0, we say that M is of the first kind and Ω assumes the particular form Ω=dθ−ω∧θ. Such an M is a 2-contact manifold with the structure forms (ω,θ, and it has a vertical 2-dimensional foliation V. If V is regular, we can give a fibration theorem which shows that M is a T2-principal bundle over a symplectic manifold. Particularly, V is regular for some homogeneous l. c. s, manifolds, and this leads to a general construction of compact homogeneous l. c. s, manifolds. Various related geometric results, including reductivity theorems for Lie algebras of i. a. are also given. Most of the proofs are adaptations of corresponding proofs in symplectic and contact geometry. The paper ends with an Appendix which states an analogous fibration theorem in Riemannian geometry.

  19. Conformational analysis and vibrational spectroscopic studies on dapsone

    Science.gov (United States)

    Ildiz, Gulce Ogruc; Akyuz, Sevim

    2012-11-01

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

  20. Programmed Switching of Single Polymer Conformation on DNA Origami

    DEFF Research Database (Denmark)

    Krissanaprasit, Abhichart; Madsen, Mikael; Knudsen, Jakob Bach

    2016-01-01

    DNA nanotechnology offers precise geometrical control of the positioning of materials, and it is increasingly also being used in the development of nanomechanical devices. Here we describe the development of a nanomechanical device that allows switching of the position of a single...... successively. This controlled nanomechanical switching of conjugated organic polymer conformation demonstrates unique control of the shape of a single polymer molecule, and it may constitute a new component for the development of reconfigurable nanophotonic and nanoelectronic devices.......) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold...

  1. Conformational cooling dynamics in matrix-isolated 1,3-butanediol.

    Science.gov (United States)

    Rosado, Mário T S; Jesus, António J Lopes; Reva, Igor D; Fausto, Rui; Redinha, José S

    2009-07-02

    The complete conformational space of monomeric 1,3-butanediol has been characterized theoretically, and 73 unique stable conformers were found at the MP2/6-311++G(d,p) level. These were classified into nine families whose members share the same heavy atom backbone configurations and differ in the hydrogen atom orientations. The first and third most populated backbone families are governed by the formation of an intramolecular hydrogen bond; however, the second precludes this type of interaction and was frequently overlooked in previous studies. Its stability is determined by the relatively high entropy of its main conformers. The hydrogen bonding of four of the most important conformers was characterized by means of atoms in molecules (AIM, also known as QTAIM) and natural bond orbital (NBO) analyses. Using appropriate isodesmic reactions, hydrogen bonding energy stabilizations of 12-14 kJ mol(-1) have been found. Experimentally, monomeric molecules of 1,3-butanediol were isolated in low-temperature inert matrixes, and their infrared spectra were analyzed from the viewpoint of the conformational distribution. All the relevant transition states for the conformational interconversion reaction paths were characterized at the same level of theory to interpret the conformational cooling dynamics observed in the low-temperature matrixes. The energy barriers for rotation of the OH groups were calculated to be very low (conformers. Further increase in the substrate temperature (up to 40 K, Xe matrix) resulted in conformational cooling where the medium-height barriers (approximately 13 kJ mol(-1)) could be surmounted and all conformational population converted to the ground conformational state. Remarkably, this state turned to consist of two forms of the most stable hydrogen bonded family, which were predicted by calculations to be accidentally degenerated and were found in the annealed matrix in equal amounts. All of these experimentally observed conformational cooling

  2. [Generics: similarities, bioequivalence but no conformity].

    Science.gov (United States)

    Even-Adin, D; De Muylder, J A; Sternon, J

    2002-01-01

    The using of generic forms (GF) is presented as a potential source of budgetary "saving of money" in the field of pharmaceutical expenses. Not frequently prescribed in Belgium, they win a new interest thanks to the recent making use of the "reference repayment". Sale's authorization of GF is controlled by european rules, but some questions about their identity to original medications remain. Do similarities based only upon qualitative and quantitative composition in active molecules, pharmaceutical forms and biodisponibility give us all requested guaranties? Several cases of discordances can appear; the major elements of non conformity are the nature of excipients, notice's contents and the value of biodisponibility studies. However, in term of economy, in the drug market, development of GF appears to constitute an unavoidable phenomenon.

  3. Water Evaporation and Conformational Changes from Partially Solvated Ubiquitin

    Directory of Open Access Journals (Sweden)

    Saravana Prakash Thirumuruganandham

    2010-01-01

    Full Text Available Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes are monitored by studying a variety of intermediate partially solvated ubiquitin structures. We find that ubiquitin shrinks with decreasing hydration shell and exposes more of its hydrophilic surface area to the surrounding.

  4. 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

  5. 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.

  6. Steady states in conformal theories

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    A novel conjecture regarding the steady state behavior of conformal field theories placed between two heat baths will be presented. Some verification of the conjecture will be provided in the context of fluid dynamics and holography.

  7. Conformity Adequacy Review: Region 5

    Science.gov (United States)

    Resources are for air quality and transportation government and community leaders. Information on the conformity SIP adequacy/inadequacy of state implementation plans (SIPs) in EPA Region 5 (IL, IN, MI, OH, WI) is provided here.

  8. Falsification of Mannheim's conformal gravity

    CERN Document Server

    Yoon, Youngsub

    2013-01-01

    We show that Mannheim's conformal gravity, whose potential has a term proportional to $1/r$ and another term proportional to $r$, doesn't reduce to Newtonian gravity at short distances. Therefore, despite the claim that it successfully explains galaxy rotation curves, it seems falsified by numerous Cavendish-type experiments performed at laboratories on Earth whose work haven't found any deviations from Newton's theory. Moreover, when Mannheim used his potential to fit the galaxy rotation curve, he used the Newtonian formula to calculate the effects of the term proportional to $1/r$, not the conformal gravity one. So, he lacked consistency. After all, he would not have been able to use the conformal gravity one either since it deviates so much from the Newtonian one, which the conformal gravity one should reduce to. We also give a couple of other similar reasons why Mannheim's conformal gravity is wrong. For example, the gravitational potential of conformal gravity doesn't reduce to the Newtonian one even in ...

  9. Dynamic water patterns change the stability of the collapsed filter conformation of the KcsA K+ channel

    OpenAIRE

    Di Wu

    2017-01-01

    The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA ...

  10. Novel Applications of Buffer-gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules

    Science.gov (United States)

    Drayna, Garrett Korda

    Cold gases of atoms and molecules provide a system for the exploration of a diverse set of physical phenomena. For example, cold gasses of magnetically and electrically polar atoms and molecules are ideal systems for quantum simulation and quantum computation experiments, and cold gasses of large polar molecules allow for novel spectroscopic techniques. Buffer-gas cooling is a robust and widely applicable method for cooling atoms and molecules to temperatures of approximately 1 Kelvin. In this thesis, I present novel applications of buffer-gas cooling to obtaining gases of trapped, ultracold atoms and diatomic molecules, as well as the study of the cooling of large organic molecules. In the first experiment of this thesis, a buffer-gas beam source of atoms is used to directly load a magneto-optical trap. Due to the versatility of the buffer-gas beam source, we obtain trapped, sub-milliKelvin gases of four different lanthanide species using the same experimental apparatus. In the second experiment of this thesis, a buffer-gas beam is used as the initial stage of an experiment to directly laser cool and magneto-optically trap the diatomic molecule CaF. In the third experiment of this thesis, buffer-gas cooling is used to study the cooling of the conformational state of large organic molecules. We directly observe conformational relaxation of gas-phase 1,2-propanediol due to cold collisions with helium gas. Lastly, I present preliminary results on a variety of novel applications of buffer-gas cooling, such as mixture analysis, separation of chiral mixtures, the measurement of parity-violation in chiral molecules, and the cooling and spectroscopy of highly unstable reaction intermediates.

  11. CONFORMANCE IMPROVEMENT USING GELS

    Energy Technology Data Exchange (ETDEWEB)

    Randall S. Seright

    2003-09-01

    This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the

  12. CONFORMANCE IMPROVEMENT USING GELS

    Energy Technology Data Exchange (ETDEWEB)

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate

  13. Conformer-Specific IR Spectroscopy of Laser-Desorbed Sulfonamide Drugs: Tautomeric and Conformational Preferences of Sulfanilamide and its Derivatives

    Science.gov (United States)

    Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W.

    2017-06-01

    Molecules containing the sulfonamide group R^{1}-SO_2-NHR^{2} have a longstanding history as antimicrobial agents. Even though nowadays they are not commonly used in treating humans anymore, they continue to be studied as effective inhibitors of metalloenzyme carbonic anhydrases. These enzymes are important targets for a variety of diseases, such as, for instance, breast cancer, glaucoma, and obesity. Here we present the results of our laser desorption single-conformation UV and IR study of sulfanilamide (NH_2Ph-SO_2-NHR, R=H), a variety of singly substituted derivatives, and their monohydrated complexes. Depending on the substituent, the sulfonamide group can either adopt an amino or an imino tautomeric form. The form prevalent in the crystal is not necessarily also the tautomeric form we identified in the molecular beam after laser desorbing the sample. Furthermore, we explored the effect of complexation with a single water molecule on the tautomeric and conformational preferences of the sulfonamides. Our conformer-specific IR spectra in the NH and OH stretch region (3200-3750 \\wn) suggest that the intra- and intermolecular interactions governing the structures of the monomers and water complexes are surprisingly diverse. We have undertaken both Quantum Theory of Atoms in Molecules (QTAIM) and Interacting Quantum Atoms (IQA) analyses of calculated electron densities to quantitatively characterize the nature and strengths of the intra- and intermolecular interactions prevalent in the monomer and water complex structures.

  14. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    Science.gov (United States)

    Yu, Rongjun; Sun, Sai

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  15. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    Directory of Open Access Journals (Sweden)

    Rongjun Yu

    Full Text Available When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN, an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  16. Conformal Window and Correlation Functions in Lattice Conformal QCD

    CERN Document Server

    Iwasaki, Y

    2012-01-01

    We discuss various aspects of Conformal Field Theories on the Lattice. We investigate the SU(3) gauge theory with Nf fermions in the fundamental representation. First we make a brief review of our previous works on the phase structure of lattice gauge theories in terms of the gauge coupling constant and the quark mass. We thereby clarify the reason why we conjecture that the conformal window is 7 = 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential damping with power correction. Investigating our numerical data by a new method, the "micro-analysis" of propagators, we observe that our data are consistent with the picture that the Nf=7 case and the Nf=2 at T ~ 2Tc case are close to the meson unparticle model. On the other hand, the Nf=16 case and the Nf=2 at T= 10^2 ~10^5 Tc cases are close to the fermion unparticle model.

  17. [Biophysics of single molecules].

    Science.gov (United States)

    Serdiuk, I N; Deriusheva, E I

    2011-01-01

    The modern methods of research of biological molecules whose application led to the development of a new field of science, biophysics of single molecules, are reviewed. The measurement of the characteristics of single molecules enables one to reveal their individual features, and it is just for this reason that much more information can be obtained from one molecule than from the entire ensample of molecules. The high sensitivity of the methods considered in detail makes it possible to come close to the solution of the basic problem of practical importance, namely, the determination of the nucleotide sequence of a single DNA molecule.

  18. 40 CFR 93.154 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section 93...) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 93.154 Conformity analysis. Any Federal...

  19. CED: a conformational epitope database

    Directory of Open Access Journals (Sweden)

    Huang Jian

    2006-04-01

    Full Text Available Abstract Background Antigen epitopes provide valuable information useful for disease prevention, diagnosis, and treatment. Recently, more and more databases focusing on different types of epitopes have become available. Conformational epitopes are an important form of epitope formed by residues that are sequentially discontinuous but close together in three-dimensional space. These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes. Description We describe CED, a special database of well defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals. The database can be browsed or searched through a user-friendly web interface. Most epitopes in CED can also be viewed interactively in the context of their 3D structures. In addition, the entries are also hyperlinked to various databases such as Swiss-Prot, PDB, KEGG and PubMed, providing wide background information. Conclusion A conformational epitope database called CED has been developed as an information resource for investigators involved in both theoretical and applied immunology research. It complements other existing specialised epitope databases. The database is freely available at http://web.kuicr.kyoto-u.ac.jp/~ced

  20. Conformational transformations induced by the charge-curvature interaction: Mean-field approach

    DEFF Research Database (Denmark)

    Gaididei, Yu B.; Christiansen, Peter Leth; Zakrzewski, W.J.

    2006-01-01

    A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom of closed molecular aggregates may act as drivers giving ...... impetus to conformational dynamics of biopolymers. It is demonstrated that initially circular aggregates may undergo transformation to polygonal shapes and possible application to aggregates of bacteriochlorophyl a molecules is considered....

  1. A perspective on conformational control of electron transfer in nitric oxide synthases

    OpenAIRE

    Hedison, Tobias M.; Hay, Sam; Scrutton, Nigel S.

    2017-01-01

    This perspective reviews single molecule and ensemble fluorescence spectroscopy studies of the three tissue specific nitric oxide synthase (NOS) isoenzymes and the related diflavin oxidoreductase cytochrome P450 reductase. The focus is on the role of protein dynamics and the protein conformational landscape and we discuss how recent fluorescence-based studies have helped in illustrating how the nature of the NOS conformational landscape relates to enzyme turnover and catalysis.

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

    Science.gov (United States)

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

    2013-09-01

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

  3. CD molecules 2005: human cell differentiation molecules

    Czech Academy of Sciences Publication Activity Database

    Zola, H.; Swart, B.; Nicholson, I.; Aasted, B.; Bensussan, A.; Boumsell, L.; Buckley, C.; Clark, G.; Drbal, Karel; Engel, P.; Hart, D.; Hořejší, Václav; Isacke, C.; Macardle, P.; Malavasi, F.; Mason, D.; Olive, D.; Saalmüller, A.; Schlossman, S.F.; Schwartz-Albiez, R.; Simmons, P.; Tedder, T.F.; Uguccioni, M.; Warren, H.

    2005-01-01

    Roč. 106, č. 9 (2005), s. 3123-3126 ISSN 0006-4971 Institutional research plan: CEZ:AV0Z5052915 Keywords : CD molecules * leukocyte antigen Subject RIV: EC - Immunology Impact factor: 10.131, year: 2005

  4. 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...

  5. Logarithmic exotic conformal Galilean algebras

    Energy Technology Data Exchange (ETDEWEB)

    Henkel, Malte, E-mail: Malte.henkel@univ-lorraine.fr [Groupe de Physique Statistique, Institut Jean Lamour (CNRS UMR 7198), Université de Lorraine Nancy, B.P. 70239, F-54506 Vandoeuvre-lès-Nancy Cedex (France); Hosseiny, Ali, E-mail: al_hosseiny@sbu.ac.ir [Department of Physics, Shahid Beheshti University, G.C. Evin, Tehran 19839 (Iran, Islamic Republic of); School of Particles and Accelerators, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of); Rouhani, Shahin, E-mail: rouhani@ipm.ir [Department of Physics, Sharif University of Technology, P.O. Box 11165-9161, Tehran (Iran, Islamic Republic of); School of Particles and Accelerators, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)

    2014-02-15

    Logarithmic representations of the conformal Galilean algebra (CGA) and the Exotic Conformal Galilean algebra (ECGA) are constructed. This can be achieved by non-decomposable representations of the scaling dimensions or the rapidity indices, specific to conformal Galilean algebras. Logarithmic representations of the non-exotic CGA lead to the expected constraints on scaling dimensions and rapidities and also on the logarithmic contributions in the co-variant two-point functions. On the other hand, the ECGA admits several distinct situations which are distinguished by different sets of constraints and distinct scaling forms of the two-point functions. Two distinct realisations for the spatial rotations are identified as well. This is the first concrete example of a reducible, but non-decomposable representation, without logarithmic terms. Such cases had been anticipated before.

  6. Understanding the Structural Evolution of Single Conjugated Polymer Chain Conformers

    Directory of Open Access Journals (Sweden)

    Adam J. Wise

    2016-11-01

    Full Text Available Single molecule photoluminescence (PL spectroscopy of conjugated polymers has shed new light on the complex structure–function relationships of these materials. Although extensive work has been carried out using polarization and excitation intensity modulated experiments to elucidate conformation-dependent photophysics, surprisingly little attention has been given to information contained in the PL spectral line shapes. We investigate single molecule PL spectra of the prototypical conjugated polymer poly[2-methoxy-5-(2-ethylhexyloxy-1,4-phenylenevinylene] (MEH-PPV which exists in at least two emissive conformers and can only be observed at dilute levels. Using a model based on the well-known “Missing Mode Effect” (MIME, we show that vibronic progression intervals for MEH-PPV conformers can be explained by relative contributions from particular skeletal vibrational modes. Here, observed progression intervals do not match any ground state Raman active vibrational frequency and instead represent a coalescence of multiple modes in the frequency domain. For example, the higher energy emitting “blue” MEH-PPV form exhibits PL maxima at ~18,200 cm−1 with characteristic MIME progression intervals of ~1200–1350 cm−1, whereas the lower energy emitting “red” form peaks at ~17,100 cm−1 with intervals in the range of ~1350–1450 cm−1. The main differences in blue and red MEH-PPV chromophores lie in the intra-chain order, or, planarity of monomers within a chromophore segment. We demonstrate that the Raman-active out-of-plane C–H wag of the MEH-PPV vinylene group (~966 cm−1 has the greatest influence in determining the observed vibronic progression MIME interval. Namely, larger displacements (intensities—indicating lower intra-chain order—lower the effective MIME interval. This simple model provides useful insights into the conformational characteristics of the heterogeneous chromophore landscape without requiring costly and

  7. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

    KAUST Repository

    Feng, Yitao

    2016-10-13

    The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

  8. Torsional Arming of Thiomannosyl Donors & Conformational Control of Hexahydropyridazines via pH

    DEFF Research Database (Denmark)

    Olsen, Jacob Ingemar

    demonstrated their ability to change conformation under different conditions. These conformational changes are connected to various intramolecular interactions and can to some extent, be controlled by pH (Chapter 3). Fusing these conformationally labile compounds to the rim of a cyclodextrin would create...... and can to some extent, be controlled by pH (Chapter 3). Fusing these conformationally labile compounds to the rim of a cyclodextrin would create compounds that could release molecules at a specified change in pH conditions. To investigate this, four hexahydropyridazines were synthesized and investigated......The overall objective of the research presented in this PhD thesis was to investigate torsional arming of thiogalacto- and thiomannosyl donors (part 1) and to investigate the possible synthesis and attachment of a pH regulated conformational switch to an α-cyclodextrin (part 2). Part 1: It is well...

  9. Social influence: compliance and conformity.

    Science.gov (United States)

    Cialdini, Robert B; Goldstein, Noah J

    2004-01-01

    This review covers recent developments in the social influence literature, focusing primarily on compliance and conformity research published between 1997 and 2002. The principles and processes underlying a target's susceptibility to outside influences are considered in light of three goals fundamental to rewarding human functioning. Specifically, targets are motivated to form accurate perceptions of reality and react accordingly, to develop and preserve meaningful social relationships, and to maintain a favorable self-concept. Consistent with the current movement in compliance and conformity research, this review emphasizes the ways in which these goals interact with external forces to engender social influence processes that are subtle, indirect, and outside of awareness.

  10. Epigenetic dominance of prion conformers.

    Directory of Open Access Journals (Sweden)

    Eri Saijo

    2013-10-01

    Full Text Available Although they share certain biological properties with nucleic acid based infectious agents, prions, the causative agents of invariably fatal, transmissible neurodegenerative disorders such as bovine spongiform encephalopathy, sheep scrapie, and human Creutzfeldt Jakob disease, propagate by conformational templating of host encoded proteins. Once thought to be unique to these diseases, this mechanism is now recognized as a ubiquitous means of information transfer in biological systems, including other protein misfolding disorders such as those causing Alzheimer's and Parkinson's diseases. To address the poorly understood mechanism by which host prion protein (PrP primary structures interact with distinct prion conformations to influence pathogenesis, we produced transgenic (Tg mice expressing different sheep scrapie susceptibility alleles, varying only at a single amino acid at PrP residue 136. Tg mice expressing ovine PrP with alanine (A at (OvPrP-A136 infected with SSBP/1 scrapie prions propagated a relatively stable (S prion conformation, which accumulated as punctate aggregates in the brain, and produced prolonged incubation times. In contrast, Tg mice expressing OvPrP with valine (V at 136 (OvPrP-V136 infected with the same prions developed disease rapidly, and the converted prion was comprised of an unstable (U, diffusely distributed conformer. Infected Tg mice co-expressing both alleles manifested properties consistent with the U conformer, suggesting a dominant effect resulting from exclusive conversion of OvPrP-V136 but not OvPrP-A136. Surprisingly, however, studies with monoclonal antibody (mAb PRC5, which discriminates OvPrP-A136 from OvPrP-V136, revealed substantial conversion of OvPrP-A136. Moreover, the resulting OvPrP-A136 prion acquired the characteristics of the U conformer. These results, substantiated by in vitro analyses, indicated that co-expression of OvPrP-V136 altered the conversion potential of OvPrP-A136 from the S to

  11. Fluorine Substitution in Neurotransmitters: Microwave Spectroscopy and Modelling of the Conformational Space and Non Bonding Interactions

    Science.gov (United States)

    Melandri, S.; Maris, A.; Merloni, A.

    2011-06-01

    Fluorine substitution in molecules is a common practice in bio-organic chemistry in order to modulate physicochemical properties and biological activity of molecules and an increasing number of drugs on the market contain fluorine, the presence of which is often of major importance to modify pharmacokinetics properties and molecular activity. The rationale for such a strategy is that fluorine is generally a stronger electron acceptor than the other halogen atoms and its size is intermediate between that of hydrogen and oxygen. We have studied two fluorinated analogs of 2-phenylethylamine (PEA), the prototype molecule for adrenergic neurotransmitters, namely: 4-Fluoro (4FPEA) and 2-Fluoro-2-phenylethylamine (2FPEA) by Molecular Beam Fourier Transform Microwave Spectroscopy in the frequency range 6-18 GHz and ab initio calculations at the MP2/6311++G** level. The aim is to obtain information on the spatial arrangement of the ethylamine side chain and the effects of fluorination on the energy landscape. The conformational space is dominated by low energy gauche conformations stabilized by weak interactions between the aminic hydrogens and the electron cloud of the benzene ring and anti conformations higher in energy. In 2FPEA the presence of the fluorine atom almost duplicate the number of possible conformation with respect to 4FPEA. We observed two conformers of 4FPEA and five conformers of 2FPEA which have been classified with the guide provided by accurate ab initio calculations. The identification of the conformational species was helped by the analysis of the quadrupole hyperfine pattern which is greatly influenced by the orientation of the amino group and acts as a fingerprint for each conformation. The orientation of the dipole moment within the principal axis frame and the order of stability of the different conformations are other independent pieces of evidence for the unambiguous assignment and identification of the conformers. The order of stability was

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

    Science.gov (United States)

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

    2015-03-01

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

  13. Identification of two conformationally trapped n-propanol-water dimers in a supersonic expansion

    Science.gov (United States)

    Mead, Griffin J.; Alonso, Elena R.; Finneran, Ian A.; Carroll, P. Brandon; Blake, Geoffrey A.

    2017-05-01

    Two conformers of the n-propanol-water dimer have been observed in a supersonic expansion using chirped-pulse Fourier-transform microwave (CPFTMW) spectroscopy. Structural assignments reveal the n-propanol sub-unit is conformationally trapped, with its methyl group in both Gauche and Trans orientations. Despite different carbon backbone conformations, both dimers display the same water-donor/alcohol-acceptor hydrogen bonding motif. This work builds upon other reported alcohol-water dimers and upon previous work detailing the trapping of small molecules into multiple structural minima in rare gas supersonic expansions.

  14. 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.

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

    Science.gov (United States)

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

    2017-04-14

    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.

  16. Confinement Spectroscopy: Probing Single DNA Molecules with Tapered Nanochannels

    DEFF Research Database (Denmark)

    Persson, Karl Fredrik; Utko, Pawel; Reisner, Walter

    2009-01-01

    We demonstrate a confinement spectroscopy technique capable of probing small conformational changes of unanchored single DNA molecules in a manner analogous to force spectroscopy, in the regime corresponding to femtonewton forces. In contrast to force spectroscopy, various structural forms of DNA...

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

    Science.gov (United States)

    Durlak, Piotr; Berski, Sławomir; Latajka, Zdzisław

    2016-01-01

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

  18. Youth Conformity Regarding Institutions and Media

    Directory of Open Access Journals (Sweden)

    Nikolay Ivantchev

    2012-10-01

    Full Text Available An experiment on conformity was carried out. The participants were 95 youths. The scale “Conformity – Autonomy” from I. Karagiozov’s questionnaire for locus of control (1998 was also used. The results indicated the prevalence of youth conformity regarding institutions and media. The different types of conformity were related to each other. The subjects’ gender and the experimentators’ gender mediated the connections between the both types of conformity. The female youths conformed more with institutions than the male youths, but there were not any significant gender differences in their conform behavior regarding media (magazines. More male youths conformed for the magazines when the experimentator was a woman. More female youths conformed for the magazines when the experimentator was a man.

  19. Defects in conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Billò, Marco [Dipartimento di Fisica, Università di Torino, and Istituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Gonçalves, Vasco [Centro de Física do Porto,Departamento de Física e Astronomia Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); ICTP South American Institute for Fundamental Research Instituto de Física Teórica,UNESP - University Estadual Paulista,Rua Dr. Bento T. Ferraz 271, 01140-070, São Paulo, SP (Brazil); Lauria, Edoardo [Institute for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Meineri, Marco [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada); Scuola Normale Superiore, and Istituto Nazionale di Fisica Nucleare - sezione di Pisa,Piazza dei Cavalieri 7 I-56126 Pisa (Italy)

    2016-04-15

    We discuss consequences of the breaking of conformal symmetry by a flat or spherical extended operator. We adapt the embedding formalism to the study of correlation functions of symmetric traceless tensors in the presence of the defect. Two-point functions of a bulk and a defect primary are fixed by conformal invariance up to a set of OPE coefficients, and we identify the allowed tensor structures. A correlator of two bulk primaries depends on two cross-ratios, and we study its conformal block decomposition in the case of external scalars. The Casimir equation in the defect channel reduces to a hypergeometric equation, while the bulk channel blocks are recursively determined in the light-cone limit. In the special case of a defect of codimension two, we map the Casimir equation in the bulk channel to the one of a four-point function without defect. Finally, we analyze the contact terms of the stress-tensor with the extended operator, and we deduce constraints on the CFT data. In two dimensions, we relate the displacement operator, which appears among the contact terms, to the reflection coefficient of a conformal interface, and we find unitarity bounds for the latter.

  20. Conformation analysis of oligomeric flavanoids

    Science.gov (United States)

    Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

    1995-01-01

    The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

  1. Conformal symmetry and holographic cosmology

    NARCIS (Netherlands)

    Bzowski, A.W.

    2013-01-01

    This thesis presents a novel approach to cosmology using gauge/gravity duality. Analysis of the implications of conformal invariance in field theories leads to quantitative cosmological predictions which are in agreement with current data. Furthermore, holographic cosmology extends the theory of

  2. Exceptional and Spinorial Conformal Windows

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Ryttov, Thomas

    2012-01-01

    We study the conformal window of gauge theories containing fermionic matter fields, where the gauge group is any of the exceptional groups with the fermions transforming according to the fundamental and adjoint representations and the orthogonal groups where the fermions transform according...

  3. Anomalous Dimensions of Conformal Baryons

    DEFF Research Database (Denmark)

    Pica, Claudio; Sannino, Francesco

    2016-01-01

    We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small, within...

  4. How the generalized anomeric effect influences the conformational preference.

    Science.gov (United States)

    Wang, Changwei; Chen, Zhenhua; Wu, Wei; Mo, Yirong

    2013-01-21

    The generalized anomeric effect refers to the conformational preference of a gauche structure over an anti structure for molecules with a R-X-C-Y moiety. Whereas there are conflicting reports regarding the origin of this ubiquitous effect, a general consensus is that both the steric (more specifically electrostatic) and hyperconjugative interactions contribute. Here we employed the block-localized wavefunction (BLW) method, which is the simplest variant of ab initio valence bond (VB) theory and can define reference electron-localized states self-consistently, to evaluate the magnitude of the hyperconjugation effect in a number of acyclic molecules exhibiting the generalized anomeric effect. The BLW-based energy decomposition analysis revealed that both the steric and hyperconjugation effects contribute to the conformational preferences of methoxymethyl fluoride and methoxymethyl chlorides. But for the other systems under investigation, including methanediol, methanediamine, aminomethanol and dimethoxymethane, the hyperconjugative interactions play a negative role in the conformational preferences and the steric effect is solely responsible for the generalized anomeric effect. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

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

    2012-08-01

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

  6. Stabilization of the peptide conformation on the micellar surface.

    Science.gov (United States)

    Shapiro YuE; Gorbatyuk VYa; Mazurov, A A; Andronati, S A

    1994-04-01

    The conformational mobility of peptide molecules plays a significant role in peptide-receptor interactions and quantitative structure-activity relationships. As a receptor mimetic system, bis(2-ethylhexyl) sodium succinate (AOT) reversed micelles containing an aqueous solution of one of the melanotrophine inhibiting factor analogues prolyltyrosyl-glycinamide hydrochloride in the inner cavity have been used. Two-dimensional nuclear magnetic resonance spectroscopy (NOESY) and 13C spin-lattice relaxation time measurements have been used to establish that the peptide molecule assumes the biologically active beta II turn conformation when it is adsorbed at the surfactant-water border. This conformation is stabilized by intramolecular H-bonding between the proline carbonyl oxygen atom and amide protons. Moreover, it has been shown that the phenyl ring of tyrosine was inserted into the AOT intermolecular cavity, which is located between the polar AOT groups and the branches of iso-octane fragments. By and large, the phenyl ring acts as a hydrophobic anchor. Reversed micelles can be regarded as providing a realistic model of the receptor.

  7. "Star" morphologies of charged nanodrops comprised of conformational isomers.

    Science.gov (United States)

    In Oh, Myong; Paliy, Maxim; Consta, Styliani

    2018-01-14

    We study the spatial distribution of conformational isomers surrounding a central macroion in a charged droplet with linear dimensions in the nanometer range. Dimethyl carbonate and formic acid are selected as typical solvents that undergo isomerization and a charged buckyball (C60) is selected as a representative example of a macroion. The study is performed by atomistic molecular dynamics simulations. We find that when the charge of the buckyball is above a threshold value, it induces the formation of concentric shells of different conformational isomers surrounding the macroion. The presence of layers with different dielectric properties necessitates the use of different state equations for the solvent polarization in each layer. We find that at a high charge state of the buckyball, the nearest layer to the macroion comprises the conformers with the highest dipole moment. The interface of the outer layers of conformers is characterized by "ray"-forming structures of the higher dielectric constant isomers penetrating into the layer of the lowest dielectric constant isomers. For high values of the solvent dielectric constant, the charged droplet acquires a "star"-like global shape. We demonstrate that these distinct droplet structures are a manifestation of charge-induced instability. We describe this simulation-based phenomenology by an analytical theory that supports this conclusion. The findings suggest new experimental research venues that may explore the reactivity and assembly of molecules within regions of different dielectric properties in droplets.

  8. A surprising role for conformational entropy in protein function

    Science.gov (United States)

    Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

    2014-01-01

    Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

  9. Functional roles of slow enzyme conformational changes in network dynamics.

    Science.gov (United States)

    Wu, Zhanghan; Xing, Jianhua

    2012-09-05

    Extensive studies from different fields reveal that many macromolecules, especially enzymes, show slow transitions among different conformations. This phenomenon is named such things as dynamic disorder, heterogeneity, hysteretic or mnemonic enzymes across these different fields, and has been directly demonstrated by single molecule enzymology and NMR studies recently. We analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can filter upstream network noises, and can either resonantly respond to the system stimulus at certain frequencies or respond adaptively for sustained input signals of the network fluctuations. It thus can serve as a basic functional motif with properties that are normally for larger intermolecular networks in the field of systems biology. We further analyzed examples including enzymes functioning against pH fluctuations, metabolic state change of Artemia embryos, and kinetic insulation of fluctuations in metabolic networks. The study also suggests that hysteretic enzymes may be building blocks of synthetic networks with various properties such as narrow-banded filtering. The work fills the missing gap between studies on enzyme biophysics and network level dynamics, and reveals that the coupling between the two is functionally important; it also suggests that the conformational dynamics of some enzymes may be evolutionally selected. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Dopamine-induced conformational changes in alpha-synuclein.

    Directory of Open Access Journals (Sweden)

    Tiago F Outeiro

    2009-09-01

    Full Text Available Oligomerization and aggregation of alpha-synuclein molecules play a major role in neuronal dysfunction and loss in Parkinson's disease [1]. However, alpha-synuclein oligomerization and aggregation have mostly been detected indirectly in cells using detergent extraction methods [2], [3], [4]. A number of in vitro studies showed that dopamine can modulate the aggregation of alpha-synuclein by inhibiting the formation of or by disaggregating amyloid fibrils [5], [6], [7].Here, we show that alpha-synuclein adopts a variety of conformations in primary neuronal cultures using fluorescence lifetime imaging microscopy (FLIM. Importantly, we found that dopamine, but not dopamine agonists, induced conformational changes in alpha-synuclein which could be prevented by blocking dopamine transport into the cell. Dopamine also induced conformational changes in alpha-synuclein expressed in neuronal cell lines, and these changes were also associated with alterations in oligomeric/aggregated species.Our results show, for the first time, a direct effect of dopamine on the conformation of alpha-synuclein in neurons, which may help explain the increased vulnerability of dopaminergic neurons in Parkinson's disease.

  11. Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.

    Directory of Open Access Journals (Sweden)

    Daniel Seeliger

    2010-01-01

    Full Text Available Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures, however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 A backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 A backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available.

  12. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  13. Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

    Science.gov (United States)

    2015-01-01

    Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data. PMID:25360896

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

    Science.gov (United States)

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

    2012-11-02

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

  15. 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.

  16. Ultracold Polar Molecules

    Science.gov (United States)

    2016-04-01

    formation of ultracold 87RbCs molecules in their rovibrational ground state by magnetoassociation followed by STIRAP, resulting in 14 papers acknowledging...produce at high densities. We revealed broad Feshbach resonances that we hope will allow production of higher-density 85Rb clouds. We are now...attempting to achieve the next step, formation of 85RbCs molecules. 15. SUBJECT TERMS EOARD, ultracold polar molecules, Feshbach resonance 16. SECURITY

  17. Restricted amide rotation with steric hindrance induced multiple conformations

    Science.gov (United States)

    Krishnan, V. V.; Vazquez, Salvador; Maitra, Kalyani; Maitra, Santanu

    2017-12-01

    The Csbnd N bond character is dependent directly upon the resonance-contributor structure population driven by the delocalized nitrogen lone-pair of electrons. In the case of N, N-dibenzyl-ortho-toluamide (o-DBET), the molecule adopts subpopulations of conformers with distinct NMR spectral features, particularly at low temperatures. This conformational adaptation is unique to o-DBET, while the corresponding meta- and para- forms do not show such behavior. Variable-temperature (VT) NMR, two-dimensional exchange spectroscopy (EXSY), and qualitative molecular modeling studies are used to demonstrate how multiple competing interactions such as restricted amide rotation and steric hindrance effects can lead to versatile molecular adaptations in the solution state.

  18. Conformal Bootstrap in Mellin Space

    Science.gov (United States)

    Gopakumar, Rajesh; Kaviraj, Apratim; Sen, Kallol; Sinha, Aninda

    2017-02-01

    We propose a new approach towards analytically solving for the dynamical content of conformal field theories (CFTs) using the bootstrap philosophy. This combines the original bootstrap idea of Polyakov with the modern technology of the Mellin representation of CFT amplitudes. We employ exchange Witten diagrams with built-in crossing symmetry as our basic building blocks rather than the conventional conformal blocks in a particular channel. Demanding consistency with the operator product expansion (OPE) implies an infinite set of constraints on operator dimensions and OPE coefficients. We illustrate the power of this method in the ɛ expansion of the Wilson-Fisher fixed point by reproducing anomalous dimensions and, strikingly, obtaining OPE coefficients to higher orders in ɛ than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement between certain observables in the 3D Ising model and the precise numerical values that have been recently obtained.

  19. Conformal FDTD modeling wake fields

    Energy Technology Data Exchange (ETDEWEB)

    Jurgens, T.; Harfoush, F.

    1991-05-01

    Many computer codes have been written to model wake fields. Here we describe the use of the Conformal Finite Difference Time Domain (CFDTD) method to model the wake fields generated by a rigid beam traveling through various accelerating structures. The non- cylindrical symmetry of some of the problems considered here requires the use of a three dimensional code. In traditional FDTD codes, curved surfaces are approximated by rectangular steps. The errors introduced in wake field calculations by such an approximation can be reduced by increasing the mesh size, therefore increasing the cost of computing. Another approach, validated here, deforms Ampere and Faraday contours near a media interface so as to conform to the interface. These improvements of the FDTD method result in better accuracy of the fields at asymptotically no computational cost. This method is also capable of modeling thin wires as found in beam profile monitors, and slots and cracks as found in resistive wall motions. 4 refs., 5 figs.

  20. Conformal gravity and "gravitational bubbles"

    CERN Document Server

    Berezin, V A; Eroshenko, Yu N

    2015-01-01

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

  1. Gel dosimetry for conformal radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Gambarini, G. [Department of Physics of the University and INFN, Milan (Italy)]. e-mail: grazia.gambarini@mi.infn.it

    2005-07-01

    With the continuum development of conformal radio therapies, aimed at delivering high dose to tumor tissue and low dose to the healthy tissue around, the necessities has appeared of suitable improvement of dosimetry techniques giving the possibility of obtaining dose images to be compared with diagnostic images. Also if wide software has been developed for calculating dose distributions in the fields of various radiotherapy units, experimental verifications are necessary, in particular in the case of complex geometries in conformal radiotherapy. Gel dosimetry is a promising method for imaging the absorbed dose in tissue-equivalent phantoms, with the possibility of 3D reconstruction of the spatial dose distribution, with milli metric resolution. Optical imaging of gel dosimeters, based on visible light absorbance analysis, has shown to be a reliable technique for achieving dose distributions. (Author)

  2. 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.

  3. Gluon Amplitudes as 2d Conformal Correlators

    OpenAIRE

    Pasterski, Sabrina; Shao, Shu-Heng; Strominger, Andrew

    2017-01-01

    Recently, spin-one wavefunctions in four dimensions that are conformal primaries of the Lorentz group SL(2,C) were constructed. We compute low-point, tree-level gluon scattering amplitudes in the space of these conformal primary wavefunctions. The answers have the same conformal covariance as correlators of spin-one primaries in a 2d CFT. The BCFW recursion relation between three- and four-point gluon amplitudes is recast into this conformal basis.

  4. 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.

  5. Camera-based single-molecule FRET detection with improved time resolution

    NARCIS (Netherlands)

    Farooq, S.; Hohlbein, J.C.

    2015-01-01

    The achievable time resolution of camera-based single-molecule detection is often limited by the frame rate of the camera. Especially in experiments utilizing single-molecule Fo¨rster resonance energy transfer (smFRET) to probe conformational dynamics of biomolecules, increasing the frame rate by

  6. Objective interpretation as conforming interpretation

    Directory of Open Access Journals (Sweden)

    Lidka Rodak

    2011-12-01

    Full Text Available The practical discourse willingly uses the formula of “objective interpretation”, with no regards to its controversial nature that has been discussed in literature.The main aim of the article is to investigate what “objective interpretation” could mean and how it could be understood in the practical discourse, focusing on the understanding offered by judicature.The thesis of the article is that objective interpretation, as identified with textualists’ position, is not possible to uphold, and should be rather linked with conforming interpretation. And what this actually implies is that it is not the virtue of certainty and predictability – which are usually associated with objectivity- but coherence that makes the foundation of applicability of objectivity in law.What could be observed from the analyses, is that both the phenomenon of conforming interpretation and objective interpretation play the role of arguments in the interpretive discourse, arguments that provide justification that interpretation is not arbitrary or subjective. With regards to the important part of the ideology of legal application which is the conviction that decisions should be taken on the basis of law in order to exclude arbitrariness, objective interpretation could be read as a question “what kind of authority “supports” certain interpretation”? that is almost never free of judicial creativity and judicial activism.One can say that, objective and conforming interpretation are just another arguments used in legal discourse.

  7. Electrophysiological precursors of social conformity.

    Science.gov (United States)

    Shestakova, Anna; Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-10-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment.

  8. Electrophysiological precursors of social conformity

    Science.gov (United States)

    Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-01-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment. PMID:22683703

  9. Reinforcement learning signal predicts social conformity.

    NARCIS (Netherlands)

    Klucharev, V.; Hytonen, K.A.; Rijpkema, M.J.P.; Smidts, A.; Fernandez, G.S.E.

    2009-01-01

    We often change our decisions and judgments to conform with normative group behavior. However, the neural mechanisms of social conformity remain unclear. Here we show, using functional magnetic resonance imaging, that conformity is based on mechanisms that comply with principles of reinforcement

  10. Herding, Social Preferences and (Non-) Conformity

    OpenAIRE

    Luca Corazzini; Ben Greiner

    2005-01-01

    We study the role of social preferences and conformity in explaining herding behavior in anonymous risky environments. In an experiment similar to information cascade settings, but with no private information, we find no evidence for conformity. On the contrary, we observe a significant amount of non-conforming behavior, which cannot be attributed to errors.

  11. 40 CFR 52.2133 - General conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false General conformity. 52.2133 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South Carolina State Implementation Plan which...

  12. Conformity in Christ | Waaijman | Acta Theologica

    African Journals Online (AJOL)

    This essay investigates the notion of conformity in Christ as it is part of a comprehensive, multilayered process of transformation. In the first part it focuses on the process of transformation in creation, re-creation, conformity, love and glory. In the second part it discusses transformation in Christ by looking at conformation and ...

  13. 40 CFR 52.938 - General conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 3 2010-07-01 2010-07-01 false General conformity. 52.938 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November 10, 1995, and adopted into the Kentucky State...

  14. CONFORMITY IN CHRIST 1. THE TRANSFORMATION PROCESS

    African Journals Online (AJOL)

    This essay investigates the notion of conformity in Christ as it is part of a compre- hensive, multilayered process of transformation. In the first part it focuses on the process of transformation in creation, re-creation, conformity, love and glory. In the second part it discusses transformation in Christ by looking at conformation and ...

  15. 40 CFR 51.854 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Conformity analysis. 51.854 Section 51... FOR PREPARATION, ADOPTION, AND SUBMITTAL OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 51.854 Conformity analysis. Link to an...

  16. Conformation and stretching of end-tethered polymers in pressure-driven flow under confinement

    Science.gov (United States)

    Roy, Tamal; Hardt, Steffen; InstituteNano-; Microfludics, Technische Universität Darmstadt Team

    2016-11-01

    Understanding of the conformation and dynamics of polymers under confinement is important for both fundamental studies and applications. We experimentally study the conformation and stretching of surface-tethered polymer chains confined between parallel surfaces and exposed to a pressure-driven flow. λ-DNA molecules are tethered to the wall of a microchannel of height smaller than the contour lengths of the molecules. The DNA molecules, stained with a fluorescent dye, are visualized by epifluorescence and laser-scanning confocal microscopy (LSCM). The effects of the channel height, flow rate and contour length on the extension of the molecules are determined from epifluorescence images. From LSCM images the complete conformation and orientation of the DNA molecules is inferred. We find that the fractional extension of the molecules is uniquely determined by the fluid shear stress at the tethering surface and the chain contour length. There is no explicit influence of the channel height in the range of contour lengths we consider. We also derive analytical scaling relationships (in the weak and strong extension limits) that explain the experimentally observed stretching characteristics. This work is supported by Deutsche Forschungsgemeinschaft (Grant No. HA 2696/33-1).

  17. The effect of chlorination of nucleotide bases on the conformational properties of thymidine monophosphate

    Directory of Open Access Journals (Sweden)

    T. M. Mukhina

    2015-04-01

    Full Text Available Recent studies on Escherichia coli bacteria cultivation, in which DNA thymine was replaced with 5-chlorouracil have refreshed the problem of understanding the changes to physical properties of DNA monomers resultant from chemical modifications. These studies have shown that the replacement did not affect the normal activities and division of the bacteria, but has significantly reduced its life span. In this paper a comparative analysis was carried out by the methods of computational experiment of a set of 687 possible conformers of natural monomeric DNA unit (2′-deoxyribonucleotide thymidine monophosphate and 660 conformers of 5-chloro-2′-deoxyuridine monophosphate – a similar molecules in which the natural nitrogenous base thymine is substituted with 5-chlorouracil. Structures of stable conformers of the modified deoxyribonucleotide have been obtained and physical factors, which determine their variation from the conformers of the unmodified molecule have been analyzed. A comparative analysis of the elastic properties of conformers­ of investigated molecules and non-covalent interactions present in them was conducted. The results can be used for planning experiments on synthesis of artificial DNA suitable for incorporation into living organisms.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1992-01-01

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

  19. Functionalized molecules studied by STM: motion, switching and reactivity

    Energy Technology Data Exchange (ETDEWEB)

    Grill, Leonhard [Institut fuer Experimentalphysik, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin (Germany)

    2008-02-06

    Functionalized molecules represent the central issue of molecular nanotechnology. Scanning tunnelling microscopy (STM) is a powerful method to investigate such molecules, because it allows us to image them with sub-molecular resolution when adsorbed on a surface and can be used at the same time as a tool to manipulate single molecules in a controlled way. Such studies permit deep insight into the conformational, mechanical and electronic structure and thus functionalities of the molecules. In this review, recent experiments on specially designed molecules, acting as model systems for molecular nanotechnology, are reviewed. The presented studies focus on key functionalities: lateral rolling and hopping motion on a supporting surface, the switching behaviour of azobenzene derivatives by using the STM tip and the controlled reactivity of molecular side groups, which enable the formation of covalently bound molecular nanoarchitectures. (topical review)

  20. Molecule of the Month

    Indian Academy of Sciences (India)

    The most logical way to reduce the reactivity of a molecule of 1 would be to put a single molecule of 1 in an unreactive "cage". Chemistry Nobel winner Donald J. Cram (1987) has shown that it is indeed possible (Angew. Chem. Int. Ed. Engl., 30, 1028. 1991)!. Cram and co-workers synthesized a variety of spheroidal molecu-.

  1. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  2. Algebraic theory of molecules

    CERN Document Server

    Iachello, F

    1995-01-01

    1. The Wave Mechanics of Diatomic Molecules. 2. Summary of Elements of Algebraic Theory. 3. Mechanics of Molecules. 4. Three-Body Algebraic Theory. 5. Four-Body Algebraic Theory. 6. Classical Limit and Coordinate Representation. 8. Prologue to the Future. Appendices. Properties of Lie Algebras; Coupling of Algebras; Hamiltonian Parameters

  3. ISOLATED MOLECULES IN METALS

    NARCIS (Netherlands)

    1992-01-01

    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  4. Electrons in Molecules

    Indian Academy of Sciences (India)

    “What are electrons doing in molecules?” This is a deceptively simple question that scientists have been trying to answer for more than eighty years. With the advent of quantum mechanics in 1926, it became clear that we must understand the dynamics of electronic motion in atoms, molecules and solids in order to explain ...

  5. Molecule of the Month

    Indian Academy of Sciences (India)

    Atoms in a molecule generally prefer, particularly among the neighbouring ones, certain optimmn geometrical relationships. These are manifested in specific ranges of bond lengths, bond angles, torsion angles etc. As it always happens, chemists are interested in making molecules where these 'standard relationships' are ...

  6. Phase transformation in conformational polymorphs of nimesulide.

    Science.gov (United States)

    Sanphui, Palash; Sarma, Bipul; Nangia, Ashwini

    2011-06-01

    Nimesulide is a nonsteroidal anti-inflammatory drug (NSAID) and a COX-2 inhibitor. The native crystal structure of nimesulide (or Form I) has been characterized in the literature by X-ray powder diffraction (XRPD) lines, whereas full three-dimensional coordinates are known for a second polymorph (Form II). A detailed structural characterization and phase stability of nimesulide polymorphs were carried out. Rod-like crystals of Form I (space group Pca2(1); number of symmetry-independent molecules, Z' = 2) were crystallized from EtOH concomitantly with Form II (C2/c, Z' = 1). These conformational polymorphs have different torsion angles at the phenoxy and sulfonamide groups. The crystal structures are stabilized by N-H · · · O hydrogen bonds and C-H · · · O, C-H · · · π interactions. Phase transition from the metastable Form (II) to the stable modification (I) was studied using differential scanning calorimetry, hot-stage microscopy, solid-state grinding, solvent-drop grinding, and slurry crystallization. The phase transition was monitored by infrared, Raman, and ss-nuclear magnetic resonance spectroscopy; and XRPD and single-crystal X-ray diffraction. The stable polymorph I was obtained in excess during solution crystallization, grinding, and slurry methods. Intrinsic dissolution and equilibrium solubility experiments showed that the metastable Form II dissolves much faster than the stable Form I. Copyright © 2011 Wiley-Liss, Inc.

  7. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers.

    Science.gov (United States)

    Satoh, Hiroko; Oda, Tomohiro; Nakakoji, Kumiyo; Uno, Takeaki; Tanaka, Hiroaki; Iwata, Satoru; Ohno, Koichi

    2016-11-08

    This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4 and 4C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1 conformations; that is, the potential energy of the global minimum of 4C1 is lower than that of 1C4 (thermodynamic predominance) and that

  8. Molecules and Models The molecular structures of main group element compounds

    CERN Document Server

    Haaland, Arne

    2008-01-01

    This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

  9. Quantitative multi-parameter analysis of single molecule dynamics by PIE FastFLIM microscopy

    Science.gov (United States)

    Sun, Yuansheng; Coskun, Ulas; Tsoi, Phoebe S.; Ferreon, Josephine C.; Ferreon, Allan Chris; Barbieri, Beniamino; Liao, Shih-Chu Jeff

    2017-02-01

    PIE FastFLIM microscopy allows the quantitative multi-parameter measurement of single molecule protein folding and dynamics. Using donor-acceptor FRET pair-labeled proteins, we detect changes in protein conformation and dynamics by monitoring FRET efficiency, stoichiometry and lifetime. Together with anisotropy decay information, we acquire rotational relaxation times for single molecules. By applying antibunching, FLCS and burst analysis, multi-parameters (such as copy numbers in protein complexes), diffusion coefficient and molecular brightness can be fitted for deeper understanding of the conformational dynamic behavior of single protein molecules. In this paper, we'll focus on the multiparameters of FRET efficiency, stoichiometry and lifetime.

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

    Directory of Open Access Journals (Sweden)

    Çenesiz Yücel

    2015-12-01

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

  11. Single molecule electronic devices.

    Science.gov (United States)

    Song, Hyunwook; Reed, Mark A; Lee, Takhee

    2011-04-12

    Single molecule electronic devices in which individual molecules are utilized as active electronic components constitute a promising approach for the ultimate miniaturization and integration of electronic devices in nanotechnology through the bottom-up strategy. Thus, the ability to understand, control, and exploit charge transport at the level of single molecules has become a long-standing desire of scientists and engineers from different disciplines for various potential device applications. Indeed, a study on charge transport through single molecules attached to metallic electrodes is a very challenging task, but rapid advances have been made in recent years. This review article focuses on experimental aspects of electronic devices made with single molecules, with a primary focus on the characterization and manipulation of charge transport in this regime. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database.

    Science.gov (United States)

    Hawkins, Paul C D; Skillman, A Geoffrey; Warren, Gregory L; Ellingson, Benjamin A; Stahl, Matthew T

    2010-04-26

    Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based conformer generator. The algorithm consists of three phases: assembly of an initial 3D structure from a library of fragments; exhaustive enumeration of all rotatable torsions using values drawn from a knowledge-based list of angles, thereby generating a large set of conformations; and sampling of this set by geometric and energy criteria. Validation of conformer generators like OMEGA has often been undertaken by comparing computed conformer sets to experimental molecular conformations from crystallography, usually from the Protein Databank (PDB). Such an approach is fraught with difficulty due to the systematic problems with small molecule structures in the PDB. Methods are presented to identify a diverse set of small molecule structures from cocomplexes in the PDB that has maximal reliability. A challenging set of 197 high quality, carefully selected ligand structures from well-solved models was obtained using these methods. This set will provide a sound basis for comparison and validation of conformer generators in the future. Validation results from this set are compared to the results using structures of a set of druglike molecules extracted from the Cambridge Structural Database (CSD). OMEGA is found to perform very well in reproducing the crystallographic conformations from both these data sets using two complementary metrics of success.

  13. Conformal symmetry inheritance in null fluid spacetimes

    CERN Document Server

    Tupper, B O J; Hall, G S; Coley, Alan A; Carot, J

    2003-01-01

    We define inheriting conformal Killing vectors for null fluid spacetimes and find the maximum dimension of the associated inheriting Lie algebra. We show that for non-conformally flat null fluid spacetimes, the maximum dimension of the inheriting algebra is seven and for conformally flat null fluid spacetimes the maximum dimension is eight. In addition, it is shown that there are two distinct classes of non-conformally flat generalized plane wave spacetimes which possess the maximum dimension, and one class in the conformally flat case.

  14. Single-Molecule Stochastic Resonance

    Directory of Open Access Journals (Sweden)

    K. Hayashi

    2012-08-01

    Full Text Available Stochastic resonance (SR is a well-known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic (random or probabilistic noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively transitions from folded to unfolded configurations under the action of an oscillating mechanical force applied with optical tweezers. By varying the frequency of the force oscillation, we investigate the folding and unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measure several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that a good quantifier of the SR is the signal-to-noise ratio (SNR of the spectral density of measured fluctuations in molecular extension of the DNA hairpins. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance-matching condition. Finally, we carry out experiments on short hairpins that show how SR might be useful for enhancing the detection of conformational molecular transitions of low SNR.

  15. Core-substituted naphthalene diimides: influence of\\ud substituent conformation on strong visible absorption

    OpenAIRE

    Quinn, Samuel; Davies, E. Stephen; Pfeiffer, Constance R.; Lewis, William; McMaster, Jonathan; Champness, Neil R.

    2017-01-01

    Substitution of the aromatic core of naphthalene diimide (NDI) chromophores by morpholine leads to molecules with strong absorbance in the visible spectrum. The shift of absorption maxima to lower energy is determined not only by the degree of substitution but also by the relative conformation and orientation of the tertiary amine with respect to the plane of the NDI.

  16. The effect of gauche molecular conformations on the phase diagram of a Langmuir monolayer

    NARCIS (Netherlands)

    Zangi, R; Rice, SA

    2003-01-01

    Experimental and simulation studies have shown that the gauche conformational degrees of freedom of long-chain amphiphile molecules assembled in a dense Langmuir monolayer play an important role in determining the structures of the several phases that the monolayer supports. Nevertheless, for

  17. Conformational Flexibility of a Rotaxane Thread Probed by Electronic Spectroscopy in Helium Nanodroplets

    NARCIS (Netherlands)

    Smolarek, S.; Rijs, A. M.; Hannam, J. S.; Leigh, D. A.; Drabbels, M.; Buma, W. J.

    2009-01-01

    Ultrahigh-resolution spectroscopic studies have been performed to elucidate the conformational landscape of the succinamide-based thread 1 that is frequently employed in mechanically interlocked molecular assemblies. We show how dissolving single molecules into a helium nanodroplet enables us to

  18. Conformational flexibility of a rotaxane thread probed by electronic spectroscopy in helium nanodroplets

    NARCIS (Netherlands)

    Smolarek, S.; Rijs, A.M.; Hannam, J.S.; Leigh, D.A.; Drabbels, M.; Buma, W.J.

    2009-01-01

    Ultrahigh-resolution spectroscopic studies have been performed to elucidate the conformational landscape of the succinamide-based thread [1] that is frequently employed in mechanically interlocked molecular assemblies. We show how dissolving single molecules into a helium nanodroplet enables us to

  19. On the equivalence of conformational and enantiomeric changes of atomic configuration for vibrational circular dichroism

    NARCIS (Netherlands)

    Heshmat, M.; Nicu, V.P.; Baerends, E.J.

    2012-01-01

    We study systematically the vibrational circular dichroism (VCD) spectra of the conformers of a simple chiral molecule, with one chiral carbon and an "achiral" alkyl substituent of varying length. The vibrational modes can be divided into a group involving the chiral center and its direct neighbors

  20. 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.)

  1. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  2. Intramolecular pi-type hydrogen bonding and conformations of 3-cyclopenten-1-ol. 1. Theoretical calculations.

    Science.gov (United States)

    Al-Saadi, Abdulaziz A; Ocola, Esther J; Laane, Jaan

    2010-07-22

    The 3-cyclopenten-1-ol (3CPOL) molecule possesses two large-amplitude, low-frequency vibrations, namely, the ring-puckering and OH internal rotation, which can interconvert its four conformers into each other. Ab initio and density functional theory (DFT) calculations have been carried out to understand the energetics of these conformational changes. The lowest energy 3CPOL conformer possesses weak pi-type intramolecular hydrogen bonding between the hydroxyl hydrogen and the carbon-carbon double bond, and this lies 274 cm(-1) (0.78 kcal/mol) to 420 cm(-1) (1.20 kcal/mol) lower in energy than the other three conformations according to CCSD/6-311++G(d,p) computations. The two-dimensional potential energy surface for 3CPOL was computed as a function of the ring-puckering and OH internal rotation coordinates with the MP2/6-31+G(d,p) model.

  3. Conformation Effects of CpG Methylation on Single-Stranded DNA Oligonucleotides : Analysis of the Opioid Peptide Dynorphin-Coding Sequences

    NARCIS (Netherlands)

    Taqi, Malik Mumtaz; Warmlander, Sebastian K. T. S.; Yamskova, Olga; Madani, Fatemeh; Bazov, Igor; Luo, Jinghui; Zubarev, Roman; Verbeek, Dineke; Graslund, Astrid; Bakalkin, Georgy

    2012-01-01

    Single-stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to

  4. Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

    CERN Document Server

    Alizadehheidari, M; Noble, C; Reiter-Schad, M; Nyberg, L K; Fritzsche, J; Mehlig, B; Tegenfeldt, J O; Ambjörnsson, T; Persson, F; Westerlund, F

    2016-01-01

    Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA....

  5. The Biological Bases of Conformity

    Science.gov (United States)

    Morgan, T. J. H.; Laland, K. N.

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects’ behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning. PMID:22712006

  6. Gauge choice in conformal gravity

    Science.gov (United States)

    Sultana, Joseph; Kazanas, Demosthenes

    2017-04-01

    In a recent paper, K. Horne examined the effect of a conformally coupled scalar field (referred to as Higgs field) on the Mannheim-Kazanas metric gμν, i.e. the static spherically symmetric metric within the context of conformal gravity, and studied its effect on the rotation curves of galaxies. He showed that for a Higgs field of the form S(r) = S0a/(r + a), where a is a radial length-scale, the equivalent Higgs-frame Mannheim-Kazanas metric \\tilde{g}_{μ ν } = Ω ^2 g_{μ ν }, with Ω = S(r)/S0, lacks the linear γr term, which has been employed in the fitting of the galactic rotation curves without the need to invoke dark matter. In this brief note, we point out that the representation of the Mannheim-Kazanas metric in a gauge, where it lacks the linear term, has already been presented by others, including Mannheim and Kazanas themselves, without the need to introduce a conformally coupled Higgs field. Furthermore, Horne argues that the absence of the linear term resolves the issue of light bending in the wrong direction, i.e. away from the gravitating mass, if γr > 0 in the Mannheim-Kazanas metric, a condition necessary to resolve the galactic dynamics in the absence of dark matter. In this case, we also point out that the elimination of the linear term is not even required because the sign of the γr term in the metric can be easily reversed by a simple gauge transformation, and also that the effects of this term are indeed too small to be observed.

  7. The Biological Bases of Conformity

    Directory of Open Access Journals (Sweden)

    Thomas Joshau Henry Morgan

    2012-06-01

    Full Text Available Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favour adaptive learning strategies that facilitate effective use of social information in decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behaviour in nonhuman animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history and ontogeny of conformity and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behaviour conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subject’s behaviour is the result of both social and asocial influences, the resultant behaviour may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for

  8. The biological bases of conformity.

    Science.gov (United States)

    Morgan, T J H; Laland, K N

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects' behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning.

  9. Electron correlation in molecules

    CERN Document Server

    Wilson, S

    2007-01-01

    Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio

  10. Heavy exotic molecules

    Science.gov (United States)

    Liu, Yizhuang; Zahed, Ismail

    We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general structures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with JPC = 1++ binds, which we identify as the reported neutral X(3872). The bottom isotriplet exotic with JPC = 1+1 binds, and is identified as a mixed state of the reported charged exotics Zb+(10610) and Zb-(10650). The bound bottom isosinglet molecule with JPC = 1++ is a possible neutral Xb(10532) to be observed.

  11. Conformal ghosts on the sphere

    Energy Technology Data Exchange (ETDEWEB)

    Vogeler, Kirsten

    2010-07-16

    This thesis is about the relation of geometry and logarithmic conformal field theories. I consider two different geometric settings: in part I the topological A-model with embedding x:R x S{sup 1}{yields}CP{sup 1}, and in part II conformal, fermionic ghosts on the torus. The A-model can be transformed such that the path integral yields a {delta} distribution on the moduli space of instantons. Integrating out the dependency on S{sup 1}, one obtains Morse theory on the universal cover LCP{sup 1} of loop space. Its low-energy state space can be derived perturbatively in cells of this manifold, and can be modelled by the representations of the chiral de Rham complex. Assuming that the representation theory of the A-model and the chiral de Rham complex are identical, I consider the chiral de Rham complex in the following. The state spaces are local, induced representations of the symmetry generated by the gradient vector field of the Morse function. According to a conjecture of E. Frenkel, A. Losev and N. Nekrasov, a generalization of these local representations as distributions on LCP{sup 1} leads to nonperturbative states of the theory. On these states, the Hamiltonian must be corrected by additional terms. I discuss the representation theory of the nonperturbative states and determine the terms which deform the Hamiltonian. They have a geometric significance as cohomology operators in a complex of globally extended local representation spaces. Eventually, I prove that a logarithmic extension of the chiral de Rham complex corresponds the additional terms in the Hamiltonian. The conformal, fermionic ghosts of part II transform in irreducible representations of the monodromy group Z{sub 2}. I show that the conformal field theory of these fields has to be logarithmically extended as soon as the representations of the monodromy group are allowed to move freely on the parameter space CP{sup 1} backslash {l_brace}0,1,{infinity}{r_brace} of the torus. The triplet model

  12. Ligand-modulated conformational switching in a fully synthetic membrane-bound receptor

    Science.gov (United States)

    Lister, Francis G. A.; Le Bailly, Bryden A. F.; Webb, Simon J.; Clayden, Jonathan

    2017-05-01

    Signal transduction through G-protein-coupled receptors (GPCRs) involves binding to signalling molecules at the cell surface, which leads to global changes in molecular conformation that are communicated through the membrane. Artificial mechanisms for communication involving ligand binding and global conformational switching have been demonstrated so far only in the solution phase. Here, we report a membrane-bound synthetic receptor that responds to binding of a ligand by undergoing a conformational change that is propagated over several nanometres, deep into the phospholipid bilayer. Our design uses a helical foldamer core, with structural features borrowed from a class of membrane-active fungal antibiotics, ligated to a water-compatible, metal-centred binding site and a conformationally responsive fluorophore. Using the fluorophore as a remote reporter of conformational change, we find that binding of specific carboxylate ligands to a Cu(II) cofactor at the binding site perturbs the foldamer's global conformation, mimicking the conformational response of a GPCR to ligand binding.

  13. Isomers and conformational barriers of gas phase nicotine, nornicotine and their protonated forms

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Tomoki; Farone, William A.; Xantheas, Sotiris S.

    2014-07-17

    We report extensive conformational searches of the neutral nicotine, nornicotine and their protonated analogs that are based on ab-initio second order Møller-Plesset perturbation (MP2) electronic structure calculations. Initial searches were performed with the 6-31G(d,p) and the energetics of the most important structures were further refined from geometry optimizations with the aug-cc-pVTZ basis set. Based on the calculated free energies at T=298 K for the gas phase molecules, neutral nicotine has two dominant trans conformers, whereas neutral nornicotine is a mixture of several conformers. For nicotine, the protonation on both the pyridine and the pyrrolidine sites is energetically competitive, whereas nornicotine prefers protonation on the pyridine nitrogen. The protonated form of nicotine is mainly a mixture of two pyridine-protonated trans conformers and two pyrrolidine-protonated trans conformers, whereas the protonated form of nornicotine is a mixture of four pyridine-protonated trans conformers. Nornicotine is conformationally more flexible than nicotine, however it is less protonated at the biologically important pyrrolidine nitrogen site. The lowest energy isomers for each case were found to interconvert via low (< 6 kcal/mol) rotational barriers around the pyridine-pyrrolidine bond.

  14. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  15. Quantum dot molecules

    CERN Document Server

    Wu, Jiang

    2014-01-01

    This book reviews recent advances in the exciting and rapidly growing field of quantum dot molecules (QDMs). It offers state-of-the-art coverage of novel techniques and connects fundamental physical properties with device design.

  16. Electron-molecule collisions

    CERN Document Server

    Takayanagi, Kazuo

    1984-01-01

    Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

  17. Conformal Gauge Transformations in Thermodynamics

    Directory of Open Access Journals (Sweden)

    Alessandro Bravetti

    2015-09-01

    Full Text Available In this work, we show that the thermodynamic phase space is naturally endowed with a non-integrable connection, defined by all of those processes that annihilate the Gibbs one-form, i.e., reversible processes. We argue that such a connection is invariant under re-scalings of the connection one-form, whilst, as a consequence of the non-integrability of the connection, its curvature is not and, therefore, neither is the associated pseudo-Riemannian geometry. We claim that this is not surprising, since these two objects are associated with irreversible processes. Moreover, we provide the explicit form in which all of the elements of the geometric structure of the thermodynamic phase space change under a re-scaling of the connection one-form. We call this transformation of the geometric structure a conformal gauge transformation. As an example, we revisit the change of the thermodynamic representation and consider the resulting change between the two metrics on the thermodynamic phase space, which induce Weinhold’s energy metric and Ruppeiner’s entropy metric. As a by-product, we obtain a proof of the well-known conformal relation between Weinhold’s and Ruppeiner’s metrics along the equilibrium directions. Finally, we find interesting properties of the almost para-contact structure and of its eigenvectors, which may be of physical interest.

  18. A quantitative measure for protein conformational heterogeneity.

    Science.gov (United States)

    Lyle, Nicholas; Das, Rahul K; Pappu, Rohit V

    2013-09-28

    Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.

  19. Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis

    Directory of Open Access Journals (Sweden)

    Kim Sunghwan

    2012-11-01

    Full Text Available Abstract Background To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D descriptions to the small-molecule records contained in the PubChem Compound database and provides various search and analysis tools that exploit 3-D molecular similarity. Therefore, the efficient use of PubChem3D resources requires an understanding of the statistical and biological meaning of computed 3-D molecular similarity scores between molecules. Results The present study investigated effects of employing multiple conformers per compound upon the 3-D similarity scores between ten thousand randomly selected biologically-tested compounds (10-K set and between non-inactive compounds in a given biological assay (156-K set. When the “best-conformer-pair” approach, in which a 3-D similarity score between two compounds is represented by the greatest similarity score among all possible conformer pairs arising from a compound pair, was employed with ten diverse conformers per compound, the average 3-D similarity scores for the 10-K set increased by 0.11, 0.09, 0.15, 0.16, 0.07, and 0.18 for STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, and ComboTCT-opt, respectively, relative to the corresponding averages computed using a single conformer per compound. Interestingly, the best-conformer-pair approach also increased the average 3-D similarity scores for the non-inactive–non-inactive (NN pairs for a given assay, by comparable amounts to those for the random compound pairs, although some assays showed a pronounced increase in the per-assay NN-pair 3-D similarity scores, compared to the average increase for the random compound pairs. Conclusion These results suggest that the use of ten diverse conformers per compound in PubChem bioassay data analysis using 3-D molecular similarity is not expected to increase the separation of non

  20. Machine learning estimates of natural product conformational energies.

    Directory of Open Access Journals (Sweden)

    Matthias Rupp

    2014-01-01

    Full Text Available Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. Our model estimates energies of new conformations by exploiting information from previous calculations via Gaussian process regression. Predictive variance is used to assess whether a conformation is in the interpolation region, allowing a controlled trade-off between prediction accuracy and computational speed-up. For energies of relaxed conformations at the density functional level of theory (implicit solvent, DFT/BLYP-disp3/def2-TZVP, mean absolute errors of less than 1 kcal/mol were achieved. The study demonstrates that predictive machine learning models can be developed for structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of larger molecular structures.

  1. A new interpretative paradigm for Conformational Protein Diseases.

    Science.gov (United States)

    Agnati, Luigi Francesco; Guidolin, Diego; Woods, Amina S; Ciruela, Francisco; Carone, Chiara; Vallelunga, Annamaria; Escuela, Dasiel Oscar Borroto; Genedani, Susanna; Fuxe, Kjell

    2013-03-01

    Conformational Protein Diseases (CPDs) comprise over forty clinically and pathologically diverse disorders in which specific altered proteins accumulate in cells or tissues of the body. The most studied are Alzheimerβ's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, prion diseases, inclusion body myopathy, and the systemic amyloidoses. They are characterised by three dimensional conformational alterations, which are often rich in β- structure. Proteins in this non-native conformation are highly stable, resistant to degradation, and have an enhanced tendency to aggregate with like protein molecules. The misfolded proteins can impart their anomalous properties to soluble, monomeric proteins with the same amino acid sequence by a process that has been likened to seeded crystallization. However, these potentially pathogenic proteins also have important physiological actions, which have not completely characterized. This opens up the question of what process transforms physiological actions into pathological actions and most intriguing, is why potentially dangerous proteins have been maintained during evolution and are present from yeasts to humans. In the present paper, we introduce the concept of mis-exaptation and of mis-tinkering since they may help in clarifying some of the double edged sword aspects of these proteins. Against this background an original interpretative paradigm for CPDs will be given in the frame of the previously proposed Red Queen Theory of Aging.

  2. Conformal basis for flat space amplitudes

    Science.gov (United States)

    Pasterski, Sabrina; Shao, Shu-Heng

    2017-09-01

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

  3. Reinforcement learning signal predicts social conformity.

    Science.gov (United States)

    Klucharev, Vasily; Hytönen, Kaisa; Rijpkema, Mark; Smidts, Ale; Fernández, Guillén

    2009-01-15

    We often change our decisions and judgments to conform with normative group behavior. However, the neural mechanisms of social conformity remain unclear. Here we show, using functional magnetic resonance imaging, that conformity is based on mechanisms that comply with principles of reinforcement learning. We found that individual judgments of facial attractiveness are adjusted in line with group opinion. Conflict with group opinion triggered a neuronal response in the rostral cingulate zone and the ventral striatum similar to the "prediction error" signal suggested by neuroscientific models of reinforcement learning. The amplitude of the conflict-related signal predicted subsequent conforming behavioral adjustments. Furthermore, the individual amplitude of the conflict-related signal in the ventral striatum correlated with differences in conforming behavior across subjects. These findings provide evidence that social group norms evoke conformity via learning mechanisms reflected in the activity of the rostral cingulate zone and ventral striatum.

  4. Single homopolypeptide chains collapse into mechanically rigid conformations

    Science.gov (United States)

    Dougan, Lorna; Li, Jingyuan; Badilla, Carmen L.; Berne, B. J.; Fernandez, Julio M.

    2009-01-01

    Huntington's disease is linked to the insertion of glutamine (Q) in the protein huntingtin, resulting in polyglutamine (polyQ) expansions that self-associate to form aggregates. While polyQ aggregation has been the subject of intense study, a correspondingly thorough understanding of individual polyQ chains is lacking. Here we demonstrate a single molecule force-clamp technique that directly probes the mechanical properties of single polyQ chains. We have made polyQ constructs of varying lengths that span the length range of normal and diseased polyQ expansions. Each polyQ construct is flanked by the I27 titin module, providing a clear mechanical fingerprint of the molecule being pulled. Remarkably, under the application of force, no extension is observed for any of the polyQ constructs. This is in direct contrast with the random coil protein PEVK of titin, which readily extends under force. Our measurements suggest that polyQ chains form mechanically stable collapsed structures. We test this hypothesis by disrupting polyQ chains with insertions of proline residues and find that their mechanical extensibility is sensitive to the position of the proline interruption. These experiments demonstrate that polyQ chains collapse to form a heterogeneous ensemble of conformations that are mechanically resilient. We further use a heat-annealing molecular dynamics protocol to extensively search the conformation space and find that polyQ can exist in highly mechanically stable compact globular conformations. The mechanical rigidity of these collapsed structures may exceed the functional ability of eukaryotic proteasomes, resulting in the accumulation of undigested polyQ sequences in vivo. PMID:19549822

  5. Conformational changes in glycine tri- and hexapeptide

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2006-01-01

    conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods...... also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids....

  6. Challenges of Agro-Food Standards Conformity

    DEFF Research Database (Denmark)

    Bolwig, Simon; Riisgaard, Lone; Gibbon, Peter

    2013-01-01

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

  7. Directly measuring single molecule heterogeneity using force spectroscopy

    CERN Document Server

    Hinczewski, Michael; Thirumalai, D

    2016-01-01

    One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with random interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Though we now have proof of functional heterogeneity in a handful of systems---enzymes, motors, adhesion complexes---identifying and measuring it remains a formidable challenge. Here we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single molecule techniques: AFM or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This re...

  8. Using FLIM-FRET to measure conformational changes of transglutaminase type 2 in live cells.

    Directory of Open Access Journals (Sweden)

    Nicholas S Caron

    Full Text Available Transglutaminase type 2 (TG2 is a ubiquitously expressed member of the transglutaminase family, capable of mediating a transamidation reaction between a variety of protein substrates. TG2 also has a unique role as a G-protein with GTPase activity. In response to GDP/GTP binding and increases in intracellular calcium levels, TG2 can undergo a large conformational change that reciprocally modulates the enzymatic activities of TG2. We have generated a TG2 biosensor that allows for quantitative assessment of TG2 conformational changes in live cells using Förster resonance energy transfer (FRET, as measured by fluorescence lifetime imaging microscopy (FLIM. Quantifying FRET efficiency with this biosensor provides a robust assay to quickly measure the effects of cell stress, changes in calcium levels, point mutations and chemical inhibitors on the conformation and localization of TG2 in living cells. The TG2 FRET biosensor was validated using established TG2 conformational point mutants, as well as cell stress events known to elevate intracellular calcium levels. We demonstrate in live cells that inhibitors of TG2 transamidation activity can differentially influence the conformation of the enzyme. The irreversible inhibitor of TG2, NC9, forces the enzyme into an open conformation, whereas the reversible inhibitor CP4d traps TG2 in the closed conformation. Thus, this biosensor provides new mechanistic insights into the action of two TG2 inhibitors and defines two new classes based on ability to alter TG2 conformation in addition to inhibiting transamidation activity. Future applications of this biosensor could be to discover small molecules that specifically alter TG2 conformation to affect GDP/GTP or calcium binding.

  9. Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain.

    Directory of Open Access Journals (Sweden)

    Chao-Yie Yang

    Full Text Available Suppression of Tumorigenicity 2 (ST2, a member of the interleukin-1 receptor (IL-1R family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2ECD models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2ECD (containing D1-D3 domains in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2ECD contributes predominantly to the interaction between ST2ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2ECD and modulation sites conformed to ST2ECD conformations. Our study provides structural models and analyses of ST2ECD that could be useful for inhibitor discovery.

  10. Ensemble QSAR: a QSAR method based on conformational ensembles and metric descriptors.

    Science.gov (United States)

    Pissurlenkar, Raghuvir R S; Khedkar, Vijay M; Iyer, Radhakrishnan P; Coutinho, Evans C

    2011-07-30

    Quantitative structure-activity relationship (QSAR) is the most versatile tool in computer-assisted molecular design. One conceptual drawback seen in QSAR approaches is the "one chemical-one structure-one parameter value" dogma where the model development is based on physicochemical description for a single molecular conformation, while ignoring the rest of the conformational space. It is well known that molecules have several low-energy conformations populated at physiological temperature, and each conformer makes a significant impact on associated properties such as biological activity. At the level of molecular interaction, the dynamics around the molecular structure is of prime essence rather than the average structure. As a step toward understanding the role of these discrete microscopic states in biological activity, we have put together a theoretically rigorous and computationally tractable formalism coined as eQSAR. In this approach, the biological activity is modeled as a function of physicochemical description for a selected set of low-energy conformers, rather than that's for a single lowest energy conformation. Eigenvalues derived from the "Physicochemical property integrated distance matrices" (PD-matrices) that encompass both 3D structure and physicochemical properties, have been used as descriptors; is a novel addition. eQSAR is validated on three peptide datasets and explicitly elaborated for bradykinin-potentiating peptides. The conformational ensembles were generated by a simple molecular dynamics and consensus dynamics approaches. The eQSAR models are statistically significant and possess the ability to select the most biologically relevant conformation(s) with the relevant physicochemical attributes that have the greatest meaning for description of the biological activity. Copyright © 2011 Wiley Periodicals, Inc.

  11. Earle K. Plyler Prize for Molecular Spectroscopy and Dynamics Lecture: 2D IR Spectroscopy of Peptide Conformation

    Science.gov (United States)

    Tokmakoff, Andrei

    2012-02-01

    Descriptions of protein and peptide conformation are colored by the methods we use to study them. Protein x-ray and NMR structures often lead to impressions of rigid or well-defined conformations, even though these are dynamic molecules. The conformational fluctuations and disorder of proteins and peptides is more difficult to quantify. This presentation will describe an approach toward characterizing and quantifying structural heterogeneity and disorder in peptides using 2D IR spectroscopy. Using amide I vibrational spectroscopy, isotope labeling strategies, and computational modeling based on molecular dynamics simulations and Markov state models allows us to characterize distinct peptide conformers and conformational variation. The examples illustrated include the beta-hairpin tripzip2 and elastin-like peptides.

  12. Novel conformation of an RNA structural switch.

    Science.gov (United States)

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

    2012-11-20

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

  13. Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline

    Science.gov (United States)

    Cabezas, C.; Cortijo, V.; Mata, S.; Lopez, J. C.; Alonso, J. L.

    2013-06-01

    Recent improvements in our LA-MB-FTMW instrumentation have allowed the characterization of eleven and eight conformers for the neurotransmitters adrenaline and noradrenaline respectively. The observation of this rich conformational behavior is in accordance with the recent observation of seven conformers for dopamine and in sharp contrast with the conformational reduction proposed for catecholamines. C. Cabezas, I. Peña, J. C. López, J. L. Alonso J. Phys. Chem. Lett. 2013, 4, 486. H. Mitsuda, M. Miyazaki, I. B. Nielsen, P. Carcabal,C. Dedonder, C. Jouvet, S. Ishiuchi, M. Fujii J. Phys. Chem. Lett. 2010, 1, 1130.

  14. A Framework for Online Conformance Checking

    DEFF Research Database (Denmark)

    Burattin, Andrea; Carmona, Josep

    2017-01-01

    Conformance checking – a branch of process mining – focuses on establishing to what extent actual executions of a process are in line with the expected behavior of a reference model. Current conformancechecking techniques only allow for a-posteriori analysis: the amount of (non-)conformant behavior...... is quantified after the completion of the process instance. In this paper we propose a framework for online conformance checking: not only do we quantify (non-)conformant behavior as the execution is running, we also restrict the computation to constant time complexity per event analyzed, thus enabling...

  15. NMR in natural products: understanding conformation, configuration and receptor interactions.

    Science.gov (United States)

    Carlomagno, Teresa

    2012-05-01

    Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of

  16. Prediction of conformationally dependent atomic multipole moments in carbohydrates.

    Science.gov (United States)

    Cardamone, Salvatore; Popelier, Paul L A

    2015-12-15

    The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings. © 2015 Wiley Periodicals, Inc.

  17. Conformable eddy current array delivery

    Science.gov (United States)

    Summan, Rahul; Pierce, Gareth; Macleod, Charles; Mineo, Carmelo; Riise, Jonathan; Morozov, Maxim; Dobie, Gordon; Bolton, Gary; Raude, Angélique; Dalpé, Colombe; Braumann, Johannes

    2016-02-01

    The external surface of stainless steel containers used for the interim storage of nuclear material may be subject to Atmospherically Induced Stress Corrosion Cracking (AISCC). The inspection of such containers poses a significant challenge due to the large quantities involved; therefore, automating the inspection process is of considerable interest. This paper reports upon a proof-of-concept project concerning the automated NDT of a set of test containers containing artificially generated AISCCs. An Eddy current array probe with a conformable padded surface from Eddyfi was used as the NDT sensor and end effector on a KUKA KR5 arc HW robot. A kinematically valid cylindrical raster scan path was designed using the KUKA|PRC path planning software. Custom software was then written to interface measurement acquisition from the Eddyfi hardware with the motion control of the robot. Preliminary results and analysis are presented from scanning two canisters.

  18. Technidilaton at the conformal edge

    Science.gov (United States)

    Hashimoto, Michio; Yamawaki, Koichi

    2011-01-01

    Technidilaton (TD) was proposed long ago in the technicolor near criticality/conformality. To reveal the critical behavior of TD, we explicitly compute the nonperturbative contributions to the scale anomaly ⟨θμμ⟩ and to the technigluon condensate ⟨αGμν2⟩, which are generated by the dynamical mass m of the technifermions. Our computation is based on the (improved) ladder Schwinger-Dyson equation, with the gauge coupling α replaced by the two-loop running coupling α(μ) having the Caswell-Banks-Zaks infrared fixed point α*: α(μ)≃α=α* for the infrared region mHaba-Matsuzaki-Yamawaki. The decoupled TD can be a candidate of dark matter.

  19. Approaching Conformality with Ten Flavors

    Energy Technology Data Exchange (ETDEWEB)

    Appelquist, Thomas; Brower, Richard C.; Buchoff, Michael I.; Cheng, Michael; Cohen, Saul D.; Fleming, George T.; Kiskis, Joe; Lin, Meifeng; Na, Heechang; Neil, Ethan T.; Osborn, James C.

    2012-04-01

    We present first results for lattice simulations, on a single volume, of the low-lying spectrum of an SU(3) Yang-Mills gauge theory with N{sub f} = 10 light fermions in the fundamental representation. Fits to the fermion mass dependence of various observables are found to be globally consistent with the hypothesis that this theory is within or just outside the strongly-coupled edge of the conformal window, with mass anomalous dimension {gamma}* {approx} 1 over the range of scales simulated. We stress that we cannot rule out the possibility of spontaneous chiral-symmetry breaking at scales well below our infrared cutoff. We discuss important systematic effects, including finite-volume corrections, and consider directions for future improvement.

  20. Gravitomagnetic effects in conformal gravity

    CERN Document Server

    Said, Jackson Levi; Adami, Kristian Zarb

    2014-01-01

    Gravitomagnetic effects are characterized by two phenomena: first, the geodetic effect which describes the precession of the spin of a gyroscope in a free orbit around a massive object, second, the Lense-Thirring effect which describes the precession of the orbital plane about a rotating source mass. We calculate both these effects in the fourth-order theory of conformal Weyl gravity for the test case of circular orbits. We show that for the geodetic effect a linear term arises which may be interesting for high radial orbits, whereas for the Lense-Thirring effect the additional term has a diminishing effect for most orbits. Circular orbits are also considered in general leading up to a generalization of Kepler's third law.

  1. Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator.

    Science.gov (United States)

    Kromann-Hansen, Tobias; Louise Lange, Eva; Peter Sørensen, Hans; Hassanzadeh-Ghassabeh, Gholamreza; Huang, Mingdong; Jensen, Jan K; Muyldermans, Serge; Declerck, Paul J; Komives, Elizabeth A; Andreasen, Peter A

    2017-06-13

    Although trypsin-like serine proteases have flexible surface-exposed loops and are known to adopt higher and lower activity conformations, structural determinants for the different conformations have remained largely obscure. The trypsin-like serine protease, urokinase-type plasminogen activator (uPA), is central in tissue remodeling processes and also strongly implicated in tumor metastasis. We solved five X-ray crystal structures of murine uPA (muPA) in the absence and presence of allosteric molecules and/or substrate-like molecules. The structure of unbound muPA revealed an unsuspected non-chymotrypsin-like protease conformation in which two β-strands in the core of the protease domain undergoes a major antiparallel-to-parallel conformational transition. We next isolated two anti-muPA nanobodies; an active-site binding nanobody and an allosteric nanobody. Crystal structures of the muPA:nanobody complexes and hydrogen-deuterium exchange mass spectrometry revealed molecular insights about molecular factors controlling the antiparallel-to-parallel equilibrium in muPA. Together with muPA activity assays, the data provide valuable insights into regulatory mechanisms and conformational flexibility of uPA and trypsin-like serine proteases in general.

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

    Science.gov (United States)

    Das, Gunajyoti

    2013-08-01

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

  3. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase

    Directory of Open Access Journals (Sweden)

    Schmid Rolf D

    2009-05-01

    observed in simulations in toluene. The conformational transition of the lid was not correlated to the motions of the β-hairpin structure. Conclusion Conformational transitions between the experimentally observed closed and open conformation of the lid were observed by multiple molecular dynamics simulations of B. cepacia lipase. Transitions in both directions occurred without applying restraints or external forces. The opening and closing were driven by the solvent and independent of a bound substrate molecule.

  4. MOLECULES IN {eta} CARINAE

    Energy Technology Data Exchange (ETDEWEB)

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf [Max-Planck Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Zapata, Luis A.; Rodriguez, Luis F. [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 3-72, 58090 Morelia, Michoacan (Mexico)

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

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

    Science.gov (United States)

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

    2015-09-18

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

  6. Small molecule-guided thermoresponsive supramolecular assemblies

    KAUST Repository

    Rancatore, Benjamin J.

    2012-10-23

    Small organic molecules with strong intermolecular interactions have a wide range of desirable optical and electronic properties and rich phase behaviors. Incorporating them into block copolymer (BCP)-based supramolecules opens new routes to generate functional responsive materials. Using oligothiophene- containing supramolecules, we present systematic studies of critical thermodynamic parameters and kinetic pathway that govern the coassemblies of BCP and strongly interacting small molecules. A number of potentially useful morphologies for optoelectronic materials, including a nanoscopic network of oligothiophene and nanoscopic crystalline lamellae, were obtained by varying the assembly pathway. Hierarchical coassemblies of oligothiophene and BCP, rather than macrophase separation, can be obtained. Crystallization of the oligothiophene not only induces chain stretching of the BCP block the oligothiophene is hydrogen bonded to but also changes the conformation of the other BCP coil block. This leads to an over 70% change in the BCP periodicity (e.g., from 31 to 53 nm) as the oligothiophene changes from a melt to a crystalline state, which provides access to a large BCP periodicity using fairly low molecular weight BCP. The present studies have demonstrated the experimental feasibility of generating thermoresponsive materials that convert heat into mechanical energy. Incorporating strongly interacting small molecules into BCP supramolecules effectively increases the BCP periodicity and may also open new opportunities to tailor their optical properties without the need for high molecular weight BCP. © 2012 American Chemical Society.

  7. Fixman compensating potential for general branched molecules

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States); Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States)

    2013-12-28

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

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

    OpenAIRE

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

    2006-01-01

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

  9. Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

    Science.gov (United States)

    Shim, Jihyun; Mackerell, Alexander D

    2011-05-01

    A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of the target molecule or its 3D structure. In such cases computational ligand-based drug design (LBDD) can accelerate the drug discovery processes. LBDD is a general approach to elucidate the relationship of a compound's structure and physicochemical attributes to its biological activity. The resulting structure-activity relationship (SAR) may then act as the basis for the prediction of compounds with improved biological attributes. LBDD methods range from pharmacophore models identifying essential features of ligands responsible for their activity, quantitative structure-activity relationships (QSAR) yielding quantitative estimates of activities based on physiochemical properties, and to similarity searching, which explores compounds with similar properties as well as various combinations of the above. A number of recent LBDD approaches involve the use of multiple conformations of the ligands being studied. One of the basic components to generate multiple conformations in LBDD is molecular mechanics (MM), which apply an empirical energy function to relate conformation to energies and forces. The collection of conformations for ligands is then combined with functional data using methods ranging from regression analysis to neural networks, from which the SAR is determined. Accordingly, for effective application of LBDD for SAR determinations it is important that the compounds be accurately modelled such that the appropriate range of conformations accessible to the ligands is identified. Such accurate modelling is largely based on use of the appropriate empirical force field for the molecules being investigated and the approaches used to generate the conformations. The present chapter includes a brief overview of currently used SAR methods in LBDD followed by a more

  10. Effects of Select Anions from the Hofmeister Series on the Gas-Phase Conformations of Protein Ions Measured with Traveling-Wave Ion Mobility Spectrometry/Mass Spectrometry

    Science.gov (United States)

    Merenbloom, Samuel I.; Flick, Tawnya G.; Daly, Michael P.; Williams, Evan R.

    2011-11-01

    The gas-phase conformations of ubiquitin, cytochrome c, lysozyme, and α-lactalbumin ions, formed by electrospray ionization (ESI) from aqueous solutions containing 5 mM ammonium perchlorate, ammonium iodide, ammonium sulfate, ammonium chloride, ammonium thiocyanate, or guanidinium chloride, are examined using traveling-wave ion mobility spectrometry (TWIMS) coupled to time-of-flight (TOF) mass spectrometry (MS). For ubiquitin, cytochrome c, and α-lactalbumin, adduction of multiple acid molecules results in no significant conformational changes to the highest and lowest charge states formed from aqueous solutions, whereas the intermediate charge states become more compact. The transition to more compact conformers for the intermediate charge states occurs with fewer bound H2SO4 molecules than HClO4 or HI molecules, suggesting ion-ion or salt-bridge interactions are stabilizing more compact forms of the gaseous protein. However, the drift time distributions for protein ions of the same net charge with the highest levels of adduction of each acid are comparable, indicating that these protein ions all adopt similarly compact conformations or families of conformers. No significant change in conformation is observed upon the adduction of multiple acid molecules to charge states of lysozyme. These results show that the attachment of HClO4, HI, or H2SO4 to multiply protonated proteins can induce compact conformations in the resulting gas-phase protein ions. In contrast, differing Hofmeister effects are observed for the corresponding anions in solution at higher concentrations.

  11. On the structural intricacies of a metabolic precursor: Direct spectroscopic detection of water-induced conformational reshaping of mevalonolactone

    Science.gov (United States)

    Domingos, Sérgio R.; Pérez, Cristóbal; Schnell, Melanie

    2017-09-01

    We use high-resolution rotational spectroscopy to investigate the structural intricacies of the lactone form of mevalonic acid, precursor of the mevalonate pathway. By combining microwave spectroscopy with supersonic expansions and quantum-chemical calculations, we determine the two most stable conformations of the precursor. Complementary micro-solvation studies reveal that aggregation of the first water molecule induces a substantial structural rearrangement comprising a hydroxy rotation and an endocyclic core torsion to create a favourable geometry to accommodate the water molecule. We discuss the conformational aspects of the precursor in isolation and under micro-hydrated conditions.

  12. Developing Single-Molecule Technique with Microsecond Resolution

    Science.gov (United States)

    Akhterov, Maxim V.

    Molecular machines like proteins are responsible for many regulatory and catalytic functions. Specifically, molecular motions of proteins and their flexibility determine conformational states required for enzyme catalysis, signal transduction, and protein-protein interactions. However, the mechanisms for protein transitions between conformational states are often poorly understood, especially in the milli- to microsecond ranges where conventional optical techniques and computational modeling are most limited. This work describes development of an electronic single-molecule technique for monitoring microsecond motions of biological molecules. Dynamic changes of conductance through a transistor made of a single-walled carbon nanotube (SWNT-FET) report conformational changes of a protein molecule tethered to the SWNT sidewall. In principle, the high operating speed of SWNT-FETs could allow this technique to resolve molecular events with nanosecond resolution. This project focused on improving the technique to a 200 kHz effective bandwidth in order to resolve microsecond-scale dynamics. The improvement was achieved with a home-built electrochemical flow cell. By minimizing parasitic capacitance due to liquid coupling to electrodes and eliminating noise pickup, the flow cell enabled low-noise, high bandwidth measurement of molecular events as short as 2 mus. The apparatus was used to observe closing and opening motions of lysozyme. Preliminary results suggest that lysozyme has a distribution of possible velocities with the most probable speed approaching our experimental resolution of 2 mus.

  13. 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.

  14. Fluorine conformational effects in organocatalysis: an emerging strategy for molecular design.

    Science.gov (United States)

    Zimmer, Lucie E; Sparr, Christof; Gilmour, Ryan

    2011-12-09

    Molecular design strategies that profit from the intrinsic stereoelectronic and electrostatic effects of fluorinated organic molecules have mainly been restricted to bio-organic chemistry. Indeed, many fluorine conformational effects remain academic curiosities with no immediate application. However, the renaissance of organocatalysis offers the possibility to exploit many of these well-described phenomena for molecular preorganization. In this minireview, we highlight examples of catalyst refinement by introduction of an aliphatic C-F bond which functions as a chemically inert steering group for conformational control. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Structure of adsorption layers and conformation transformations of ethylhydroxyethylcellulose on surfaces of titanium and iron oxides

    Science.gov (United States)

    Bulychev, N. A.; Fomin, V. N.; Malyukova, E. B.; Ur'ev, N. B.

    2011-01-01

    Regularities of the adsorption of ethylhydroxyethylcellulose (EHEC) hydrophilic polymer on a surface of inorganic pigments of TiO2 and Fe2O3 were investigated by infrared spectroscopy. It was found that the adsorption interaction between EHEC and a surface of oxides is accompanied by conformation transformations of the adsorbed molecules of EHEC. The means by which macromolecules bind with active centers on a surface of metal oxides and the influence of the oxides' nature on the EHEC macromolecule conformation transformations determining the structure of the adsorption layer upon adsorption were established.

  16. Measuring two at the same time: combining magnetic tweezers with single-molecule FRET.

    Science.gov (United States)

    Swoboda, Marko; Grieb, Maj Svea; Hahn, Steffen; Schlierf, Michael

    2014-01-01

    Molecular machines are the workhorses of the cell that efficiently convert chemical energy into mechanical motion through conformational changes. They can be considered powerful machines, exerting forces and torque on the molecular level of several piconewtons and piconewton-nanometer, respectively. For studying translocation and conformational changes of these machines, fluorescence methods, like FRET, as well as "mechanical" methods, like optical and magnetic tweezers, have proven well suited over the past decades. One of the current challenges in the field of molecular machines is gaining maximal information from single-molecule experiments by simultaneously measuring translocation, conformational changes, and forces exerted by these machines. In this chapter, we describe the combination of magnetic tweezers with single-molecule FRET for orthogonal simultaneous readout to maximize the information gained in single-molecule experiments.

  17. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 2. Molecule of the Month Isomers of Benzene - Still Pursuing Dreams. J Chandrasekhar. Feature Article Volume 1 Issue 2 February 1996 pp 80-83. Fulltext. Click here to view fulltext PDF. Permanent link:

  18. Molecule-based magnets

    Indian Academy of Sciences (India)

    Keywords. Molecular lattices; spin–spin interaction; photo-induced magnetism; single molecule magnets. ... Since the first successful synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be categorized on the basis of the chemical nature of the magnetic units involved: organic-, ...

  19. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  20. Quantum Interference of Molecules

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL │ ARTICLE. Quantum Interference of Molecules. Probing the Wave Nature of Matter. Anu Venugopalan. Keywords. Matter waves, wave-particle du- ality, electron interference, decoherence. Anu Venugopalan is on the faculty of the School of. Basic and Applied. Sciences, GGS. Indraprastha University,. Delhi.

  1. On quark molecules

    CERN Document Server

    Dolgov, A D; Okun, Lev Borisovich

    1974-01-01

    A nonrelativistic quark model with three triplets and an octet of coloured gluons is considered. The interaction energy is calculated for some quark molecules. It is shown that states of the type qqqq and qqqqq are bounded more tightly than qq and qqq, respectively. This may indicate an existence of exotic particles in the nature or, perhaps, that the model is invalid. (11 refs).

  2. Atoms, Molecules and Radiation

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course in Applications of Quantum Mechanics to 'Atoms, Molecules and Radiation' will be held at the Indian Academy of Sciences, Bangalore from December 8 to 20. 2014. The Course is primarily aimed at teachers teaching quantum mechanics and/ or atomic and molecular physics at the UG / PG level.

  3. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - Molecular-Chameleon: Solvatochromism at its Iridescent Best! Photon Rao. Volume 16 Issue 12 December 2011 pp 1303-1306. Fulltext. Click here to view fulltext PDF. Permanent link:

  4. Molecule of the Month

    Indian Academy of Sciences (India)

    attempting to adapt the success of organic chemistry in the study of organosilicon compounds. Nevertheless chemists persisted with a sense of doggedness to try and mimic organic molecules with non- carbon elements. The year 1981 marks a watershed in the efforts to prepare and stabilise multiply-bonded compounds of ...

  5. Atoms, Molecules and Radiation

    Indian Academy of Sciences (India)

    IAS Admin

    2015-11-10

    Nov 10, 2015 ... Module 3: Interaction of electromagnetic radiation with matter: Quantum theory of radiation, spontaneous, stimulated emission and absorption probabilities, electric dipole selection rules, Einstein A and B coefficients, Rabi coefficients, Thomson Scattering, Jaynes-Cummings Model. Module 4: Molecules ...

  6. Molecule of the Month

    Indian Academy of Sciences (India)

    ethanol, blue in isopropyl alcohol, green in acetone and greenish-yellow in anisole. The electronic absorption spectrum of a molecule often depends on the solvent used. The change in position (and, sometimes, intensity) of the UVNis band accompanying a change in the polarity of the medium is called solvatochromism.

  7. Excitons: Molecules in flatland

    Science.gov (United States)

    Yao, Wang

    2015-06-01

    Forming molecules from atoms is commonplace in dense atomic gases. But it now seems that some two-dimensional materials provide a suitable environment for creating complex molecular states from the hydrogen-like electron-hole pairs that form in semiconductors.

  8. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 9. Molecule of the Month Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Feature Article Volume 1 Issue 9 September 1996 pp 66-71. Fulltext. Click here to view fulltext PDF. Permanent link:

  9. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    a heterogeneous medium the local environment of each molecule may be different. This gives rise to large vari- ations of those properties which depend on the medium. (e.g., local polarity or viscosity). For instance, in a bio- logical cell the local environment at the membrane may be drastically different from that in the ...

  10. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Volume 16 Issue 12 December 2011 pp 1232-1237. Fulltext. Click here to view fulltext PDF. Permanent link:

  11. Chemical chaperone and inhibitor discovery: potential treatments for protein conformational diseases.

    Science.gov (United States)

    Zhao, Jian-Hua; Liu, Hsuan-Liang; Lin, Hsin-Yi; Huang, Chih-Hung; Fang, Hsu-Wei; Chen, Shiao-Shing; Ho, Yih; Tsai, Wei-Bor; Chen, Wen-Yih

    2007-12-11

    Protein misfolding and aggregation cause a large number of neurodegenerative diseases in humans due to (i) gain of function as observed in Alzheimer's disease, Huntington's disease, Parkinson's disease, and Prion's disease or (ii) loss of function as observed in cystic fibrosis and alpha1-antitrypsin deficiency. These misfolded proteins could either lead to the formation of harmful amyloids that become toxic for the cells or to be recognized and prematurely degraded by the protein quality control system. An increasing number of studies has indicated that some low-molecular-weight compounds named as chemical chaperones can reverse the mislocalization and/or aggregation of proteins associated with human conformational diseases. These small molecules are thought to non-selectively stabilize proteins and facilitate their folding. In this review, we summarize the probable mechanisms of protein conformational diseases in humans and the use of chemical chaperones and inhibitors as potential therapeutic agents against these diseases. Furthermore, recent advanced experimental and theoretical approaches underlying the detailed mechanisms of protein conformational changes and current structure-based drug designs towards protein conformational diseases are also discussed. It is believed that a better understanding of the mechanisms of conformational changes as well as the biological functions of these proteins will lead to the development and design of potential interfering compounds against amyloid formation associated with protein conformational diseases.

  12. The butane condensed matter conformational problem

    NARCIS (Netherlands)

    Weber, A.C.J.; de Lange, C.A.; Meerts, W.L.; Burnell, E.E.

    2010-01-01

    From the dipolar couplings of orientationally ordered n-butane obtained by NMR spectroscopy we have calculated conformer probabilities using the modified Chord (Cd) and Size-and-Shape (CI) models to estimate the conformational dependence of the order matrix. All calculation methods make use of

  13. Conformity to Peer Pressure in Preschool Children

    Science.gov (United States)

    Haun, Daniel B. M.; Tomasello, Michael

    2011-01-01

    Both adults and adolescents often conform their behavior and opinions to peer groups, even when they themselves know better. The current study investigated this phenomenon in 24 groups of 4 children between 4;2 and 4;9 years of age. Children often made their judgments conform to those of 3 peers, who had made obviously erroneous but unanimous…

  14. Group Cohesiveness, Deviation, Stress, and Conformity

    Science.gov (United States)

    1993-08-11

    productivity. ~ Relations, I. 599-519 . Blake , R. R., & Mouton , J. 5, (1961) . Conformity. resistance, and conversion. In I. A. Berg , & B. M. Bass...conversion ( Blake & HoutQn. 1961). Conformity without a true change in private acceptance has been termed compliance (Kiesler, 1969 ; Kiesler

  15. Chaotropes trigger conformational rearrangements differently in ...

    Indian Academy of Sciences (India)

    SHREYASI ASTHANA

    Abstract. Concanavalin A (ConA) is a plant lectin having industrial and biological applications. Concanavalin. A changes conformation upon exposure to different stress conditions, like exposure to sodium dodecyl sulphate, guanidine hydrochloride, varying hydronium ion potential, etc. The conformational changes were ...

  16. Asymptotic symmetry algebra of conformal gravity

    Science.gov (United States)

    Irakleidou, Maria; Lovrekovic, Iva

    2017-11-01

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

  17. Conformity to the Surviving Sepsis Campaign International ...

    African Journals Online (AJOL)

    They had moderate conformity rates for blood cultures prior to administering antibiotics (57%) and administration of antibiotics within first hour of recognition of septic shock (54%). There was high conformity rate to the glucose control policy (81%), use of protective lung strategy in acute lung injury/Acute respiratory distress ...

  18. Conformation of hindered piperidines: Spectroscopic evidence for ...

    Indian Academy of Sciences (India)

    Administrator

    C NMR; conformational analysis; boat forms. 1. Introduction. Many piperidine derivatives are found to possess pharmacological activity and form an essential part of the molecular structure of important drugs. 1. Most of the piperidine precursors are known to exist in chair conformation. Electron withdrawing groups. (–NO ...

  19. Conformational Explosion: Understanding the Complexity of the Para-Dialkylbenzene Potential Energy Surfaces

    Science.gov (United States)

    Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

    2017-06-01

    This talk focuses on the single-conformation spectroscopy of small-chain para-dialkylbenzenes. This work builds on previous studies from our group on long-chain n-alkylbenzenes that identified the first folded structure in octylbenzene. The dialkylbenzenes are representative of a class of molecules that are common components of coal and aviation fuel and are known to be present in vehicle exhaust. We bring the molecules para-diethylbenzene, para-dipropylbenzene and para-dibutylbenzene into the gas phase and cool the molecules in a supersonic expansion. The jet-cooled molecules are then interrogated using laser-induced fluorescence excitation, fluorescence dip IR spectroscopy (FDIRS) and dispersed fluorescence. The LIF spectra in the S_{0}-S_{1} origin region show dramatic increases in the number of resolved transitions with increasing length of alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an 'egg carton' shape to the potential energy surface. We use a combination of electronic frequency shift and alkyl CH stretch infrared spectra to generate a consistent set of conformational assignments.

  20. OMG: Open Molecule Generator

    Directory of Open Access Journals (Sweden)

    Peironcely Julio E

    2012-09-01

    Full Text Available Abstract Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG, which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  1. Wormholes in conformal gravity arXiv

    CERN Document Server

    Hohmann, Manuel; Raidal, Martti; Veermäe, Hardi

    We present a new class of solutions for static spherically symmetric wormhole spacetimes in conformal gravity and outline a detailed method for their construction. As an explicit example, we construct a class of traversable and non-traversable wormholes that are locally conformal to Schwarzschild-(anti) de Sitter spacetimes. These wormhole spacetimes are exact vacuum solutions in, but not being limited to, Weyl gravity and conformal scalar-tensor theories. Importantly, the method implies that every conformal gravity theory with local field equations will trivially contain wormholes without the need for exotic matter. Applying those results on gravitational theories that possess conformal symmetry in the ultraviolet regime, the central singularities of black holes can be replaced with wormhole throats. We speculate on possible phenomenological consequences.

  2. 5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

    Science.gov (United States)

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

    2005-02-01

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

  3. Bacterial invasion reconstructed molecule by molecule

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the

  4. Conformational structures in dry ionomers

    Science.gov (United States)

    Allahyarov, Elshad; Taylor, Philip

    2007-03-01

    The molecular architecture of polymer electrolyte membranes (PEM), which consist of hydrophobic and hydrophilic segments, leads to its own self-assembled structure through a partial phase segregation. Controlling these structures is necessary for improving the performance of fuel cells. We have used computer simulation to analyze the relationship between the hydrophilic cluster structure and the parameters describing the pendant side chains in dry Nafion-like materials. We investigate the morphology of a dry PEM system within different coarse-grained models: a free-proton model, a dipolar model for side chains, and a branched-chain model. We conclude that the free-proton model, where the proton-proton correlations are decoupled from the sulfonate-sulfonate correlations, has the potential to explain the experimentally observed conformational structures of PEM. We find that the geometry of domains with a high concentration of sulfonate groups depends only weakly on the form of the distance-dependent dielectric permittivity, but strongly depends on the partial charge and monomeric unit sequence distribution along the ionomer chain. We predict a nanophase separation with a lamellar-like morphology in ionomers carrying a divalent salt.

  5. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Limitation on Declaration of Conformity. 2.1072... Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The Declaration of Conformity signifies that...'s rules. (b) A Declaration of Conformity by the responsible party is effective until a termination...

  6. Fast electron transfer through a single molecule natively structured redox protein

    DEFF Research Database (Denmark)

    Della Pia, Eduardo Antonio; Chi, Qijin; Macdonald, J. Emyr

    2012-01-01

    of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between...... and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role...

  7. 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.

  8. Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

    Science.gov (United States)

    Egli, M.; Usman, N.; Rich, A.

    1993-01-01

    We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

  9. Scanning tunnelling spectroscopy and manipulation of double-decker phthalocyanine molecules on a semiconductor surface

    Science.gov (United States)

    Pan, Yi; Kanisawa, Kiyoshi; Ishikawa, Naoto; Fölsch, Stefan

    2017-09-01

    A scanning tunnelling microscope (STM) operated at 5 K was used to study dysprosium biphthalocyanine (DyPc2) molecules adsorbed on the inert III-V semiconductor surface InAs(1 1 1)A. Orbital imaging and scanning tunnelling spectroscopy measurements reveal that the molecular electronic structure remains largely unperturbed, indicating a weak molecule-surface binding. The molecule adsorbs at the In vacancy site of the (2  ×  2)-reconstructed surface and is highly sensitive to current-induced excitations leading to random rotational fluctuations. Owing to the weak surface binding, individual molecules can be precisely repositioned and arranged by the STM tip via attractive tip-molecule interaction. In this way, DyPc2 dimers of well-defined internal structure can be assembled which exist in two conformations of equivalent appearance. A binary switching between these two conformers can be induced by injecting electrons into one of the two molecules. The conformational change of the dimer proceeds via a concerted molecular rotation and minor lateral displacement. The synchronised switching observed here is attributed to steric interactions between the two molecules constituting the dimer.

  10. Conformational landscape, photochemistry, and infrared spectra of sulfanilamide.

    Science.gov (United States)

    Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

    2013-01-31

    A combined matrix isolation FTIR and theoretical DFT(B3LYP)/6-311++G(3df,3pd) study of sulfanilamide (SA) was performed. The full conformational search on the potential energy surface of the compound allowed the identification of four different minima, all of them bearing the sulfamide nitrogen atom placed in the perpendicular orientation relatively to the aromatic ring and differing from each other in the orientation of the hydrogen atoms connected to the two nitrogen atoms of the molecule. All conformers were predicted to be significantly populated in the gas phase (at 100 °C, their relative populations were estimated as being 1:0.9:0.3:0.2). However, in agreement with the theoretically calculated low-energy barriers for conformational isomerization, in the low-temperature matrices, only the most stable conformer could be observed, with the remaining forms being converted into this form during matrix deposition (conformational cooling). The unimolecular photochemistry of matrix-isolated SA (in both argon and xenon) was also investigated. Upon broadband UV irradiation (λ > 215 nm), two photofragmentation pathways were observed: the prevalent pathway (A), leading to extrusion of sulfur dioxide and simultaneous formation of benzene-1,4-diamine, which then converts to 2,5-cyclohexadiene-1,4-diimine, and the minor pathway (B), conducting an γ-cleavage plus [1,3] H-atom migration from the sulfamide group to the aromatic ring, which leads to formation of iminosulfane dioxide and aniline, the latter undergoing subsequent phototransformation into cyclohexa-2,5-dien-1-imine. Finally, the crystalline polymorph of SA resulting from warming (265 K) the amorphous solid obtained from fast cooling of the vapor of the compound onto the cold (13 K) substrate of the cryostat was identified spectroscopically, and found to be the γ-crystalline phase, the one exhibiting in average longer H-bonds and an infrared spectrum resembling more that of the low temperature SA glass. Full

  11. Stereoelectronic Effect-Induced Conductance Switching in Aromatic Chain Single-Molecule Junctions.

    Science.gov (United States)

    Xin, Na; Wang, Jinying; Jia, Chuancheng; Liu, Zitong; Zhang, Xisha; Yu, Chenmin; Li, Mingliang; Wang, Shuopei; Gong, Yao; Sun, Hantao; Zhang, Guanxin; Liu, Zhirong; Zhang, Guangyu; Liao, Jianhui; Zhang, Deqing; Guo, Xuefeng

    2017-02-08

    Biphenyl, as the elementary unit of organic functional materials, has been widely used in electronic and optoelectronic devices. However, over decades little has been fundamentally understood regarding how the intramolecular conformation of biphenyl dynamically affects its transport properties at the single-molecule level. Here, we establish the stereoelectronic effect of biphenyl on its electrical conductance based on the platform of graphene-molecule single-molecule junctions, where a specifically designed hexaphenyl aromatic chain molecule is covalently sandwiched between nanogapped graphene point contacts to create stable single-molecule junctions. Both theoretical and temperature-dependent experimental results consistently demonstrate that phenyl twisting in the aromatic chain molecule produces different microstates with different degrees of conjugation, thus leading to stochastic switching between high- and low-conductance states. These investigations offer new molecular design insights into building functional single-molecule electrical devices.

  12. Atoms, molecules & elements

    CERN Document Server

    Graybill, George

    2007-01-01

    Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.

  13. Conformational Properties of β-PrP*

    Science.gov (United States)

    Hosszu, Laszlo L. P.; Trevitt, Clare R.; Jones, Samantha; Batchelor, Mark; Scott, David J.; Jackson, Graham S.; Collinge, John; Waltho, Jonathan P.; Clarke, Anthony R.

    2009-01-01

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly α-helical conformation to one dominated by β-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91–231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant β-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a β-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126–227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state. PMID:19369250

  14. Conformational properties of beta-PrP.

    Science.gov (United States)

    Hosszu, Laszlo L P; Trevitt, Clare R; Jones, Samantha; Batchelor, Mark; Scott, David J; Jackson, Graham S; Collinge, John; Waltho, Jonathan P; Clarke, Anthony R

    2009-08-14

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.

  15. Conformational effects in photoelectron circular dichroism

    Science.gov (United States)

    Turchini, S.

    2017-12-01

    Photoelectron circular dichroism (PECD) is a novel type of spectroscopy, which presents surprising sensitivity to conformational effects in chiral systems. While classical photoelectron spectroscopy mainly responds to conformational effects in terms of energy level shifts, PECD provides a rich and detailed response to tiny changes in electronic and structural properties by means of the intensity dispersion of the circular dichroism as a function of photoelectron kinetic energy. In this work, the basics of PECD will be outlined, emphasizing the role of interference from the l,l+/- 1 outgoing partial wave of the photoelectron in the PECD transition matrix element, which is responsible for the extreme sensitivity to conformational effects. Examples using molecular systems and interfaces will shed light on the powerful application of PECD to classical conformational effects such as group substitution, isomerism, conformer population and clustering. Moreover, the PECD results will be reported in challenging new fields where conformations play a key role, such as vibrational effects, transient chirality and time- resolved experiments. To date, PECD has mostly been based on synchrotron radiation facilities, but it also has a future as a table-top lab experiment by means of multiphoton ionization. An important application of PECD as an analytical tool will be reported. The aim of this review is to illustrate that in PECD, the presence of conformational effects is essential for understanding a wide range of effects from a new perspective, making it different from classical spectroscopy.

  16. On functional representations of the conformal algebra

    Energy Technology Data Exchange (ETDEWEB)

    Rosten, Oliver J.

    2017-07-15

    Starting with conformally covariant correlation functions, a sequence of functional representations of the conformal algebra is constructed. A key step is the introduction of representations which involve an auxiliary functional. It is observed that these functionals are not arbitrary but rather must satisfy a pair of consistency equations corresponding to dilatation and special conformal invariance. In a particular representation, the former corresponds to the canonical form of the exact renormalization group equation specialized to a fixed point whereas the latter is new. This provides a concrete understanding of how conformal invariance is realized as a property of the Wilsonian effective action and the relationship to action-free formulations of conformal field theory. Subsequently, it is argued that the conformal Ward Identities serve to define a particular representation of the energy-momentum tensor. Consistency of this construction implies Polchinski's conditions for improving the energy-momentum tensor of a conformal field theory such that it is traceless. In the Wilsonian approach, the exactly marginal, redundant field which generates lines of physically equivalent fixed points is identified as the trace of the energy-momentum tensor. (orig.)

  17. Photonic Molecule Lasers Revisited

    Science.gov (United States)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  18. Distance measurement along DNA molecules using fluorecent quantum dots

    Science.gov (United States)

    Strey, Helmut

    2005-03-01

    To create and design better micro- and nanofluidic devices, we need to understand how macromolecules behave when squeezed by lateral barriers to create pseudo-two-dimensional confinement. We present experiments in which we visualize DNA molecules of varying sizes (2 kbp - 50 kbp) trapped in 10 micrometer wide slits, the slit height varying from the radius of gyration of the unconfined molecule (micrometer) down to 25 nm (half the persistence length of DNA). We present data on the diffusion coefficient and electrophoretic mobility (no electroosmotic flow) of SYBR-gold labeled DNA molecules as a function of slit height. Simultaneously, we have assessed the DNA conformation by examining molecules that are end-labeled with differently colored fluorescent quantum dots. By determining the distance between labels, we measure directly the end-to-end distance - a conformational measure much discussed but rarely measured. Using the same approach but turning the problem around, we determined if contour length can be estimated from visualization experiments. The answer to this question becomes important when the distance between specific binding sites on the DNA backbone must be measured. One such application, for example, is the determination of haplotypes (genetic variability due to blocks of single nucleotide polymorphisms (SNP)) in diploid individuals.

  19. Spectra of conformal sigma models

    Energy Technology Data Exchange (ETDEWEB)

    Tlapak, Vaclav

    2015-04-15

    In this thesis the spectra of conformal sigma models defined on (generalized) symmetric spaces are analysed. The spaces where sigma models are conformal without the addition of a Wess-Zumino term are supermanifolds, in other words spaces that include fermionic directions. After a brief review of the general construction of vertex operators and the background field expansion, we compute the diagonal terms of the one-loop anomalous dimensions of sigma models on semi-symmetric spaces. We find that the results are formally identical to the symmetric case. However, unlike for sigma models on symmetric spaces, off diagonal terms that lead to operator mixing are also present. These are not computed here. We then present a detailed analysis of the one-loop spectrum of the supersphere S{sup 3} {sup vertical} {sup stroke} {sup 2} sigma model as one of the simplest examples. The analysis illustrates the power and simplicity of the construction. We use this data to revisit a duality with the OSP(4 vertical stroke 2) Gross-Neveu model that was proposed by Candu and Saleur. With the help of a recent all-loop result for the anomalous dimension of (1)/(2)BPS operators of Gross-Neveu models, we are able to recover the entire zero-mode spectrum of the supersphere model. We also argue that the sigma model constraints and its equations of motion are implemented correctly in the Gross-Neveu model, including the one-loop data. The duality is further supported by a new all-loop result for the anomalous dimension of the ground states of the sigma model. However, higher-gradient operators cannot be completely recovered. It is possible that this discrepancy is related to a known instability of the sigma model. The instability of sigma models is due to symmetry preserving high-gradient operators that become relevant at arbitrarily small values of the coupling. This feature has been observed long ago in one-loop calculations of the O(N)-vector model and soon been realized to be a generic

  20. Conformational analysis of the anomeric forms of kojibiose, nigerose, and maltose using MM3.

    Science.gov (United States)

    Dowd, M K; Zeng, J; French, A D; Reilly, P J

    1992-06-16

    Energy surfaces were computed for relative orientations of the relaxed pyranosyl rings of the two anomeric forms of kojibiose, nigerose, and maltose, the (1----2)-alpha, (1----3)-alpha, and (1----4)-alpha-linked D-glucosyl disaccharides, respectively. Twenty-four combinations of starting conformations of the rotatable side-groups were considered for each disaccharide. Optimized structures were calculated using MM3 on a 20 degree grid spacing of the torsional angles about the glycosidic bonds. The energy surfaces of the six disaccharides were similar in many respects but differed in detail within the low-energy regions. The maps also illustrate the importance of the exo-anomeric effect and linkage type in determining the conformational flexibility of disaccharides. Torsional conformations of known crystal structures of maltosyl-containing molecules lie in a lower MM3 energy range than previously reported.

  1. The nature of persistent conformational chirality, racemization mechanisms, and predictions in diarylether heptanoid cyclophane natural products.

    Science.gov (United States)

    Pattawong, Ommidala; Salih, M Quamar; Rosson, Nicholas T; Beaudry, Christopher M; Cheong, Paul Ha-Yeon

    2014-05-28

    Restricted rotations of chemical bonds can lead to the presence of persistent conformational chirality in molecules lacking stereocenters. We report the development of first-of-a-kind predictive rules that enable identification of conformational chirality and prediction of racemization barriers in the diarylether heptanoid (DAEH) natural products that do not possess stereocenters. These empirical rules-of-thumb are based on quantum mechanical computations (SCS-MP2/∞//B3LYP/6-31G*/PCM) of racemization barriers of four representative DAEHs. Specifically, the local symmetry of ring B and the E/Z configuration of the vinylogous acid/ester are critical in determining conformational chirality in the DAEH natural product family.

  2. Multiresolution Computation of Conformal Structures of Surfaces

    Directory of Open Access Journals (Sweden)

    Xianfeng Gu

    2003-10-01

    Full Text Available An efficient multiresolution method to compute global conformal structures of nonzero genus triangle meshes is introduced. The homology, cohomology groups of meshes are computed explicitly, then a basis of harmonic one forms and a basis of holomorphic one forms are constructed. A progressive mesh is generated to represent the original surface at different resolutions. The conformal structure is computed for the coarse level first, then used as the estimation for that of the finer level, by using conjugate gradient method it can be refined to the conformal structure of the finer level.

  3. Conformal field theory with gauge symmetry

    CERN Document Server

    Ueno, Kenji

    2008-01-01

    This book presents a systematic approach to conformal field theory with gauge symmetry from the point of view of complex algebraic geometry. After presenting the basic facts of the theory of compact Riemann surfaces and the representation theory of affine Lie algebras in Chapters 1 and 2, conformal blocks for pointed Riemann surfaces with coordinates are constructed in Chapter 3. In Chapter 4 the sheaf of conformal blocks associated to a family of pointed Riemann surfaces with coordinates is constructed, and in Chapter 5 it is shown that this sheaf supports a projective flat connection-one of

  4. Conformable Fractional Nikiforov—Uvarov Method

    Science.gov (United States)

    Karayer, H.; Demirhan, D.; Büyükkılıç, F.

    2016-07-01

    We introduce conformable fractional Nikiforov—Uvarov (NU) method by means of conformable fractional derivative which is the most natural definition in non-integer calculus. Since, NU method gives exact eigenstate solutions of Schrödinger equation (SE) for certain potentials in quantum mechanics, this method is carried into the domain of fractional calculus to obtain the solutions of fractional SE. In order to demonstrate the applicability of the conformable fractional NU method, we solve fractional SE for harmonic oscillator potential, Woods—Saxon potential, and Hulthen potential.

  5. Conformal Gravity: Dark Matter and Dark Energy

    Directory of Open Access Journals (Sweden)

    Robert K. Nesbet

    2013-01-01

    Full Text Available This short review examines recent progress in understanding dark matter, dark energy, and galactic halos using theory that departs minimally from standard particle physics and cosmology. Strict conformal symmetry (local Weyl scaling covariance, postulated for all elementary massless fields, retains standard fermion and gauge boson theory but modifies Einstein–Hilbert general relativity and the Higgs scalar field model, with no new physical fields. Subgalactic phenomenology is retained. Without invoking dark matter, conformal gravity and a conformal Higgs model fit empirical data on galactic rotational velocities, galactic halos, and Hubble expansion including dark energy.

  6. The decomposition of global conformal invariants

    CERN Document Server

    Alexakis, Spyros

    2012-01-01

    This book addresses a basic question in differential geometry that was first considered by physicists Stanley Deser and Adam Schwimmer in 1993 in their study of conformal anomalies. The question concerns conformally invariant functionals on the space of Riemannian metrics over a given manifold. These functionals act on a metric by first constructing a Riemannian scalar out of it, and then integrating this scalar over the manifold. Suppose this integral remains invariant under conformal re-scalings of the underlying metric. What information can one then deduce about the Riemannian scalar? Dese

  7. Conformal invariance in quantum field theory

    CERN Document Server

    Todorov, Ivan T; Petkova, Valentina B

    1978-01-01

    The present volume is an extended and up-to-date version of two sets of lectures by the first author and it reviews more recent work. The notes aim to present a self-contained exposition of a constructive approach to conformal invariant quantum field theory. Other parts in application of the conformal group to quantum physics are only briefly mentioned. The relevant mathematical material (harmonic analysis on Euclidean conformal groups) is briefly summarized. A new exposition of physical applications is given, which includes an explicit construction of the vacuum operator product expansion for the free zero mass fields.

  8. Static validation of licence conformance policies

    DEFF Research Database (Denmark)

    Hansen, Rene Rydhof; Nielson, Flemming; Nielson, Hanne Riis

    2008-01-01

    Policy conformance is a security property gaining importance due to commercial interest like Digital Rights Management. It is well known that static analysis can be used to validate a number of more classical security policies, such as discretionary and mandatory access control policies, as well...... as communication protocols using symmetric and asymmetric cryptography. In this work we show how to develop a Flow Logic for validating the conformance of client software with respect to a licence conformance policy. Our approach is sufficiently flexible that it extends to fully open systems that can admit new...

  9. Scalar scattering via conformal higher spin exchange

    Energy Technology Data Exchange (ETDEWEB)

    Joung, Euihun [School of Physics and Astronomy,Seoul National University, Seoul 151-747 (Korea, Republic of); Gauge, Gravity & Strings, Center for Theoretical Physics of the Universe,Institute for Basic Sciences, Daejeon 34047 (Korea, Republic of); Nakach, Simon; Tseytlin, Arkady A. [Theoretical physics group, Blackett Laboratory,Imperial College London, SW7 2AZ (United Kingdom)

    2016-02-18

    Theories containing infinite number of higher spin fields require a particular definition of summation over spins consistent with their underlying symmetries. We consider a model of massless scalars interacting (via bilinear conserved currents) with conformal higher spin fields in flat space. We compute the tree-level four-scalar scattering amplitude using a natural prescription for summation over an infinite set of conformal higher spin exchanges and find that it vanishes. Independently, we show that the vanishing of the scalar scattering amplitude is, in fact, implied by the global conformal higher spin symmetry of this model. We also discuss one-loop corrections to the four-scalar scattering amplitude.

  10. Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

    Science.gov (United States)

    Flechsig, Holger

    2016-02-01

    ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

  11. Preparation of Low Entropy Correlated Many-body States via Conformal Cooling Quenches

    CERN Document Server

    Zaletel, Michael P; Yao, Norman Y

    2016-01-01

    We analyze a method for preparing low-entropy many-body states in isolated quantum optical systems of atoms, ions and molecules. Our approach is based upon shifting entropy between different regions of a system by spatially modulating the magnitude of the effective Hamiltonian. We conduct two case studies, on a topological spin chain and the spinful fermionic Hubbard model, focusing on the key question: can a "conformal cooling quench" remove sufficient entropy within experimentally accessible timescales? Finite temperature, time-dependent matrix product state calculations reveal that even moderately sized "bath" regions can remove enough energy and entropy density to expose coherent low temperature physics. The protocol is particularly natural in systems with long-range interactions such lattice-trapped polar molecules and Rydberg dressed atoms where the magnitude of the Hamiltonian scales directly with the density. To this end, we propose a simple implementation of conformal cooling quenches in a dilutely-f...

  12. The broadband microwave spectra of the monoterpenoids thymol and carvacrol: Conformational landscape and internal dynamics

    Science.gov (United States)

    Schmitz, D.; Shubert, V. A.; Giuliano, B. M.; Schnell, M.

    2014-07-01

    The rotational spectra of the monoterpenoids thymol and carvacrol are reported in the frequency range 2-8.5 GHz, obtained with broadband Fourier-transform microwave spectroscopy. For carvacrol four different conformations were identified in the cold conditions of the molecular jet, whereas only three conformations were observed for thymol. The rotational constants and other molecular parameters are reported and compared with quantum chemical calculations. For both molecules, line splittings due to methyl group internal rotation were observed and the resulting barrier heights could be determined. The experimental barrier heights, 4.0863(25) kJ/mol for trans-carvacrol-A, 4.4024(16) kJ/mol for trans-carvacrol-B, and 0.3699(11) kJ/mol for trans-thymol-A, are compared with similar molecules.

  13. The broadband microwave spectra of the monoterpenoids thymol and carvacrol: Conformational landscape and internal dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schmitz, D.; Shubert, V. A. [Max Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany); The Center for Free-Electron Laser Science, Hamburg (Germany); Giuliano, B. M. [Center for Astrobiology, INTA-CSIC, Torrejón de Ardoz, Madrid (Spain); Schnell, M., E-mail: melanie.schnell@mpsd.mpg.de [Max Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany); The Center for Free-Electron Laser Science, Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Hamburg (Germany)

    2014-07-21

    The rotational spectra of the monoterpenoids thymol and carvacrol are reported in the frequency range 2–8.5 GHz, obtained with broadband Fourier-transform microwave spectroscopy. For carvacrol four different conformations were identified in the cold conditions of the molecular jet, whereas only three conformations were observed for thymol. The rotational constants and other molecular parameters are reported and compared with quantum chemical calculations. For both molecules, line splittings due to methyl group internal rotation were observed and the resulting barrier heights could be determined. The experimental barrier heights, 4.0863(25) kJ/mol for trans-carvacrol-A, 4.4024(16) kJ/mol for trans-carvacrol-B, and 0.3699(11) kJ/mol for trans-thymol-A, are compared with similar molecules.

  14. Antigenic determinants of influenza virus hemagglutinin. XI. Conformational changes detected by monoclonal antibodies.

    Science.gov (United States)

    Jackson, D C; Nestorowicz, A

    1985-08-01

    At pH 5 influenza virus hemagglutinin undergoes an irreversible conformational change (J.J. Skehel, P. M. Bayley, E. B. Brown, S. R. Martin, M. D. Waterfield, J. M. White, I. A. Wilson, and D. C. Wiley (1982). Proc. Natl. Acad. Sci. USA 79, 968-972) which parallels the appearance of fusion activity of this molecule. This paper describes experiments which explore the conformational change using a panel of monoclonal antibodies which define four of the major antigenic sites of this protein. The results indicate that three of the major antigenic sites of hemagglutinin undergo changes when exposed to acid pH. These changes have little effect on the binding avidity of influenza virus to glycophorin, the major receptor present on the red blood cell surface. These findings have been used to postulate a mechanism where the molecule flexes around a central region resulting in rearrangement in space of its component domains on exposure to low pH.

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

    Science.gov (United States)

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

    2005-03-10

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

  16. Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus.

    Directory of Open Access Journals (Sweden)

    Raffaella Nativio

    2009-11-01

    Full Text Available Cohesin is a chromatin-associated protein complex that mediates sister chromatid cohesion by connecting replicated DNA molecules. Cohesin also has important roles in gene regulation, but the mechanistic basis of this function is poorly understood. In mammalian genomes, cohesin co-localizes with CCCTC binding factor (CTCF, a zinc finger protein implicated in multiple gene regulatory events. At the imprinted IGF2-H19 locus, CTCF plays an important role in organizing allele-specific higher-order chromatin conformation and functions as an enhancer blocking transcriptional insulator. Here we have used chromosome conformation capture (3C assays and RNAi-mediated depletion of cohesin to address whether cohesin affects higher order chromatin conformation at the IGF2-H19 locus in human cells. Our data show that cohesin has a critical role in maintaining CTCF-mediated chromatin conformation at the locus and that disruption of this conformation coincides with changes in IGF2 expression. We show that the cohesin-dependent, higher-order chromatin conformation of the locus exists in both G1 and G2 phases of the cell cycle and is therefore independent of cohesin's function in sister chromatid cohesion. We propose that cohesin can mediate interactions between DNA molecules in cis to insulate genes through the formation of chromatin loops, analogous to the cohesin mediated interaction with sister chromatids in trans to establish cohesion.

  17. Conserved linear dynamics of single-molecule Brownian motion

    KAUST Repository

    Serag, Maged F.

    2017-06-06

    Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

  18. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

    Science.gov (United States)

    Cao, Chan; Long, Yi-Tao

    2018-02-20

    Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

  19. Single Molecule Study of Photoconversion and Spectral Heterogeneities of Fluorophores

    DEFF Research Database (Denmark)

    Liao, Zhiyu

    of conformational changes and dynamics. The photophysical properties of organic dyes directly determine the quality of the experiments. So the better understanding of the photophysical properties of organic dyes, the better we are able to design the experiments and interpret the data, especially in single molecule...... 104 single molecule measurements. A simple and practical method is introduced to study the characteristics of the photoproducts at the ensemble level. Control experiments reveal that the reaction leading to photobleaching is oxygen related, but the composition of the photoproducts remains inconclusive...... stimulate new pathways in engineering and designing photoconvertible fluorophores, based on the reaction with oxygen or other chemicals. Besides, this results show that dyes that convert into other emissive species could give problems when interpreting single molecule FRET systems. The revealed mechanism...

  20. Density Functional Theory of Polymer Structure and Conformations

    Directory of Open Access Journals (Sweden)

    Zhaoyang Wei

    2016-04-01

    Full Text Available We present a density functional approach to quantitatively evaluate the microscopic conformations of polymer chains with consideration of the effects of chain stiffness, polymer concentration, and short chain molecules. For polystyrene (PS, poly(ethylene oxide (PEO, and poly(methyl methacrylate (PMMA melts with low-polymerization degree, as chain length increases, they display different stretching ratios and show non-universal scaling exponents due to their different chain stiffnesses. In good solvent, increase of PS concentration induces the decline of gyration radius. For PS blends containing short (m1 = 1 − 100 and long (m = 100 chains, the expansion of long chains becomes unobvious once m 1 is larger than 40, which is also different to the scaling properties of ideal chain blends.