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

Universal hydrodynamics of non-conformal branes

International Nuclear Information System (INIS)

Kanitscheider, Ingmar; Skenderis, Kostas

2009-01-01

We examine the hydrodynamic limit of non-conformal branes using the recently developed precise holographic dictionary. We first streamline the discussion of holography for backgrounds that asymptote locally to non-conformal brane solutions by showing that all such solutions can be obtained from higher dimensional asymptotically locally AdS solutions by suitable dimensional reduction and continuation in the dimension. As a consequence, many holographic results for such backgrounds follow from the corresponding results of the Asymptotically AdS case. In particular, the hydrodynamics of non-conformal branes is fully determined in terms of conformal hydrodynamics. Using previous results on the latter we predict the form of the non-conformal hydrodynamic stress tensor to second order in derivatives. Furthermore we show that the ratio between bulk and shear viscosity is fixed by the generalized conformal structure to be ζ/η = 2(1/(d-1)-c s 2 ), where c s is the speed of sound in the fluid.

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...

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-08-15

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

An evaluation of canonical forms for non-rigid 3D shape retrieval

OpenAIRE

Pickup, David; Liu, Juncheng; Sun, Xianfang; Rosin, Paul L.; Martin, Ralph R.; Cheng, Zhiquan; Lian, Zhouhui; Nie, Sipin; Jin, Longcun; Shamai, Gil; Sahillioğlu, Yusuf; Kavan, Ladislav

2018-01-01

Canonical forms attempt to factor out a non-rigid shape’s pose, giving a pose-neutral shape. This opens up the\\ud possibility of using methods originally designed for rigid shape retrieval for the task of non-rigid shape retrieval.\\ud We extend our recent benchmark for testing canonical form algorithms. Our new benchmark is used to evaluate a\\ud greater number of state-of-the-art canonical forms, on five recent non-rigid retrieval datasets, within two different\\ud retrieval frameworks. A tota...

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

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

How Diverse are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?

Science.gov (United States)

Friedrich, Nils-Ole; Simsir, Méliné; Kirchmair, Johannes

2018-03-01

Knowledge of the bioactive conformations of small molecules or the ability to predict them with theoretical methods is of key importance to the design of bioactive compounds such as drugs, agrochemicals and cosmetics. Using an elaborate cheminformatics pipeline, which also evaluates the support of individual atom coordinates by the measured electron density, we compiled a complete set (“Sperrylite Dataset”) of high-quality structures of protein-bound ligand conformations from the PDB. The Sperrylite Dataset consists of a total of 10,936 high-quality structures of 4548 unique ligands. Based on this dataset, we assessed the variability of the bioactive conformations of 91 small molecules—each represented by a minimum of ten structures—and found it to be largely independent of the number of rotatable bonds. Sixty-nine molecules had at least two distinct conformations (defined by an RMSD greater than 1 Å). For a representative subset of 17 approved drugs and cofactors we observed a clear trend for the formation of few clusters of highly similar conformers. Even for proteins that share a very low sequence identity, ligands were regularly found to adopt similar conformations. For cofactors, a clear trend for extended conformations was measured, although in few cases also coiled conformers were observed. The Sperrylite Dataset is available for download from http://www.zbh.uni-hamburg.de/sperrylite_dataset.

Orbital energies and structural non-rigidity of complex hydrides according to data on ab initio calculations

Energy Technology Data Exchange (ETDEWEB)

Boldyrev, A I; Sukhanov, L P; Charkin, O P [AN SSSR, Moscow. Inst. Novykh Khimicheskikh Problem

1982-01-01

In approximation by the Hartree-Fock-Routine method using several Gauss type bases ionization potentials of complex hydrides LiBeH/sub 3/, NaBeH/sub 3/, LiMgH/sub 3/, LiBH/sub 4/, NaBH/sub 4/ and LiAlH/sub 4/ have been calculated. A problem of the show of structural non-rigidity of complex molecules L(MX/sub 4/) with tetrahedral anions (MX/sub 4/)/sup -/ in photoelectron spectra is considered.

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

Energy Technology Data Exchange (ETDEWEB)

Ngo, Anh T.; Skeini, Timur [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Iancu, Violeta [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Redfern, Paul C.; Curtiss, Larry A.; Hla, Saw Wai [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States

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 beta-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 beta-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of beta-carotene/chlorophyll-a clsuters, with intimate structural details highlighting how they pair: beta-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.

Mechanics of responsive polymers via conformationally switchable molecules

Science.gov (United States)

Brighenti, Roberto; Artoni, Federico; Vernerey, Franck; Torelli, Martina; Pedrini, Alessandro; Domenichelli, Ilaria; Dalcanale, Enrico

2018-04-01

Active materials are those capable of giving some physical reaction under external stimuli coming from the environment such as temperature, pH, light, mechanical stress, etc. Reactive polymeric materials can be obtained through the introduction of switchable molecules in their network, i.e. molecules having two distinct stable conformations: if properly linked to the hosting polymer chains, the switching from one state to the other can promote a mechanical reaction of the material, detectable at the macroscale, and thus enables us to tune the response according to a desired functionality. In the present paper, the main aspects of the mechanical behavior of polymeric materials with embedded switchable molecules-properly linked to the polymer's chains-are presented and discussed. Starting from the micro mechanisms occurring in such active material, a continuum model is developed, providing a straightforward implementation in computational approaches. Finally, some experimental outcomes related to a switchable molecules (known as quinoxaline cavitands) added to an elastomeric PDMS under chemical stimuli, are presented and quantitatively discussed through the use of the developed mechanical framework.

Single molecule insights on conformational selection and induced fit mechanism

DEFF Research Database (Denmark)

Hatzakis, Nikos

2014-01-01

. To describe the molecular basis of this behavior, two main mechanisms have been advanced: 'induced fit' and 'conformational selection'. Our understanding of these models relies primarily on NMR, computational studies and kinetic measurements. These techniques report the average behavior of a large ensemble...... 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...

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

CT-3DRA registration for radiosurgery treatments: a comparison among rigid, affine and non rigid approaches

International Nuclear Information System (INIS)

Stancanello, J.; Loeckx, D.; Francescon, P.; Calvedon, C.; Avanzo, M.; Cora, S.; Scalchi, P.; Cerveri, P.; Ferrigno, G.

2004-01-01

This work aims at comparing rigid, affine and Local Non Rigid (LNR) CT-3D Rotational Angiography (CT-3DRA) registrations based on mutual information. 10 cranial and 1 spinal cases have been registered by rigid and affine transformations; while LNR has been applied to the cases where residual deformation must be corrected. An example of CT-3DRA registration without regularization term and an example of LNR using the similarity criterion and the regularization term as well as 3D superposition of the 3DRA before and after the registration without the regularization term are presented. All the registrations performed by rigid transformation converged to an acceptable solution. The results about the robustness test in axial direction are reported. Conclusions: For cranial cases, affine transformation endowed with threshold-segmentation pre-processing can be considered the most favourable solution for almost all registrations; for some cases, LNR provides more accurate results. For the spinal case rigid transformation is the most suitable when immobilizing patient during examinations; in this case the increase of accuracy by using LNR registrations seems to be not significant

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...

Preference of small molecules for local minimum conformations when binding to proteins.

Directory of Open Access Journals (Sweden)

Qi Wang

2007-09-01

Full Text Available It is well known that small molecules (ligands do not necessarily adopt their lowest potential energy conformations when binding to proteins. Analyses of protein-bound ligand crystal structures have reportedly shown that many of them do not even adopt the conformations at local minima of their potential energy surfaces (local minimum conformations. The results of these analyses raise a concern regarding the validity of virtual screening methods that use ligands in local minimum conformations. Here we report a normal-mode-analysis (NMA study of 100 crystal structures of protein-bound ligands. Our data show that the energy minimization of a ligand alone does not automatically stop at a local minimum conformation if the minimum of the potential energy surface is shallow, thus leading to the folding of the ligand. Furthermore, our data show that all 100 ligand conformations in their protein-bound ligand crystal structures are nearly identical to their local minimum conformations obtained from NMA-monitored energy minimization, suggesting that ligands prefer to adopt local minimum conformations when binding to proteins. These results both support virtual screening methods that use ligands in local minimum conformations and caution about possible adverse effect of excessive energy minimization when generating a database of ligand conformations for virtual screening.

Extracting a Purely Non-rigid Deformation Field of a Single Structure

Science.gov (United States)

Demirci, Stefanie; Manstad-Hulaas, Frode; Navab, Nassir

During endovascular aortic repair (EVAR) treatment, the aortic shape is subject to severe deformation that is imposed by medical instruments such as guide wires, catheters, and the stent graft. The problem definition of deformable registration of images covering the entire abdominal region, however, is highly ill-posed. We present a new method for extracting the deformation of an aneurysmatic aorta. The outline of the procedure includes initial rigid alignment of two abdominal scans, segmentation of abdominal vessel trees, and automatic reduction of their centerline structures to one specified region of interest around the aorta. Our non-rigid registration procedure then only computes local non-rigid deformation and leaves out all remaining global rigid transformations. In order to evaluate our method, experiments for the extraction of aortic deformation fields are conducted on 15 patient datasets from endovascular aortic repair (EVAR) treatment. A visual assessment of the registration results were performed by two vascular surgeons and one interventional radiologist who are all experts in EVAR procedures.

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

Science.gov (United States)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers

DEFF Research Database (Denmark)

Nuermaimaiti, Ajiguli; Schultz-Falk, Vickie; Lind Cramer, Jacob

2016-01-01

Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self-assembly of lamel......Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self......-assembly of lamellae structures. From statistical analysis of Scanning Tunnelling Microscopy (STM) data we observe a clear selection of specific conformational states after self-assembly. Using Density Functional Theory (DFT) calculations we rationalise how this selection is correlated to the orientation of the alkyl...

RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules.

Science.gov (United States)

Neveu, Emilie; Popov, Petr; Hoffmann, Alexandre; Migliosi, Angelo; Besseron, Xavier; Danoy, Grégoire; Bouvry, Pascal; Grudinin, Sergei

2018-03-15

The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of spatially proximate molecular conformations. Previously we introduced the RigidRMSD algorithm to compute the RMSD corresponding to the rigid-body motion of a molecule. In this study we go beyond the limits of the rigid-body approximation by taking into account conformational flexibility of the molecule. We model the flexibility with a reduced set of collective motions computed with e.g. normal modes or principal component analysis. The initialization of our algorithm is linear in the number of atoms and all the subsequent evaluations of RMSD values between flexible molecular conformations depend only on the number of collective motions that are selected to model the flexibility. Therefore, our algorithm is much faster compared to the standard RMSD computation for large-scale modeling applications. We demonstrate the efficiency of our method on several clustering examples, including clustering of flexible docking results and molecular dynamics (MD) trajectories. We also demonstrate how to use the presented formalism to generate pseudo-random constant-RMSD structural molecular ensembles and how to use these in cross-docking. We provide the algorithm written in C ++ as the open-source RapidRMSD library governed by the BSD-compatible license, which is available at http://team.inria.fr/nano-d/software/RapidRMSD/. The constant-RMSD structural ensemble application and clustering of MD trajectories is available at http://team.inria.fr/nano-d/software/nolb-normal-modes/. sergei.grudinin@inria.fr. Supplementary data are available at Bioinformatics.

Testing non-rigid registration of nuclear medicine data using synthetic derived SPECT images

International Nuclear Information System (INIS)

Todd-Pokropek, A.

2002-01-01

Aim: Non-rigid registration is needed to build atlas data to make statistical tests of significance of uptake in nuclear medicine (NM). Non-rigid registration is much more difficult than rigid registration to validate since some kind of matching function must be defined throughout the volume being registered, and no suitable gold standards exist. The aim here has been to assess non-rigid methods of registration and deformation for NM to NM and NM to MRI data. An additional aim has been to derive good synthetic SPECT images from other NM and MRI data to be used after as reference standards. Material and Methods: Phantom and patient test images have been acquired for both NM and MRI, which are then used to generate projections, where the characteristics of the images are modified to change both signal and noise properties. These derived images are different in character but perfectly registered with the original data, and can then be deformed in a known manner. The registration algorithm is then run backwards to re-register the modified deformed data with the original images. A technique has been developed to assess the vector fields of the original deformation to the reverse non-rigid registration field. Results: The main purpose of this paper is to describe a methodology for optimising algorithms, not to develop the algorithms themselves. Two different algorithms based on optic flow and thin plate spline interpolation have been intercompared and in particular the constraints imposed tested. Considerable differences in matching can be observed in different regions for example edge and centre of brain. Conclusions: Quadratic distance between known makers is a bad estimate to use to assess non-rigid registration. A robust statistic has been developed which can be used to optimise non-rigid algorithms based on the use of synthetic SPECT reference datasets. While the task being tested is simpler than the real clinical task, it is the first essential step in the

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 Summary: 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. : Yang et al. revealed significant conformational dynamics of Cas9 at global and local scales using single-molecule FRET. They uncovered surprising long-range allosteric communication between the HNH nuclease domain and the RNA/DNA heteroduplex at the PAM-distal end that serves as a proofreading checkpoint to govern the nuclease activity and specificity of Cas9. Keywords: CRISPR, Cas9, single-molecule, FRET, conformational dynamics, proofreading, off-target, allosteric communication, genome editing

Measuring the mechanical properties of molecular conformers

Science.gov (United States)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

In silico single-molecule manipulation of DNA with rigid body dynamics.

Directory of Open Access Journals (Sweden)

Pascal Carrivain

2014-02-01

Full Text Available We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally.

Non-rigid connector: The wand to allay the stresses on abutment

OpenAIRE

Banerjee, Saurav; Khongshei, Arlingstone; Gupta, Tapas; Banerjee, Ardhendu

2011-01-01

The use of rigid connectors in 5-unit fixed dental prosthesis with a pier abutment can result in failure of weaker retainer in the long run as the pier abutment acts as a fulcrum. Non-rigid connector placed on the distal aspect of pier seems to reduce potentially excess stress concentration on the pier abutment.

Optimized imaging using non-rigid registration

International Nuclear Information System (INIS)

Berkels, Benjamin; Binev, Peter; Blom, Douglas A.; Dahmen, Wolfgang; Sharpley, Robert C.; Vogt, Thomas

2014-01-01

The extraordinary improvements of modern imaging devices offer access to data with unprecedented information content. However, widely used image processing methodologies fall far short of exploiting the full breadth of information offered by numerous types of scanning probe, optical, and electron microscopies. In many applications, it is necessary to keep measurement intensities below a desired threshold. We propose a methodology for extracting an increased level of information by processing a series of data sets suffering, in particular, from high degree of spatial uncertainty caused by complex multiscale motion during the acquisition process. An important role is played by a non-rigid pixel-wise registration method that can cope with low signal-to-noise ratios. This is accompanied by formulating objective quality measures which replace human intervention and visual inspection in the processing chain. Scanning transmission electron microscopy of siliceous zeolite material exhibits the above-mentioned obstructions and therefore serves as orientation and a test of our procedures. - Highlights: • Developed a new process for extracting more information from a series of STEM images. • An objective non-rigid registration process copes with distortions. • Images of zeolite Y show retrieval of all information available from the data set. • Quantitative measures of registration quality were implemented. • Applicable to any serially acquired data, e.g. STM, AFM, STXM, etc

Non-rigid ultrasound image registration using generalized relaxation labeling process

Science.gov (United States)

Lee, Jong-Ha; Seong, Yeong Kyeong; Park, MoonHo; Woo, Kyoung-Gu; Ku, Jeonghun; Park, Hee-Jun

2013-03-01

This research proposes a novel non-rigid registration method for ultrasound images. The most predominant anatomical features in medical images are tissue boundaries, which appear as edges. In ultrasound images, however, other features can be identified as well due to the specular reflections that appear as bright lines superimposed on the ideal edge location. In this work, an image's local phase information (via the frequency domain) is used to find the ideal edge location. The generalized relaxation labeling process is then formulated to align the feature points extracted from the ideal edge location. In this work, the original relaxation labeling method was generalized by taking n compatibility coefficient values to improve non-rigid registration performance. This contextual information combined with a relaxation labeling process is used to search for a correspondence. Then the transformation is calculated by the thin plate spline (TPS) model. These two processes are iterated until the optimal correspondence and transformation are found. We have tested our proposed method and the state-of-the-art algorithms with synthetic data and bladder ultrasound images of in vivo human subjects. Experiments show that the proposed method improves registration performance significantly, as compared to other state-of-the-art non-rigid registration algorithms.

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.

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

Science.gov (United States)

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

2014-08-14

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

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.

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

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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.

Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET

NARCIS (Netherlands)

Hohlbein, J.; Kapanidis, A.N.

2016-01-01

Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open

A non-renormalization theorem for conformal anomalies

International Nuclear Information System (INIS)

Petkou, Anastasios; Skenderis, Kostas

1999-01-01

We provide a non-renormalization theorem for the coefficients of the conformal anomaly associated with operators with vanishing anomalous dimensions. Such operators include conserved currents and chiral operators in superconformal field theories. We illustrate the theorem by computing the conformal anomaly of 2-point functions both by a computation in the conformal field theory and via the AdS/CFT correspondence. Our results imply that 2- and 3-point functions of chiral primary operators in N=4 SU(N) SYM will not renormalize provided that a 'generalized Adler-Bardeen theorem' holds. We further show that recent arguments connecting the non-renormalizability of the above-mentioned correlation functions to a bonus U(1) Y symmetry are incomplete due to possible U(1) Y violating contact terms. The tree level contribution to the contact terms may be set to zero by considering appropriately normalized operators. Non-renormalizability of the above-mentioned correlation functions, however, will follow only if these contact terms saturate by free fields

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

Directory of Open Access Journals (Sweden)

Jiang Hualiang

2010-11-01

Full Text Available Abstract Background 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. Results 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. Conclusions By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational

Dynamic Non-Rigid Objects Reconstruction with a Single RGB-D Sensor

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Sen Wang

2018-03-01

Full Text Available This paper deals with the 3D reconstruction problem for dynamic non-rigid objects with a single RGB-D sensor. It is a challenging task as we consider the almost inevitable accumulation error issue in some previous sequential fusion methods and also the possible failure of surface tracking in a long sequence. Therefore, we propose a global non-rigid registration framework and tackle the drifting problem via an explicit loop closure. Our novel scheme starts with a fusion step to get multiple partial scans from the input sequence, followed by a pairwise non-rigid registration and loop detection step to obtain correspondences between neighboring partial pieces and those pieces that form a loop. Then, we perform a global registration procedure to align all those pieces together into a consistent canonical space as guided by those matches that we have established. Finally, our proposed model-update step helps fixing potential misalignments that still exist after the global registration. Both geometric and appearance constraints are enforced during our alignment; therefore, we are able to get the recovered model with accurate geometry as well as high fidelity color maps for the mesh. Experiments on both synthetic and various real datasets have demonstrated the capability of our approach to reconstruct complete and watertight deformable objects.

Efficient Constrained Local Model Fitting for Non-Rigid Face Alignment.

Science.gov (United States)

Lucey, Simon; Wang, Yang; Cox, Mark; Sridharan, Sridha; Cohn, Jeffery F

2009-11-01

Active appearance models (AAMs) have demonstrated great utility when being employed for non-rigid face alignment/tracking. The "simultaneous" algorithm for fitting an AAM achieves good non-rigid face registration performance, but has poor real time performance (2-3 fps). The "project-out" algorithm for fitting an AAM achieves faster than real time performance (> 200 fps) but suffers from poor generic alignment performance. In this paper we introduce an extension to a discriminative method for non-rigid face registration/tracking referred to as a constrained local model (CLM). Our proposed method is able to achieve superior performance to the "simultaneous" AAM algorithm along with real time fitting speeds (35 fps). We improve upon the canonical CLM formulation, to gain this performance, in a number of ways by employing: (i) linear SVMs as patch-experts, (ii) a simplified optimization criteria, and (iii) a composite rather than additive warp update step. Most notably, our simplified optimization criteria for fitting the CLM divides the problem of finding a single complex registration/warp displacement into that of finding N simple warp displacements. From these N simple warp displacements, a single complex warp displacement is estimated using a weighted least-squares constraint. Another major advantage of this simplified optimization lends from its ability to be parallelized, a step which we also theoretically explore in this paper. We refer to our approach for fitting the CLM as the "exhaustive local search" (ELS) algorithm. Experiments were conducted on the CMU Multi-PIE database.

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

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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.

Non-relativistic conformal symmetries and Newton-Cartan structures

International Nuclear Information System (INIS)

Duval, C; Horvathy, P A

2009-01-01

This paper provides us with a unifying classification of the conformal infinitesimal symmetries of non-relativistic Newton-Cartan spacetime. The Lie algebras of non-relativistic conformal transformations are introduced via the Galilei structure. They form a family of infinite-dimensional Lie algebras labeled by a rational 'dynamical exponent', z. The Schroedinger-Virasoro algebra of Henkel et al corresponds to z = 2. Viewed as projective Newton-Cartan symmetries, they yield, for timelike geodesics, the usual Schroedinger Lie algebra, for which z = 2. For lightlike geodesics, they yield, in turn, the Conformal Galilean Algebra (CGA) of Lukierski, Stichel and Zakrzewski (alias 'alt' of Henkel), with z = 1. Physical systems realizing these symmetries include, e.g. classical systems of massive and massless non-relativistic particles, and also hydrodynamics, as well as Galilean electromagnetism.

Paths to equilibrium in non-conformal collisions

Directory of Open Access Journals (Sweden)

Attems Maximilian

2018-01-01

Full Text Available Ever since fast hydrodynamization has been observed in heavy ion collisions the understanding of the hot early out-of-equilibrium stage of such collisions has been a topic of intense research. We use the gauge/gravity duality to model the creation of a strongly coupled Quark-Gluon plasma in a non-conformal gauge theory. This numerical relativity study is the first non-conformal holographic simulation of a heavy ion collision and reveals the existence of new relaxation channels due to the presence of non-vanishing bulk viscosity. We study shock wave collisions at different energies in gauge theories with different degrees of non-conformality and compare three relaxation times which can occur in different orderings: the hydrodynamization time (when hydrodynamics becomes applicable, the EoSization time (when the average pressure approaches its equilibrium value and the condensate relaxation time (when the expectation value of a scalar operator approaches its equilibrium value. We find that these processes can occur in several different orderings. In particular, the condensate can remain far from equilibrium even long after the plasma has hydrodynamized and EoSized.

Non-rigid registration of tomographic images with Fourier transforms

International Nuclear Information System (INIS)

Osorio, Ar; Isoardi, Ra; Mato, G

2007-01-01

Spatial image registration of deformable body parts such as thorax and abdomen has important medical applications, but at the same time, it represents an important computational challenge. In this work we propose an automatic algorithm to perform non-rigid registration of tomographic images using a non-rigid model based on Fourier transforms. As a measure of similarity, we use the correlation coefficient, finding that the optimal order of the transformation is n = 3 (36 parameters). We apply this method to a digital phantom and to 7 pairs of patient images corresponding to clinical CT scans. The preliminary results indicate a fairly good agreement according to medical experts, with an average registration error of 2 mm for the case of clinical images. For 2D images (dimensions 512x512), the average running time for the algorithm is 15 seconds using a standard personal computer. Summarizing, we find that intra-modality registration of the abdomen can be achieved with acceptable accuracy for slight deformations and can be extended to 3D with a reasonable execution time

Molecular dynamics simulation investigations of H2/D2 dissocitive chemisorption dynamics on Cun(n=13-14) Rigid/nonrigid clusters

International Nuclear Information System (INIS)

Elzein, N.

2004-01-01

In this work with a use of molecular dynamic simulations we have reported the results of a quasiclassical simulation study of the interaction of H2/(D2) with Cu N (N=13-14) atoms in both rigid /(non rigid) clusters.The geometry of the cluster is obtained by an embedded-atom (EA) mode potential, and the interaction between the molecule and cIuster is described by a LEPS -London-Eyring -Polanyi-Sato) potential energy function.Both channels the reactive dissociative adsorption of the molecule on the cIuster) and non reactive (scattering of the molecule from the cluster) are considered. The dissociative chemisorption probability, cross section and rate constant are studied as functions of the initial quantal rovibrational state of the molecule, collision energy, impact parameter and the temperature (OK,296K,834K ,1014K,1554K) of the clusters

Model analysis of molecular conformations in terms of weak interactions between non bonded atoms

International Nuclear Information System (INIS)

Lombardi, E.

1988-01-01

The aim of the present paper is to establish a reliable basis for the evaluation of stable conformations and rotational barriers for molecules, with possible applications to systems of biological interest. It is proceeded in two steps: first, the effect of chemical environment on orbitals of a given atom is studied for diatomic units, adopting a valence-bond approach and considering, as prototypes, the two simplest series of diatomic molecules with one valence electron each, i.e. the alkali diatomics and the alkali hydrides. In the model, the orbital of the hydrogen atom by a simple (''1S'') gaussian function, the valence orbital of an alkali atom by a function (r 2 -a 2 ) times a simple gaussian (''2S'' gaussian). Dissociation energies D e and equilibrium distances R e are calculated using a scanning procedure. Agreement with experiment is quantitative for the alkali diatomics. For alkali hydrides, good agreement is obtained only if validity of a rule β e R e =constant, for the two atoms separately, is postulated; β e is the characteristic parameter of a ''1S'' gaussian (hydrogen) or a ''2S'' gaussian (alkali atom) function. In a second step, the authors assume validity of the same rule in conformational analysis for any single bonded A-B molecule with A=C, O, N, P, Si, Ge and B=H, or a halogen atom. Gauge β e values for H, F and C are obtained by fitting experimental rotational barriers in C 2 H 6 , C 2 F 6 and C 3 H 8 . Stable conformation of, and barriers to rotation in, ethane-like rotors are determined, applying first-order exchange perturbation theory, in terms of two- and many-center exchange interactions in cluster of non-bonded atoms. Some 60 molecules are analyzed. Agreement with experiments is strikngly good except for a few systematic deviation. Reasons for such discrepancies are discussed

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...

Conformal Invariance, Dark Energy, and CMB Non-Gaussianity

CERN Document Server

Antoniadis, Ignatios; Mottola, Emil

2012-01-01

We show that in addition to simple scale invariance, a universe dominated by dark energy naturally gives rise to correlation functions possessing full conformal invariance. This is due to the mathematical isomorphism between the conformal group of certain three dimensional slices of de Sitter space and the de Sitter isometry group SO(4,1). In the standard homogeneous, isotropic cosmological model in which primordial density perturbations are generated during a long vacuum energy dominated de Sitter phase, the embedding of flat spatial R^3 sections in de Sitter space induces a conformal invariant perturbation spectrum and definite prediction for the shape of the non-Gaussian CMB bispectrum. In the case in which the density fluctuations are generated instead on the de Sitter horizon, conformal invariance of the S^2 horizon embedding implies a different but also quite definite prediction for the angular correlations of CMB non-Gaussianity on the sky. Each of these forms for the bispectrum is intrinsic to the sym...

Non-conformal contact mechanical characteristic analysis on spherical components

Energy Technology Data Exchange (ETDEWEB)

Zhen-zhi, G.; Bin, H.; Zheng-ming, G.; Feng-mei, Y.; Jin, Q [The 2. Artillery Engineering Univ., Xi' an (China)

2017-03-15

Non-conformal spherical-contact mechanical problems is a three-dimensional coordination or similar to the coordination spherical contact. Due to the complexity of the problem of spherical-contact and difficulties of solving higher-order partial differential equations, problems of three-dimensional coordination or similar to the coordination spherical-contact is still no exact analytical method for solving. It is based on three-dimensional taper model is proposed a model based on the contour surface of the spherical contact and concluded of the formula of the contact pressure and constructed of finite element model by contact pressure distribution under the non-conformal spherical. The results shows spherical contact model can reflect non-conformal spherical-contacting mechanical problems more than taper-contacting model, and apply for the actual project.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Science.gov (United States)

Nayar, Divya; Chakravarty, Charusita

2015-08-27

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy.

Science.gov (United States)

Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

2015-10-31

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicted dual binding modes across multiple bacterial species, our approach opens up new possibilities for understanding assembly and catalytic properties of a broad range of multi-enzyme complexes.

Supergravity, Non-Conformal Field Theories and Brane-Worlds

CERN Document Server

Gherghetta, Tony; Gherghetta, Tony; Oz, Yaron

2002-01-01

We consider the supergravity dual descriptions of non-conformal super Yang-Mills theories realized on the world-volume of Dp-branes. We use the dual description to compute stress-energy tensor and current correlators. We apply the results to the study of dilatonic brane-worlds described by non-conformal field theories coupled to gravity. We find that brane-worlds based on D4 and D5 branes exhibit a localization of gauge and gravitational fields. We calculate the corrections to the Newton and Coulomb laws in these theories.

Hierarchical and successive approximate registration of the non-rigid medical image based on thin-plate splines

Science.gov (United States)

Hu, Jinyan; Li, Li; Yang, Yunfeng

2017-06-01

The hierarchical and successive approximate registration method of non-rigid medical image based on the thin-plate splines is proposed in the paper. There are two major novelties in the proposed method. First, the hierarchical registration based on Wavelet transform is used. The approximate image of Wavelet transform is selected as the registered object. Second, the successive approximation registration method is used to accomplish the non-rigid medical images registration, i.e. the local regions of the couple images are registered roughly based on the thin-plate splines, then, the current rough registration result is selected as the object to be registered in the following registration procedure. Experiments show that the proposed method is effective in the registration process of the non-rigid medical images.

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.

47 CFR 25.220 - Non-conforming transmit/receive earth station operations.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Non-conforming transmit/receive earth station operations. 25.220 Section 25.220 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Standards § 25.220 Non-conforming transmit/receive...

Second-order hydrodynamics and universality in non-conformal holographic fluids

International Nuclear Information System (INIS)

Kleinert, Philipp; Probst, Jonas

2016-01-01

We study second-order hydrodynamic transport in strongly coupled non-conformal field theories with holographic gravity duals in asymptotically anti-de Sitter space. We first derive new Kubo formulae for five second-order transport coefficients in non-conformal fluids in (3+1) dimensions. We then apply them to holographic RG flows induced by scalar operators of dimension Δ=3. For general background solutions of the dual bulk geometry, we find explicit expressions for the five transport coefficients at infinite coupling and show that a specific combination, H̃=2ητ π −2(κ−κ ∗ )−λ 2 , always vanishes. We prove analytically that the Haack-Yarom identity H=2ητ π −4λ 1 −λ 2 =0, which is known to be true for conformal holographic fluids at infinite coupling, also holds when taking into account leading non-conformal corrections. The numerical results we obtain for two specific families of RG flows suggest that H vanishes regardless of conformal symmetry. Our work provides further evidence that the Haack-Yarom identity H=0 may be universally satisfied by strongly coupled fluids.

Second-order hydrodynamics and universality in non-conformal holographic fluids

Energy Technology Data Exchange (ETDEWEB)

Kleinert, Philipp; Probst, Jonas [Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

2016-12-19

We study second-order hydrodynamic transport in strongly coupled non-conformal field theories with holographic gravity duals in asymptotically anti-de Sitter space. We first derive new Kubo formulae for five second-order transport coefficients in non-conformal fluids in (3+1) dimensions. We then apply them to holographic RG flows induced by scalar operators of dimension Δ=3. For general background solutions of the dual bulk geometry, we find explicit expressions for the five transport coefficients at infinite coupling and show that a specific combination, H̃=2ητ{sub π}−2(κ−κ{sup ∗})−λ{sub 2}, always vanishes. We prove analytically that the Haack-Yarom identity H=2ητ{sub π}−4λ{sub 1}−λ{sub 2}=0, which is known to be true for conformal holographic fluids at infinite coupling, also holds when taking into account leading non-conformal corrections. The numerical results we obtain for two specific families of RG flows suggest that H vanishes regardless of conformal symmetry. Our work provides further evidence that the Haack-Yarom identity H=0 may be universally satisfied by strongly coupled fluids.

Calculations of critical micelle concentration by dissipative particle dynamics simulations: the role of chain rigidity.

Science.gov (United States)

Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V

2013-09-05

Micelle formation in surfactant solutions is a self-assembly process governed by complex interplay of solvent-mediated interactions between hydrophilic and hydrophobic groups, which are commonly called heads and tails. However, the head-tail repulsion is not the only factor affecting the micelle formation. For the first time, we present a systematic study of the effect of chain rigidity on critical micelle concentration and micelle size, which is performed with the dissipative particle dynamics simulation method. Rigidity of the coarse-grained surfactant molecule was controlled by the harmonic bonds set between the second-neighbor beads. Compared to flexible molecules with the nearest-neighbor bonds being the only type of bonded interactions, rigid molecules exhibited a lower critical micelle concentration and formed larger and better-defined micelles. By varying the strength of head-tail repulsion and the chain rigidity, we constructed two-dimensional diagrams presenting how the critical micelle concentration and aggregation number depend on these parameters. We found that the solutions of flexible and rigid molecules that exhibited approximately the same critical micelle concentration could differ substantially in the micelle size and shape depending on the chain rigidity. With the increase of surfactant concentration, primary micelles of more rigid molecules were found less keen to agglomeration and formation of nonspherical aggregates characteristic of flexible molecules.

Dimension of non-conformal repellers: a survey

International Nuclear Information System (INIS)

Chen, Jianyu; Pesin, Yakov

2010-01-01

This paper is a survey of recent results on the dimension of repellers for expanding maps and limit sets for iterated function systems. While the case of conformal repellers is well understood, the study of non-conformal repellers is in its early stages though a number of interesting phenomena have been discovered, some remarkable results obtained and several interesting examples constructed. We will describe contemporary state of the art in the area with emphasis on some new emerging ideas and open problems. (invited article)

Conformational analysis by intersection: CONAN.

Science.gov (United States)

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

2003-01-15

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

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

Directory of Open Access Journals (Sweden)

Qian Ye

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

Non-Noether symmetries of Hamiltonian systems with conformable fractional derivatives

International Nuclear Information System (INIS)

Wang Lin-Li; Fu Jing-Li

2016-01-01

In this paper, we present the fractional Hamilton’s canonical equations and the fractional non-Noether symmetry of Hamilton systems by the conformable fractional derivative. Firstly, the exchanging relationship between isochronous variation and fractional derivatives, and the fractional Hamilton principle of the system under this fractional derivative are proposed. Secondly, the fractional Hamilton’s canonical equations of Hamilton systems based on the Hamilton principle are established. Thirdly, the fractional non-Noether symmetries, non-Noether theorem and non-Noether conserved quantities for the Hamilton systems with the conformable fractional derivatives are obtained. Finally, an example is given to illustrate the results. (paper)

Real-time motion compensated patient positioning and non-rigid deformation estimation using 4-D shape priors.

Science.gov (United States)

Wasza, Jakob; Bauer, Sebastian; Hornegger, Joachim

2012-01-01

Over the last years, range imaging (RI) techniques have been proposed for patient positioning and respiration analysis in motion compensation. Yet, current RI based approaches for patient positioning employ rigid-body transformations, thus neglecting free-form deformations induced by respiratory motion. Furthermore, RI based respiration analysis relies on non-rigid registration techniques with run-times of several seconds. In this paper we propose a real-time framework based on RI to perform respiratory motion compensated positioning and non-rigid surface deformation estimation in a joint manner. The core of our method are pre-procedurally obtained 4-D shape priors that drive the intra-procedural alignment of the patient to the reference state, simultaneously yielding a rigid-body table transformation and a free-form deformation accounting for respiratory motion. We show that our method outperforms conventional alignment strategies by a factor of 3.0 and 2.3 in the rotation and translation accuracy, respectively. Using a GPU based implementation, we achieve run-times of 40 ms.

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

Evaluation for rigidity of box construction of nuclear reactor building

International Nuclear Information System (INIS)

Yamakawa, Tetsuo

1979-01-01

A huge box-shaped structure (hereafter, called box construction) of reinforced concrete is presently utilized as the reactor building structure in nuclear power plants. Evaluation of the rigidity of the huge box construction is required for making a vibration analysis model of nuclear reactor buildings. It is necessary to handle the box construction as the plates to which the force in plane is applied. This paper describes that the bending theory in elementary beam theory is equivalent to a peculiar, orthogonally anisotropic plate, the shearing rigidity and film rigidity in y direction of which are put to infinity and the Poisson's ratio is put to zero, viewed from the two-dimensional theory of elasticity. The form factor of 1.2 for shearing deformation in rectangular cross section was calculated from the parabolic distribution of shearing stress intensity, and it is the maximum value. The factor is equal to 1.2 for slender beams, but smaller than 1.2 for short and thick beams, having tendency to converge to 1.0. The non-conformity of boundary conditions regarding the shearing force at the both ends of cantilevers does not affect very seriously the evaluation of shearing rigidity. From the above results, it was found that the application of the theory to the box construction was able to give the rigidity evaluation with sufficient engineering accuracy. The theory can also be applied to the evaluation of tube type ultrahigh buildings. (Wakatsuki, Y.)

Holographic collisions in non-conformal theories

International Nuclear Information System (INIS)

Attems, Maximilian; Casalderrey-Solana, Jorge; Mateos, David; Santos-Oliván, Daniel; Sopuerta, Carlos F.; Triana, Miquel; Zilhão, Miguel

2017-01-01

We numerically simulate gravitational shock wave collisions in a holographic model dual to a non-conformal four-dimensional gauge theory. We find two novel effects associated to the non-zero bulk viscosity of the resulting plasma. First, the hydrodynamization time increases. Second, if the bulk viscosity is large enough then the plasma becomes well described by hydrodynamics before the energy density and the average pressure begin to obey the equilibrium equation of state. We discuss implications for the quark-gluon plasma created in heavy ion collision experiments.

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

OpenAIRE

Fiegenwald , Valérie; Bassetto , Samuel; Tollenaere , Michel

2011-01-01

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

PRICE RIGIDITY AND MONETARY NON-NEUTRALITY IN DEVELOPING COUNTRIES: EVIDENCE FROM NIGERIA

Directory of Open Access Journals (Sweden)

Nathaniel E. Urama

2013-04-01

Full Text Available In an attempt to find out the degree of monetary non-neutrality in Nigeria we started from finding out the size of price rigidity in the country. Computation with Ball and Romer method showed that price rigidity is optimal decision for firms in Nigeria only when the menu cost is well above 2.28% of the firm’s revenue which is on the high side, showing the likelihood of weak price rigidity in the country. Confirming this, the IRFs of the SVAR shows that the response of inflation to nominal shock has only one period lag. These combined results led to a small though persistent response of output to the nominal shock. The result of the study therefore points towards large nominal and small real effect of monetary policy in Nigeria and conclude that monetary policy will be a better option for contractionary plan but not for an expansionary plan.

Calculating ensemble averaged descriptions of protein rigidity without sampling.

Science.gov (United States)

González, Luis C; Wang, Hui; Livesay, Dennis R; Jacobs, Donald J

2012-01-01

Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the integer body-bar Pebble Game (PG) algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations to accurately account for fluctuations in network topology. We have developed a mean field Virtual Pebble Game (VPG) that represents the ensemble of networks by a single effective network. That is, all possible number of distance constraints (or bars) that can form between a pair of rigid bodies is replaced by the average number. The resulting effective network is viewed as having weighted edges, where the weight of an edge quantifies its capacity to absorb degrees of freedom. The VPG is interpreted as a flow problem on this effective network, which eliminates the need to sample. Across a nonredundant dataset of 272 protein structures, we apply the VPG to proteins for the first time. Our results show numerically and visually that the rigidity characterizations of the VPG accurately reflect the ensemble averaged [Formula: see text] properties. This result positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability.

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

Energy Technology Data Exchange (ETDEWEB)

Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

2015-09-15

An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

GENERAL THEORY OF THE ROTATION OF THE NON-RIGID EARTH AT THE SECOND ORDER. I. THE RIGID MODEL IN ANDOYER VARIABLES

International Nuclear Information System (INIS)

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

2010-01-01

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.

Backreaction from non-conformal quantum fields in de Sitter spacetime

Energy Technology Data Exchange (ETDEWEB)

Perez-Nadal, Guillem; Verdaguer, Enric [Departament de Fisica Fonamental and Institut de Ciencies del Cosmos, Universitat de Barcelona, Av Diagonal 647, 08028 Barcelona (Spain); Roura, Albert [Theoretical Division, T-8, Los Alamos National Laboratory, M.S. B285, Los Alamos, NM 87545 (United States)

2008-08-07

We study the backreaction on the mean field geometry due to a non-conformal quantum field in a Robertson-Walker background. In the regime of small mass and small deviation from conformal coupling, we compute perturbatively the expectation value of the stress tensor of the field for a variety of vacuum states, and use it to obtain explicitly the semiclassical gravity solutions for isotropic perturbations around de Sitter spacetime, which is found to be stable. Our results clearly show the crucial role of the non-local terms that appear in the effective action: they cancel the contribution from local terms proportional to the logarithm of the scale factor which would otherwise become dominant at late times and prevent the existence of a stable self-consistent de Sitter solution. Finally, the opposite regime of a strongly non-conformal field with a large mass is also considered.

Theoretical studies on nuclear spin selective quantum dynamics of non-linear molecules; Theoretische Untersuchung zur Quantendynamik der Kernspinisomere nicht-linearer Molekuele

Energy Technology Data Exchange (ETDEWEB)

Grohmann, Thomas

2012-05-31

In this thesis the wave packet dynamics of nuclear spin isomers of polyatomic molecules after interaction with static and time-dependent magnetic fields and moderate intense nonresonant laser pulses is investigated. In particular, the process of inducing (internal) molecular rotation as well as alignment of molecules by manipulating their rotational or rotational-torsional degrees of freedom is studied. In the first part of the thesis all theoretical concepts for identifying nuclear spin isomers and for describing their quantum dynamics will be discussed. Especially the symmetrization postulate and themolecular symmetry group will be introduced and illustrated for some examples of molecules. These concepts will be extended to the case of identifying nuclear spin isomers in the presence of an external field. In the second part it is shown for nitromethane that magnetic fields are able to induce unidirectional rotations in opposite directions for different nuclear spin isomers of molecules containing methyl groups if the dipolar interaction is included. Additionally, it is demonstrated that different nuclear spin isomers of a chemical compound may show different alignment after the interaction with a moderate intense laser pulse. As shown for the rigid symmetric top propadien and the rigid asymmetric tops ethene and analogues, distinct pairs of nuclear spin isomers show at certain points in time a complementary behavior: while one isomer is showing alignment the partner isomer is showing anti-alignment. Moreover, it is illustrated that not every nuclear spin isomer can be aligned equally efficient. The alignment of non-rigid molecules is considered as well. As an example for a molecule with feasible torsion in the electronic ground state, the alignment of diboron tetrafluoride is investigated. It becomes apparent that not only rotational but also the torsional dynamics of the molecules is nuclear spin selective; different nuclear spin isomers have at distinct points

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

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

International Nuclear Information System (INIS)

Laurence, Ted Alfred

2002-01-01

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

Thermostability in rubredoxin and its relationship to mechanical rigidity

Science.gov (United States)

Rader, A. J.

2010-03-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.

Thermostability in rubredoxin and its relationship to mechanical rigidity

International Nuclear Information System (INIS)

Rader, A J

2010-01-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors

Study of the flow development of polymer solutions through capillaries

International Nuclear Information System (INIS)

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

1991-01-01

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

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

Science.gov (United States)

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

2011-01-01

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

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.

Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale

Science.gov (United States)

Kuzu, Guray; Gursoy, Attila; Nussinov, Ruth; Keskin, Ozlem

2013-01-01

Cellular functions are performed through protein-protein interactions; therefore, identification of these interactions is crucial for understanding biological processes. Recent studies suggest that knowledge-based approaches are more useful than ‘blind’ docking for modeling at large scales. However, a caveat of knowledge-based approaches is that they treat molecules as rigid structures. The Protein Data Bank (PDB) offers a wealth of conformations. Here, we exploited ensemble of the conformations in predictions by a knowledge-based method, PRISM. We tested ‘difficult’ cases in a docking-benchmark dataset, where the unbound and bound protein forms are structurally different. Considering alternative conformations for each protein, the percentage of successfully predicted interactions increased from ~26% to 66%, and 57% of the interactions were successfully predicted in an ‘unbiased’ scenario, in which data related to the bound forms were not utilized. If the appropriate conformation, or relevant template interface, is unavailable in the PDB, PRISM could not predict the interaction successfully. The pace of the growth of the PDB promises a rapid increase of ensemble conformations emphasizing the merit of such knowledge-based ensemble strategies for higher success rates in protein-protein interaction predictions on an interactome-scale. We constructed the structural network of ERK interacting proteins as a case study. PMID:23590674

Conformal invariance in harmonic superspace

International Nuclear Information System (INIS)

Galperin, A.; Ivanov, E.; Ogievetsky, V.; Sokatchev, E.

1987-01-01

In the present paper we show how the N = 2 superconformal group is realised in harmonic superspace and examine conformal invariance of N = 2 off-shell theories. We believe that the example of N = O self-dual Yang-Mills equations can serve as an instructive introduction to the subject of harmonic superspace and this is examined. The rigid N = 2 conformal supersymmetry and its local version, i.e. N = 2 conformal supergravity is also discussed. The paper is a contribution to the book commemorating the sixtieth birthday of E.S. Fradkin. (author)

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.

Conformal FDTD modeling of 3-D wake fields

International Nuclear Information System (INIS)

Jurgens, T.G.; Harfoush, F.A.

1991-01-01

Many computer codes have been written to model wake fields. Here the authors 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 so as to conform to the interface. These improvements to 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 monitors

Selective stimulation of conformational conversions in free molecules

International Nuclear Information System (INIS)

Ismailzade, G.I.; Movsumov, I.Z.; Menzeleev, M.R.; Kazymova, S.B.

2014-01-01

Application of double-resonance (RF-MW, IR-MW, MW-MW) methods to enhance studies of unstable isomeric structures was discussed. The use of infrared pump radiation to excite conformational energy levels in order to stimulate selectively conformational conversions and to correct spectral line intensities of separate conformations was substantiated. (authors)

[Non-rigid medical image registration based on mutual information and thin-plate spline].

Science.gov (United States)

Cao, Guo-gang; Luo, Li-min

2009-01-01

To get precise and complete details, the contrast in different images is needed in medical diagnosis and computer assisted treatment. The image registration is the basis of contrast, but the regular rigid registration does not satisfy the clinic requirements. A non-rigid medical image registration method based on mutual information and thin-plate spline was present. Firstly, registering two images globally based on mutual information; secondly, dividing reference image and global-registered image into blocks and registering them; then getting the thin-plate spline transformation according to the shift of blocks' center; finally, applying the transformation to the global-registered image. The results show that the method is more precise than the global rigid registration based on mutual information and it reduces the complexity of getting control points and satisfy the clinic requirements better by getting control points of the thin-plate transformation automatically.

Accuracy limit of rigid 3-point water models

Science.gov (United States)

Izadi, Saeed; Onufriev, Alexey V.

2016-08-01

Classical 3-point rigid water models are most widely used due to their computational efficiency. Recently, we introduced a new approach to constructing classical rigid water models [S. Izadi et al., J. Phys. Chem. Lett. 5, 3863 (2014)], which permits a virtually exhaustive search for globally optimal model parameters in the sub-space that is most relevant to the electrostatic properties of the water molecule in liquid phase. Here we apply the approach to develop a 3-point Optimal Point Charge (OPC3) water model. OPC3 is significantly more accurate than the commonly used water models of same class (TIP3P and SPCE) in reproducing a comprehensive set of liquid bulk properties, over a wide range of temperatures. Beyond bulk properties, we show that OPC3 predicts the intrinsic charge hydration asymmetry (CHA) of water — a characteristic dependence of hydration free energy on the sign of the solute charge — in very close agreement with experiment. Two other recent 3-point rigid water models, TIP3PFB and H2ODC, each developed by its own, completely different optimization method, approach the global accuracy optimum represented by OPC3 in both the parameter space and accuracy of bulk properties. Thus, we argue that an accuracy limit of practical 3-point rigid non-polarizable models has effectively been reached; remaining accuracy issues are discussed.

Calculating ensemble averaged descriptions of protein rigidity without sampling.

Directory of Open Access Journals (Sweden)

Luis C González

Full Text Available Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the integer body-bar Pebble Game (PG algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations to accurately account for fluctuations in network topology. We have developed a mean field Virtual Pebble Game (VPG that represents the ensemble of networks by a single effective network. That is, all possible number of distance constraints (or bars that can form between a pair of rigid bodies is replaced by the average number. The resulting effective network is viewed as having weighted edges, where the weight of an edge quantifies its capacity to absorb degrees of freedom. The VPG is interpreted as a flow problem on this effective network, which eliminates the need to sample. Across a nonredundant dataset of 272 protein structures, we apply the VPG to proteins for the first time. Our results show numerically and visually that the rigidity characterizations of the VPG accurately reflect the ensemble averaged [Formula: see text] properties. This result positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability.

Asymptotic conformal invariance in a non-Abelian Chern-Simons-matter model

Energy Technology Data Exchange (ETDEWEB)

Acebal, J.L. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil). Coordenacao de Campos e Particulas]. E-mail: acebal@cbpf.br

2002-08-01

One shows here the existence of solutions to the Callan-Symanzik equation for the non-Abelian SU(2) Chern-Simons-matter model which exhibits asymptotic conformal invariance to every order in perturbative theory. The conformal symmetry in the classical domain is shown to hold by means of a local criteria based on the trace of the energy-momentum tensor. By using recently exhibited regimes for the dependence between the several couplings in which the set of {beta}-functions vanish, the asymptotic conformal invariance of the model appears to be valid in the quantum domain. By considering the SU (n) case the possible non validity of the proof for a particular {eta} would be merely accidental. (author)

Constrained non-rigid registration for whole body image registration: method and validation

Science.gov (United States)

Li, Xia; Yankeelov, Thomas E.; Peterson, Todd E.; Gore, John C.; Dawant, Benoit M.

2007-03-01

3D intra- and inter-subject registration of image volumes is important for tasks that include measurements and quantification of temporal/longitudinal changes, atlas-based segmentation, deriving population averages, or voxel and tensor-based morphometry. A number of methods have been proposed to tackle this problem but few of them have focused on the problem of registering whole body image volumes acquired either from humans or small animals. These image volumes typically contain a large number of articulated structures, which makes registration more difficult than the registration of head images, to which the vast majority of registration algorithms have been applied. To solve this problem, we have previously proposed an approach, which initializes an intensity-based non-rigid registration algorithm with a point based registration technique [1, 2]. In this paper, we introduce new constraints into our non-rigid registration algorithm to prevent the bones from being deformed inaccurately. Results we have obtained show that the new constrained algorithm leads to better registration results than the previous one.

Analysis of non-conformity in continuous quality improvement in a Hospital Radiopharmacy Unit.

Science.gov (United States)

Martinez, T; Contreras, J F

To perform an analysis of non-conformities (NC) registered between 2012 and 2015, as a part of the review process of the Quality Management System of our Radiopharmacy Unit. Non-conformities registered in the Radiopharmacy Unit in the period 2012-2015 are analyzed and sorted by their impact on the process (critical, major, and minor), cause/origin of the non-conformity, and nature of radiopharmaceutical (PET vs. SPECT). A decrease in the NC of 20% per year is observed, especially in PET radiopharmaceuticals. Non-conformities in SPECT make up about 62-84% of the total of the NC, mainly related to the high number of doses prepared and not administered, which is about 1.5-3% in the ratio of non-administered/administered per year. Analysis of the NC can be considered as a useful indicator in assessment of quality assurance, and in our particular case, the decrease in the registration of NC indicates effectiveness in the corrective and preventive actions implemented. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

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.

Conformation Generation: The State of the Art.

Science.gov (United States)

Hawkins, Paul C D

2017-08-28

The generation of conformations for small molecules is a problem of continuing interest in cheminformatics and computational drug discovery. This review will present an overview of methods used to sample conformational space, focusing on those methods designed for organic molecules commonly of interest in drug discovery. Different approaches to both the sampling of conformational space and the scoring of conformational stability will be compared and contrasted, with an emphasis on those methods suitable for conformer sampling of large numbers of drug-like molecules. Particular attention will be devoted to the appropriate utilization of information from experimental solid-state structures in validating and evaluating the performance of these tools. The review will conclude with some areas worthy of further investigation.

OPE convergence in non-relativistic conformal field theories

Energy Technology Data Exchange (ETDEWEB)

Goldberger, Walter D.; Khandker, Zuhair University; Prabhu, Siddharth [Department of Physics, Yale University,New Haven, CT 06511 (United States); Physics Department, Boston University,Boston, MA 02215 (United States)

2015-12-09

Motivated by applications to the study of ultracold atomic gases near the unitarity limit, we investigate the structure of the operator product expansion (OPE) in non-relativistic conformal field theories (NRCFTs). The main tool used in our analysis is the representation theory of charged (i.e. non-zero particle number) operators in the NRCFT, in particular the mapping between operators and states in a non-relativistic “radial quantization” Hilbert space. Our results include: a determination of the OPE coefficients of descendant operators in terms of those of the underlying primary state, a demonstration of convergence of the (imaginary time) OPE in certain kinematic limits, and an estimate of the decay rate of the OPE tail inside matrix elements which, as in relativistic CFTs, depends exponentially on operator dimensions. To illustrate our results we consider several examples, including a strongly interacting field theory of bosons tuned to the unitarity limit, as well as a class of holographic models. Given the similarity with known statements about the OPE in SO(2,d) invariant field theories, our results suggest the existence of a bootstrap approach to constraining NRCFTs, with applications to bound state spectra and interactions. We briefly comment on a possible implementation of this non-relativistic conformal bootstrap program.

In God we trust? Neural measures reveal lower social conformity among non-religious individuals.

Science.gov (United States)

Thiruchselvam, Ravi; Gopi, Yashoda; Kilekwang, Leonard; Harper, Jessica; Gross, James J

2017-06-01

Even in predominantly religious societies, there are substantial individual differences in religious commitment. Why is this? One possibility is that differences in social conformity (i.e. the tendency to think and behave as others do) underlie inclination towards religiosity. However, the link between religiosity and conformity has not yet been directly examined. In this study, we tested the notion that non-religious individuals show dampened social conformity, using both self-reported and neural (EEG-based ERPs) measures of sensitivity to others' influence. Non-religious vs religious undergraduate subjects completed an experimental task that assessed levels of conformity in a domain unrelated to religion (i.e. in judgments of facial attractiveness). Findings showed that, although both groups yielded to conformity pressures at the self-report level, non-religious individuals did not yield to such pressures in their neural responses. These findings highlight a novel link between religiosity and social conformity, and hold implications for prominent theories about the psychological functions of religion. © The Author (2017). Published by Oxford University Press.

Ab initio investigation of isomerism in not rigid dimer molecules of (LiAB)2 salts with 20 valent electrons (AB-=BO-, AlO-, BS-, AlS-, CN-, CP-, SiN-, SiP-)

International Nuclear Information System (INIS)

Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.; Shlojer, P.R.

1999-01-01

Ab initio calculations of potential energy surfaces in neighborhood of key structures of non rigid dimer molecules of lithium salts of (LiAB) 2 type - (LiBO) 2 , (LiAlO) 2 , (LiBS) 2 , (LiAlS) 2 , (LiCN) 2 , (LiSiN) 2 , (LiCP) 2 , (LiSiP) 2 - with 20 valent electrons are done in the framework of MP2/6-31G8//HF/6-31G* + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations. Totality of low-lying isomers containing four- and six-membered cycles with lithium bridges is localized. It is shown that for all cycles not rigidity to high deformation of angles in the case of low energy changes is characterized. Equilibrium geometrical parameters, relative energy and energy of isomer decomposition, frequency and intensities of normal vibrations are determined [ru

Conformal symmetries of the Einstein-Hilbert action on horizons of stationary and axisymmetric black holes

International Nuclear Information System (INIS)

Mei Jianwei

2012-01-01

We suggest a way to study possible conformal symmetries on black hole horizons. We do this by carrying out a Kaluza-Klein-like reduction of the Einstein-Hilbert action along the ignorable coordinates of stationary and axisymmetric black holes. Rigid diffeomorphism invariance of the m-ignorable coordinates then becomes a global SL(m, R) gauge symmetry of the reduced action. Related to each non-vanishing angular velocity, there is a particular SL(2, R) subgroup, which can be extended to the Witt algebra on the black hole horizons. The classical Einstein-Hilbert action thus has k-copies of infinite-dimensional conformal symmetries on a given black hole horizon, with k being the number of non-vanishing angular velocities of the black hole. (paper)

Conformational studies of self-organized regioregular poly(3-dodecylthiophene)s using non-contact atomic force microscopy in ultra high vacuum condition

International Nuclear Information System (INIS)

Tanaka, Shukichi; Grevin, Benjamin; Rannou, Patrice; Suzuki, Hitoshi; Mashiko, Shinro

2006-01-01

Conformations of one of the variations of π-conjugated poly-alkylthiophene, poly(3-dodecylthiophene)s (P3DDT)s on the surface in ultra high vacuum (UHV) were investigated by non-contact atomic force microscopy (NC-AFM) operated by frequency-modulation mode (FM-mode). From individual molecules to several multi-layered ones, polymer chains on the surface were clearly resolved on conducting highly oriented pyrolytic graphite (HOPG) substrates and insulating mica ones, respectively. Solvent evaporation was found to have two stages, which influenced the diffusion, ordering, and adhesion processes of polymer chains on the substrate. To keep the ordered conformations of deposited polymer chains when they are transferred from ambient condition to UHV, these evaporation processes should be carefully considered. The initial conformation of polymers on the substrate was found to depend strongly on the lattice matching conditions and interactions between polymers and substrates. Formations of stripe-like structures of P3DDT polymers were found on the mica substrates, which is promising for device application

Adsorption of asymmetric rigid rods or heteronuclear diatomic moleculeson homogeneous surfaces

Science.gov (United States)

Engl, W.; Courbin, L.; Panizza, P.

2004-10-01

We treat the adsorption on homogeneous surfaces of asymmetric rigid rods (like for instance heteronuclear diatomic molecules). We show that the n→0 vector spin formalism is well suited to describe such a problem. We establish an isomorphism between the coupling constants of the magnetic Hamiltonian and the adsorption parameters of the rigid rods. By solving this Hamiltonian within a mean-field approximation, we obtain analytical expressions for the densities of the different rod’s configurations, both isotherm and isobar adsorptions curves. The most probable configurations of the molecules (normal or parallel to the surface) which depends on temperature and energy parameters are summarized in a diagram. We derive that the variation of Qv , the heat of adsorption at constant volume, with the temperature is a direct signature of the adsorbed molecules configuration change. We show that this formalism can be generalized to more complicated problems such as for instance the adsorption of symmetric and asymmetric rigid rods mixtures in the presence or not of interactions.

The two-body problem of a pseudo-rigid body and a rigid sphere

DEFF Research Database (Denmark)

Kristiansen, Kristian Uldall; Vereshchagin, M.; Gózdziewski, K.

2012-01-01

n this paper we consider the two-body problem of a spherical pseudo-rigid body and a rigid sphere. Due to the rotational and "re-labelling" symmetries, the system is shown to possess conservation of angular momentum and circulation. We follow a reduction procedure similar to that undertaken...... in the study of the two-body problem of a rigid body and a sphere so that the computed reduced non-canonical Hamiltonian takes a similar form. We then consider relative equilibria and show that the notions of locally central and planar equilibria coincide. Finally, we show that Riemann's theorem on pseudo......-rigid bodies has an extension to this system for planar relative equilibria....

Energy conditions of non-singular black hole spacetimes in conformal gravity

International Nuclear Information System (INIS)

Toshmatov, Bobir; Bambi, Cosimo; Ahmedov, Bobomurat; Abdujabbarov, Ahmadjon; Stuchlik, Zdenek

2017-01-01

Conformal gravity can elegantly solve the problem of spacetime singularities present in Einstein's gravity. For every physical spacetime, there is an infinite family of conformally equivalent singularity-free metrics. In the unbroken phase, every non-singular metric is equivalent and can be used to infer the physical properties of the spacetime. In the broken phase, a Higgs-like mechanism should select a certain vacuum, which thus becomes the physical one. However, in the absence of the complete theoretical framework we do not know how to select the right vacuum. In this paper, we study the energy conditions of non-singular black hole spacetimes obtained in conformal gravity assuming they are solutions of Einstein's gravity with an effective energy-momentum tensor. We check whether such conditions can be helpful to select the vacuum of the broken phase. (orig.)

Energy conditions of non-singular black hole spacetimes in conformal gravity

Energy Technology Data Exchange (ETDEWEB)

Toshmatov, Bobir [Silesian University in Opava, Faculty of Philosophy and Science, Institute of Physics, Opava (Czech Republic); Ulugh Beg Astronomical Institute, Tashkent (Uzbekistan); Bambi, Cosimo [Fudan University, Department of Physics, Center for Field Theory and Particle Physics, Shanghai (China); Eberhard-Karls Universitaet Tuebingen, Theoretical Astrophysics, Tuebingen (Germany); Ahmedov, Bobomurat [Ulugh Beg Astronomical Institute, Tashkent (Uzbekistan); National University of Uzbekistan, Tashkent (Uzbekistan); Abdujabbarov, Ahmadjon [Ulugh Beg Astronomical Institute, Tashkent (Uzbekistan); National University of Uzbekistan, Tashkent (Uzbekistan); Tashkent University of Information Technologies, Tashkent (Uzbekistan); Stuchlik, Zdenek [Silesian University in Opava, Faculty of Philosophy and Science, Institute of Physics, Opava (Czech Republic)

2017-08-15

Conformal gravity can elegantly solve the problem of spacetime singularities present in Einstein's gravity. For every physical spacetime, there is an infinite family of conformally equivalent singularity-free metrics. In the unbroken phase, every non-singular metric is equivalent and can be used to infer the physical properties of the spacetime. In the broken phase, a Higgs-like mechanism should select a certain vacuum, which thus becomes the physical one. However, in the absence of the complete theoretical framework we do not know how to select the right vacuum. In this paper, we study the energy conditions of non-singular black hole spacetimes obtained in conformal gravity assuming they are solutions of Einstein's gravity with an effective energy-momentum tensor. We check whether such conditions can be helpful to select the vacuum of the broken phase. (orig.)

Torsional rigidity, isospectrality and quantum graphs

International Nuclear Information System (INIS)

Colladay, Don; McDonald, Patrick; Kaganovskiy, Leon

2017-01-01

We study torsional rigidity for graph and quantum graph analogs of well-known pairs of isospectral non-isometric planar domains. We prove that such isospectral pairs are distinguished by torsional rigidity. (paper)

Free surface flow of a suspension of rigid particles in a non-Newtonian fluid

DEFF Research Database (Denmark)

Svec, Oldrich; Skocek, Jan; Stang, Henrik

2012-01-01

A numerical framework capable of predicting the free surface flow of a suspension of rigid particles in a non-Newtonian fluid is described. The framework is a combination of the lattice Boltzmann method for fluid flow, the mass tracking algorithm for free surface representation, the immersed...

Electric moments in molecule interferometry

International Nuclear Information System (INIS)

Eibenberger, Sandra; Gerlich, Stefan; Arndt, Markus; Tuexen, Jens; Mayor, Marcel

2011-01-01

We investigate the influence of different electric moments on the shift and dephasing of molecules in a matter wave interferometer. Firstly, we provide a quantitative comparison of two molecules that are non-polar yet polarizable in their thermal ground state and that differ in their stiffness and response to thermal excitations. While C 25 H 20 is rather rigid, its larger derivative C 49 H 16 F 52 is additionally equipped with floppy side chains and vibrationally activated dipole moment variations. Secondly, we elucidate the role of a permanent electric dipole momentby contrasting the quantum interference pattern of a (nearly) non-polar and a polar porphyrin derivative. We find that a high molecular polarizability and even sizeable dipole moment fluctuations are still well compatible with high-contrast quantum interference fringes. The presence of permanent electric dipole moments, however, can lead to a dephasing and rapid degradation of the quantum fringe pattern already at moderate electric fields. This finding is of high relevance for coherence experiments with large organic molecules, which are generally equipped with strong electric moments.

GPU-based stochastic-gradient optimization for non-rigid medical image registration in time-critical applications

NARCIS (Netherlands)

Staring, M.; Al-Ars, Z.; Berendsen, Floris; Angelini, Elsa D.; Landman, Bennett A.

2018-01-01

Currently, non-rigid image registration algorithms are too computationally intensive to use in time-critical applications. Existing implementations that focus on speed typically address this by either parallelization on GPU-hardware, or by introducing methodically novel techniques into

Structural, Spectroscopic (FT-IR, Raman and NMR, Non-linear Optical (NLO, HOMO-LUMO and Theoretical (DFT/CAM-B3LYP Analyses of N-Benzyloxycarbonyloxy-5-Norbornene-2,3-Dicarboximide Molecule

Directory of Open Access Journals (Sweden)

Nuri ÖZTÜRK

2018-02-01

Full Text Available The experimental spectroscopic investigation of N-benzyloxycarbonyloxy-5-norbornene-2,3-dicarboximide (C17H15NO5 molecule has been done using 1H and 13C NMR chemical shifts, FT-IR and Raman spectroscopies. Conformational forms have been determined depending on orientation of N-benzyloxycarbonyloxy and 5-norbornene-2,3-dicarboximide (NDI groups of the title compound. The structural geometric optimizations, vibrational wavenumbers, NMR chemical shifts (in vacuum and chloroform and HOMO-LUMO analyses for all conformers of the title molecule have been done with DFT/CAM-B3LYP method at the 6-311++G(d,p basis set. Additionally, based on the calculated HOMO and LUMO energy values, some molecular properties such as ionization potential (I, electron affinity (A, electronegativity (χ, chemical hardness (h, chemical softness (z, chemical potential (μ and electrophilicity index (w parameters are determined for all conformers. The non-linear optical (NLO properties have been studied for the title molecule. We can say that the experimental spectral data are in accordance with calculated values.

18 CFR 415.51 - Prior non-conforming structures.

Science.gov (United States)

2010-04-01

... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Prior non-conforming structures. 415.51 Section 415.51 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION... damaged by any means, including a flood, to the extent of 50 percent or more of its market value at that...

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.

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.

Solitons, τ-functions and hamiltonian reduction for non-Abelian conformal affine Toda theories

Science.gov (United States)

Ferreira, L. A.; Miramontes, J. Luis; Guillén, Joaquín Sánchez

1995-02-01

We consider the Hamiltonian reduction of the "two-loop" Wess-Zumino-Novikov-Witten model (WZNW) based on an untwisted affine Kac-Moody algebra G. The resulting reduced models, called Generalized Non-Abelian Conformal Affine Toda (G-CAT), are conformally invariant and a wide class of them possesses soliton solutions; these models constitute non-Abelian generalizations of the conformal affine Toda models. Their general solution is constructed by the Leznov-Saveliev method. Moreover, the dressing transformations leading to the solutions in the orbit of the vacuum are considered in detail, as well as the τ-functions, which are defined for any integrable highest weight representation of G, irrespectively of its particular realization. When the conformal symmetry is spontaneously broken, the G-CAT model becomes a generalized affine Toda model, whose soliton solutions are constructed. Their masses are obtained exploring the spontaneous breakdown of the conformal symmetry, and their relation to the fundamental particle masses is discussed. We also introduce what we call the two-loop Virasoro algebra, describing extended symmetries of the two-loop WZNW models.

A DNA Origami Mechanical Device for the Regulation of Microcosmic Structural Rigidity.

Science.gov (United States)

Wan, Neng; Hong, Zhouping; Wang, Huading; Fu, Xin; Zhang, Ziyue; Li, Chao; Xia, Han; Fang, Yan; Li, Maoteng; Zhan, Yi; Yang, Xiangliang

2017-11-01

DNA origami makes it feasible to fabricate a tremendous number of DNA nanostructures with various geometries, dimensions, and functionalities. Moreover, an increasing amount of research on DNA nanostructures is focused on biological and biomedical applications. Here, the reversible regulation of microcosmic structural rigidity is accomplished using a DNA origami device in vitro. The designed DNA origami monomer is composed of an internal central axis and an external sliding tube. Due to the external tube sliding, the device transforms between flexible and rigid states. By transporting the device into the liposome, the conformational change of the origami device induces a structural change in the liposome. The results obtained demonstrate that the programmed DNA origami device can be applied to regulate the microcosmic structural rigidity of liposomes. Because microcosmic structural rigidity is important to cell proliferation and function, the results obtained potentially provide a foundation for the regulation of cell microcosmic structural rigidity using DNA nanostructures. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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...

Effects of dielectric inhomogeneity on electrostatic twist rigidity of a helical biomolecule in Debye-Hückel regime

Science.gov (United States)

Rezaie-Dereshgi, Amir; Mohammad-Rafiee, Farshid

2018-04-01

The electrostatic interactions play a crucial role in biological systems. Here we consider an impermeable dielectric molecule in the solvent with a different dielectric constant. The electrostatic free energy in the problem is studied in the Debye-Hückel regime using the analytical Green function that is calculated in the paper. Using this electrostatic free energy, we study the electrostatic contribution to the twist rigidity of a double stranded helical molecule such as a DNA and an actin filament. The dependence of the electrostatic twist rigidity of the molecule to the dielectric inhomogeneity, structural parameters, and the salt concentration is studied. It is shown that, depending on the parameters, the electrostatic twist rigidity could be positive or negative.

Rotational Spectrum and Conformational Analysis of N-methyl-2-aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

Science.gov (United States)

Calabrese, Camilla; Maris, Assimo; Evangelisti, Luca; Piras, Anna; Parravicini, Valentina; Melandri, Sonia

2018-02-01

Abstract We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol’s family, and include 2-aminophenylethanol, 2-methylaminophenylethanol, noradrenaline, adrenaline 2-aminoethanol and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6-18 and 59.6-74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was obtained, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

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.

Molecules as quantum shapes and how they violate P and T

International Nuclear Information System (INIS)

Balachandran, A.P.; Witt, D.M.; Simoni, A.

1992-01-01

A geometric shape is a rigid shape in n-dimensional Euclidean space. These shapes commonly occur in the Born-Oppenheimer approximation in molecular physics, and collective models of nuclei. Abelian and non-Abelian generalizations of the of the vacuum angle of gauge theories are realized in the quantum theory of shapes. In this paper, such generalizations are presented in the language of modern quantum physics and it is shown that parity, P, and time reversal, T, are violated in certain of these quantum theories. However, the combined symmetry PT of parity composed with time reversal generally remains a good symmetry, just as in gauge theories. The exceptions are the quantum theories of staggered conformations which can violate only T. The mechanism responsible for the loss of these symmetries is a generalization of the vacuum angle mechanism for the same effect. An important results of the present analysis is the demonstration that geometric shapes, molecules in the Born-Oppenheimer approximation, and nuclei in the collective model description furnish concrete systems which upon quantization discriminate between left- and right-handed coordinates even though this distinction is entirely absent in their classical descriptions

Supersymmetric Yang-Mills theory on conformal supergravity backgrounds in ten dimensions

Energy Technology Data Exchange (ETDEWEB)

Medeiros, Paul de; Figueroa-O’Farrill, José [Maxwell Institute and School of Mathematics, The University of Edinburgh,James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom)

2016-03-14

We consider bosonic supersymmetric backgrounds of ten-dimensional conformal supergravity. Up to local conformal isometry, we classify the maximally supersymmetric backgrounds, determine their conformal symmetry superalgebras and show how they arise as near-horizon geometries of certain half-BPS backgrounds or as a plane-wave limit thereof. We then show how to define Yang-Mills theory with rigid supersymmetry on any supersymmetric conformal supergravity background and, in particular, on the maximally supersymmetric backgrounds. We conclude by commenting on a striking resemblance between the supersymmetric backgrounds of ten-dimensional conformal supergravity and those of eleven-dimensional Poincaré supergravity.

Research of vibration resistance of non-rigid shafts turning with various technological set-ups

Directory of Open Access Journals (Sweden)

Vasilevykh Sergey L.

2017-01-01

Full Text Available The article considers the definition of the stability range of a dynamic system for turning non-rigid shafts with different technological set-ups: standard and developed ones; they are improved as a result of this research. The topicality of the study is due to the fact that processing such parts is associated with significant difficulties caused by deformation of the workpiece under the cutting force as well as occurrence of vibration of the part during processing, they are so intense and in practice they force to significantly reduce the cutting regime, recur to multiple-pass operation, lead to premature deterioration of the cutter, as a result, reduce the productivity of machining shafts on metal-cutting machines. In this connection, the purpose of the present research is to determine the boundaries of the stability regions with intensive turning of non-rigid shafts. In the article the basic theoretical principles of construction of a mathematical system focused on the process of non-free cutting of a dynamic machine are justified. By means of the developed mathematical model interrelations are established and legitimacies of influence of various technological set-ups on stability of the dynamic system of the machine-tool-device-tool-blank are revealed. The conducted researches allow to more objectively represent difficult processes that occur in a closed dynamic system of a machine.

First Order Electroweak Phase Transition from (Non)Conformal Extensions of the Standard Model

DEFF Research Database (Denmark)

Sannino, Francesco; Virkajärvi, Jussi

2015-01-01

We analyse and compare the finite-temperature electroweak phase transition properties of classically (non)conformal extensions of the Standard Model. In the classically conformal scenarios the breaking of the electroweak symmetry is generated radiatively. The models feature new scalars coupled co...... the associated models are testable at the upcoming Large Hadron Collider run two experiments....

Reconstructing rotations and rigid body motions from exact point correspondences through reflections

NARCIS (Netherlands)

Fontijne, D.; Dorst, L.; Dorst, L.; Lasenby, J.

2011-01-01

We describe a new algorithm to reconstruct a rigid body motion from point correspondences. The algorithm works by constructing a series of reflections which align the points with their correspondences one by one. This is naturally and efficiently implemented in the conformal model of geometric

A new derivation of the conformally flat stationary cyclic non-circular spacetimes

International Nuclear Information System (INIS)

Ayon-Beato, Eloy; Campuzano, Cuauhtemoc; GarcIa, Alberto

2007-01-01

We present an alternative way to derive the conformally flat stationary cyclic non-circular spacetimes. We show that there is no room for stationary axisymmetric non-circular axisymmetric spacetimes. We reproduce the well know results for this sort of spacetimes recently reported in [1

A new derivation of the conformally flat stationary cyclic non-circular spacetimes

Energy Technology Data Exchange (ETDEWEB)

Ayon-Beato, Eloy [Departamento de Fisica, Facultad de Fisica e Inteligencia Artificial, Universidad Veracruzana, 91000 Xalapa, Veracruz (Mexico); Campuzano, Cuauhtemoc [Departamento de Fisica, Facultad de Fisica e Inteligencia Artificial, Universidad Veracruzana, 91000 Xalapa, Veracruz (Mexico); GarcIa, Alberto [Department of Physics, University of California, Davis, CA 95616 (United States)

2007-11-15

We present an alternative way to derive the conformally flat stationary cyclic non-circular spacetimes. We show that there is no room for stationary axisymmetric non-circular axisymmetric spacetimes. We reproduce the well know results for this sort of spacetimes recently reported in [1].

Conformal Ablative Thermal Protection Systems (CA-TPS) for Venus and Saturn Backshells

Science.gov (United States)

Beck, R.; Gasch, M.; Stackpoole, M.; Wilder, M.; Boghozian, T.; Chavez-Garcia, J.; Prabhu, Dinesh; Kazemba, Cole D.; Venkatapathy, E.

2016-01-01

This poster provides an overview of the work performed to date on the Conformal Ablative TPS (CA-TPS) element of the TPSM project out of GCDP. Under this element, NASA is developing improved ablative TPS materials based on flexible felt for reinforcement rather than rigid reinforcements. By replacing the reinforcements with felt, the resulting materials have much higher strain-to-failure and are much lower in thermal conductivity than their rigid counterparts. These characteristics should allow for larger tile sizes, direct bonding to aeroshells and even lower weight TPS. The conformal phenolic impregnated carbon felt (C-PICA) is a candidate for backshell TPS for both Venus and Saturn entry vehicles.

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

Science.gov (United States)

Feng, Wei; Wang, Zhigang; Zhang, Wenke

2017-02-28

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

Estimating the magnitude of steric effects in rigid systems by NMR

International Nuclear Information System (INIS)

Yoneda, Julliane Diniz; Seidl, Peter Rudolf; Leal, Katia Zaccur

2008-01-01

The rapid advance of supramolecular chemistry has led to a better understanding of the forces and interactions that are responsible for many different phenomena. Among these, steric effects play an important role in determining the constraints to association between the species involved. Although the role of steric effects has been recognized for a long time, quantitative information has been mainly related to the comparison of these effects on a chemical reaction or conformational equilibrium rather than the properties of the group of atoms that is responsible for their manifestation. This situation has been changing with the increase in power of computational methods and the accumulation of data on model compounds that can be used for the purpose of comparison. Here we present a short review of our recent work on NMR of rigid carbocyclic systems and apply this type of approach to di- and triamantane systems. Our results show how NMR can be used to locate the segment of a molecule that is subjected to steric effects and evaluate the degree to which these effects will distort its geometry. (author)

Estimating the magnitude of steric effects in rigid systems by NMR

Energy Technology Data Exchange (ETDEWEB)

Yoneda, Julliane Diniz [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Programa Pos-Graduacao em Quimica Organica; Seidl, Peter Rudolf [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Escola de Quimica; Leal, Katia Zaccur, E-mail: pseidl@eq.ufrj.br [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. de Fisico-Quimica. Programa de Pos-Graduacao em Quimica Organica

2008-07-01

The rapid advance of supramolecular chemistry has led to a better understanding of the forces and interactions that are responsible for many different phenomena. Among these, steric effects play an important role in determining the constraints to association between the species involved. Although the role of steric effects has been recognized for a long time, quantitative information has been mainly related to the comparison of these effects on a chemical reaction or conformational equilibrium rather than the properties of the group of atoms that is responsible for their manifestation. This situation has been changing with the increase in power of computational methods and the accumulation of data on model compounds that can be used for the purpose of comparison. Here we present a short review of our recent work on NMR of rigid carbocyclic systems and apply this type of approach to di- and triamantane systems. Our results show how NMR can be used to locate the segment of a molecule that is subjected to steric effects and evaluate the degree to which these effects will distort its geometry. (author)

Birationally rigid varieties

CERN Document Server

Pukhlikov, Aleksandr

2013-01-01

Birational rigidity is a striking and mysterious phenomenon in higher-dimensional algebraic geometry. It turns out that certain natural families of algebraic varieties (for example, three-dimensional quartics) belong to the same classification type as the projective space but have radically different birational geometric properties. In particular, they admit no non-trivial birational self-maps and cannot be fibred into rational varieties by a rational map. The origins of the theory of birational rigidity are in the work of Max Noether and Fano; however, it was only in 1970 that Iskovskikh and Manin proved birational superrigidity of quartic three-folds. This book gives a systematic exposition of, and a comprehensive introduction to, the theory of birational rigidity, presenting in a uniform way, ideas, techniques, and results that so far could only be found in journal papers. The recent rapid progress in birational geometry and the widening interaction with the neighboring areas generate the growing interest ...

Watching individual molecules flex within lipid membranes using SERS

Science.gov (United States)

Taylor, Richard W.; Benz, Felix; Sigle, Daniel O.; Bowman, Richard W.; Bao, Peng; Roth, Johannes S.; Heath, George R.; Evans, Stephen D.; Baumberg, Jeremy J.

2014-08-01

Interrogating individual molecules within bio-membranes is key to deepening our understanding of biological processes essential for life. Using Raman spectroscopy to map molecular vibrations is ideal to non-destructively `fingerprint' biomolecules for dynamic information on their molecular structure, composition and conformation. Such tag-free tracking of molecules within lipid bio-membranes can directly connect structure and function. In this paper, stable co-assembly with gold nano-components in a `nanoparticle-on-mirror' geometry strongly enhances the local optical field and reduces the volume probed to a few nm3, enabling repeated measurements for many tens of minutes on the same molecules. The intense gap plasmons are assembled around model bio-membranes providing molecular identification of the diffusing lipids. Our experiments clearly evidence measurement of individual lipids flexing through telltale rapid correlated vibrational shifts and intensity fluctuations in the Raman spectrum. These track molecules that undergo bending and conformational changes within the probe volume, through their interactions with the environment. This technique allows for in situ high-speed single-molecule investigations of the molecules embedded within lipid bio-membranes. It thus offers a new way to investigate the hidden dynamics of cell membranes important to a myriad of life processes.

Ground state hydrogen conformations and vibrational analysis of 1,2-dihdroxyanthraquinone (alizarin) molecule by AB initio Hartree-Fock and density functional theory calculations

International Nuclear Information System (INIS)

Delta, E.; Ucun, F.; Saglam, A.

2010-01-01

The ground state hydrogen conformations of 1,2-dihydroxyanthraquinone (alizarin) molecule have been investigated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d,p) basis set. The calculations indicate that the compound in the ground state exist with the doubly bonded O atom linked intra molecularly by the two hydrogen bonds. The vibrational analyses of the ground state conformation of the compound were also made and its optimized geometry parameters were given.

Investigating the conformation of polymeric dispersant molecules on nanoparticle surface

International Nuclear Information System (INIS)

Yasin, S.; Luckham, P.F.; Iqbal, T

2016-01-01

Block copolymers are widely used as stabilizers in industrial dispersions. These polymers adsorb on surfaces by an anchor chain and extend by a hydrophilic chain. Scaling model or de Gennes theory has been used to determine the grafting density of the block copolymers. By implementing this theory to the block copolymers, conformation of the polymer molecules as a function of distance between adjacent anchor chains can be determined. The scaling model was applied to a selection of block copolymers (PE/F 103, PE/F 108, NPE1800, Triton X100, Triton X405, Lugalvan BNO12, Hypermer LP1, Hypermer B246 and OLOA 11000) in this study. The cross sectional area sc, distance s (square root of sc) and the Flory radius (end to end dimension of polymer), Rf, for all the polymers was determined. The cross sectional area per PEO (Poly Ethylene Oxide) chain (nm2) was found to be increasing with the size of stabilizing chain. Triton X100 and Lugalvan BNO12 has the smaller stabilizing chains so occupy smaller cross sectional areas whereas PE/F108 and triton X405 have larger number of PEO units and occupy a larger cross sectional area. This shows that stabilizing chain regulates the adsorption amounts that are lower in case of lower number of EO units. The application of de Gennes theory to experimental results suggested brush configuration of adsorbed polymer molecules in case of PE/F 103, PE/F 108, Triton X100, Triton X405, NPE1800, Lugalvan BNO12, Hypermer B246 and OLOA 11000. Whereas, Hypermer LP1 is more likely found to be adsorbed on graphitic carbon black in loops and trains. (author)

Conformational sensitivity of conjugated poly(ethylene oxide)-poly(amidoamine) molecules to cations adducted upon electrospray ionization – A mass spectrometry, ion mobility and molecular modeling study

Energy Technology Data Exchange (ETDEWEB)

Tintaru, Aura [Aix-Marseille Université – CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille (France); Chendo, Christophe [Aix-Marseille Université – CNRS, FR 1739, Fédération des Sciences Chimiques de Marseille, Spectropole, Marseille (France); Wang, Qi [Aix-Marseille Université – CNRS, UMR 6114, Centre Interdisciplinaire de Nanosciences de Marseille, Marseille (France); Viel, Stéphane [Aix-Marseille Université – CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille (France); Quéléver, Gilles; Peng, Ling [Aix-Marseille Université – CNRS, UMR 6114, Centre Interdisciplinaire de Nanosciences de Marseille, Marseille (France); Posocco, Paola [University of Trieste, Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), Trieste (Italy); National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste (Italy); Pricl, Sabrina, E-mail: sabrina.pricl@di3.units.it [University of Trieste, Molecular Simulation Engineering (MOSE) Laboratory, Department of Engineering and Architecture (DEA), Trieste (Italy); National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste (Italy); Charles, Laurence, E-mail: laurence.charles@univ-amu.fr [Aix-Marseille Université – CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille (France)

2014-01-15

Graphical abstract: -- Highlights: •ESI-MS/MS, IMS and molecular modeling were combined to study PEO-PAMAM conformation. •Protonated and lithiated molecules were studied, with charge states from 2 to 4. •Protonation mostly occurred on PAMAM, with PEO units enclosing the protonated group. •Lithium adduction on PEO units lead to more expanded conformations. •Charge location strongly influenced PEO-PAMAM dissociation behavior. -- Abstract: Tandem mass spectrometry and ion mobility spectrometry experiments were performed on multiply charged molecules formed upon conjugation of a poly(amidoamine) (PAMAM) dendrimer with a poly(ethylene oxide) (PEO) linear polymer to evidence any conformational modification as a function of their charge state (2+ to 4+) and of the adducted cation (H{sup +}vs Li{sup +}). Experimental findings were rationalized by molecular dynamics simulations. The G0 PAMAM head-group could accommodate up to three protons, with protonated terminal amine group enclosed in a pseudo 18-crown-6 ring formed by the PEO segment. This particular conformation enabled a hydrogen bond network which allowed long-range proton transfer to occur during collisionally activated dissociation. In contrast, lithium adduction was found to mainly occur onto oxygen atoms of the polyether, each Li{sup +} cation being coordinated by a 12-crown-4 pseudo structure. As a result, for the studied polymeric segment (M{sub n} = 1500 g mol{sup −1}), PEO-PAMAM hybrid molecules exhibited a more expanded shape when adducted to lithium as compared to proton.

An Entropy Stable h/p Non-Conforming Discontinuous Galerkin Method with the Summation-by-Parts Property

KAUST Repository

Friedrich, Lucas

2017-12-29

This work presents an entropy stable discontinuous Galerkin (DG) spectral element approximation for systems of non-linear conservation laws with general geometric (h) and polynomial order (p) non-conforming rectangular meshes. The crux of the proofs presented is that the nodal DG method is constructed with the collocated Legendre-Gauss-Lobatto nodes. This choice ensures that the derivative/mass matrix pair is a summation-by-parts (SBP) operator such that entropy stability proofs from the continuous analysis are discretely mimicked. Special attention is given to the coupling between nonconforming elements as we demonstrate that the standard mortar approach for DG methods does not guarantee entropy stability for non-linear problems, which can lead to instabilities. As such, we describe a precise procedure and modify the mortar method to guarantee entropy stability for general non-linear hyperbolic systems on h/p non-conforming meshes. We verify the high-order accuracy and the entropy conservation/stability of fully non-conforming approximation with numerical examples.

Tribological Behavior of Oil-Lubricated Laser Textured Steel Surfaces in Conformal Flat and Non-Conformal Contacts

Energy Technology Data Exchange (ETDEWEB)

Kovalchenko, A. M. [Inst. for Problems of Materials Science, Dept. 7, 3 Krzhizhanovsky Street, Kyiv 03142, UA (Corresponding author), e-mail: andrii.kovalchenko@gatech.edu; Erdemir, A. [Argonne National Lab., Energy Systems Division, 9700 South Cass Avenue, Argonne, IL 60439 US; Ajayi, O. O. [Argonne National Lab., Energy Systems Division, 9700 South Cass Avenue, Argonne, IL 60439 US; Etsion, I. [Technion-Israel Inst. of Technology, Dept. of Mechanical Engineering, Haifa 32000, IL

2017-01-30

Changing the surface texture of sliding surfaces is an effective way to manipulate friction and wear of lubricated surfaces. Having realized its potential, we have done very extensive studies on the effects of laser surface texturing (LST, which involves the creation of an array of microdimples on a surface) on friction and wear behavior of oil-lubricated steel surfaces in the early 2000s. In this paper, we reviewed some of our research accomplishments and assessed future directions of the laser texturing field in many diverse industrial applications. Our studies specifically addressed the impact of laser texturing on friction and wear of both the flat conformal and initial non-conformal point contact configurations using a pin-on-disk test rig under fully-flooded synthetic oil lubricants with different viscosities. Electrical resistance measurement between pin and LST disks was also used to determine the operating lubrication regimes in relation to friction. In conformal contact, we confirmed that LST could significantly expand the operating conditions for hydrodynamic lubrication to significantly much higher loads and slower speeds. In particular, with LST and higher viscosity oils, the low-friction full hydrodynamic regime was shifted to the far left in the Stribeck diagram. Overall, the beneficial effects of laser surface texturing were more pronounced at higher speeds and loads and with higher viscosity oil. LST was also observed to reduce the magnitude of friction coefficients in the boundary regime. For the non-conformal contact configuration, we determined that LST would produce more abrasive wear on the rubbing counterface compared to the untreated surfaces due to a reduction in lubricant fluid film thickness, as well as the highly uneven and rough nature of the textured surfaces. However, this higher initial wear rate has led to faster generation of a conformal contact, and thus transition from the high-friction boundary to lower friction mixed

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.

Variable contact gap single-molecule conductance determination for a series of conjugated molecular bridges

DEFF Research Database (Denmark)

Haiss, W.; Wang, Christian; Jitchati, R.

2008-01-01

It is now becoming clear that the characteristics of the whole junction are important in determining the conductance of single molecules bound between two metal contacts. This paper shows through measurements on a series of seven conjugated molecular bridges that contact separation is an importan...... that conductance increases rather dramatically at higher tilt angle away from the normal for conformationally rigid molecular wires and that this increase in conductance arises from increased electronic coupling between the molecular bridge and the gold contacts.......It is now becoming clear that the characteristics of the whole junction are important in determining the conductance of single molecules bound between two metal contacts. This paper shows through measurements on a series of seven conjugated molecular bridges that contact separation is an important......-distance curves and knowledge of the terminal to terminal length of the molecular wire. The contact gap separation dependence is interpreted as arising from tilting of these molecules in the junction and this model is underpinned by ab initio transport computations. In this respect we make the general observation...

On flexible and rigid nouns

DEFF Research Database (Denmark)

Rijkhoff, Jan

2010-01-01

classes. Finally this article wants to claim that the distinction between rigid and flexible noun categories (a) adds a new dimension to current classifications of parts of speech systems, (b) correlates with certain grammatical phenomena (e.g. so-called number discord), and (c) helps to explain the parts......This article argues that in addition to the major flexible lexical categories in Hengeveld’s classification of parts of speech systems (Contentive, Non-Verb, Modifier), there are also flexible word classes within the rigid lexical category Noun (Set Noun, Sort Noun, General Noun). Members...... by the flexible item in the external world. I will then argue that flexible word classes constitute a proper category (i.e. they are not the result of a merger of some rigid word classes) in that members of flexible word categories display the same properties regarding category membership as members of rigid word...

Non-Invasive Ocular Rigidity Measurement: A Differential Tonometry Approach

Directory of Open Access Journals (Sweden)

Efstathios T. Detorakis

2015-12-01

Full Text Available Purpose: Taking into account the fact that Goldmann applanation tonometry (GAT geometrically deforms the corneal apex and displaces volume from the anterior segment whereas Dynamic Contour Tonometry (DCT does not, we aimed at developing an algorithm for the calculation of ocular rigidity (OR based on the differences in pressure and volume between deformed and non-deformed status according to the general Friedenwald principle of differential tonometry. Methods: To avoid deviations of GAT IOP from true IOP in eyes with corneas different from the “calibration cornea” we applied the previously described Orssengo-Pye algorithm to calculate an error coefficient “C/B”. To test the feasibility of the proposed model, we calculated the OR coefficient (r in 17 cataract surgery candidates (9 males and 8 females. Results: The calculated r according to our model (mean ± SD, range was 0.0174 ± 0.010 (0.0123–0.022 mmHg/μL. A negative statistically significant correlation between axial length and r was detected whereas correlations between r and other biometric parameters examined were statistically not significant. Conclusions: The proposed method may prove a valid non-invasive tool for the measurement method of OR, which could help in introducing OR in the decision-making of the routine clinical practice.

Rotational Spectrum and Conformational Analysis of N-Methyl-2-Aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

Directory of Open Access Journals (Sweden)

Camilla Calabrese

2018-02-01

Full Text Available We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol's family, and include 2-amino-1-phenylethanol, 2-methylamino-1-phenylethanol, noradrenaline, adrenaline 2-aminoethanol, and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6–18 and 59.6–74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was performed, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

Science.gov (United States)

Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

2017-11-01

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

Conformationally rigid histone deacetylase inhibitors correct DF508-CFTR protein function

DEFF Research Database (Denmark)

Vickers, Chris J.; Olsen, Christian Adam; Hutt, Darren M.

2011-01-01

and bacterial infection, therapy using HDAC inhibitors has the potential to treat and correct the underlying etiology associated with the disorder. Subsequently, we have synthesized conformationally well-defined cyclic tetrapeptide derivatives based on the natural product HDAC inhibitor Apicidin, in order...

Design-order, non-conformal low-Mach fluid algorithms using a hybrid CVFEM/DG approach

Science.gov (United States)

Domino, Stefan P.

2018-04-01

A hybrid, design-order sliding mesh algorithm, which uses a control volume finite element method (CVFEM), in conjunction with a discontinuous Galerkin (DG) approach at non-conformal interfaces, is outlined in the context of a low-Mach fluid dynamics equation set. This novel hybrid DG approach is also demonstrated to be compatible with a classic edge-based vertex centered (EBVC) scheme. For the CVFEM, element polynomial, P, promotion is used to extend the low-order P = 1 CVFEM method to higher-order, i.e., P = 2. An equal-order low-Mach pressure-stabilized methodology, with emphasis on the non-conformal interface boundary condition, is presented. A fully implicit matrix solver approach that accounts for the full stencil connectivity across the non-conformal interface is employed. A complete suite of formal verification studies using the method of manufactured solutions (MMS) is performed to verify the order of accuracy of the underlying methodology. The chosen suite of analytical verification cases range from a simple steady diffusion system to a traveling viscous vortex across mixed-order non-conformal interfaces. Results from all verification studies demonstrate either second- or third-order spatial accuracy and, for transient solutions, second-order temporal accuracy. Significant accuracy gains in manufactured solution error norms are noted even with modest promotion of the underlying polynomial order. The paper also demonstrates the CVFEM/DG methodology on two production-like simulation cases that include an inner block subjected to solid rotation, i.e., each of the simulations include a sliding mesh, non-conformal interface. The first production case presented is a turbulent flow past a high-rate-of-rotation cube (Re, 4000; RPM, 3600) on like and mixed-order polynomial interfaces. The final simulation case is a full-scale Vestas V27 225 kW wind turbine (tower and nacelle omitted) in which a hybrid topology, low-order mesh is used. Both production simulations

The First Quantum Theory of Molecules

Indian Academy of Sciences (India)

IAS Admin

rotational energies of diatomic molecules. That theory was ... resent the intensity of light emitted by a black body as a function of ... by the vibrational motion of its parts”. Bjerrum was .... −1/4; despite the fact that no molecule is a rigid rotor,.

Non-singular string-cosmologies from exact conformal field theories

International Nuclear Information System (INIS)

Vega, H.J. de; Larsen, A.L.; Sanchez, N.

2001-01-01

Non-singular two and three dimensional string cosmologies are constructed using the exact conformal field theories corresponding to SO(2,1)/SO(1,1) and SO(2,2)/SO(2,1). All semi-classical curvature singularities are canceled in the exact theories for both of these cosets, but some new quantum curvature singularities emerge. However, considering different patches of the global manifolds, allows the construction of non-singular space-times with cosmological interpretation. In both two and three dimensions, we construct non-singular oscillating cosmologies, non-singular expanding and inflationary cosmologies including a de Sitter (exponential) stage with positive scalar curvature as well as non-singular contracting and deflationary cosmologies. Similarities between the two and three dimensional cases suggest a general picture for higher dimensional coset cosmologies: Anisotropy seems to be a generic unavoidable feature, cosmological singularities are generically avoided and it is possible to construct non-singular cosmologies where some spatial dimensions are experiencing inflation while the others experience deflation

The renormalization-group flux of the conformally reduced quantum gravity; Der Renormierungsgruppen-Fluss der konform-reduzierten Quantengravitation

Energy Technology Data Exchange (ETDEWEB)

Weyer, Holger

2010-12-17

We analyze the conceptual role of background independence in the application of the effective average action to quantum gravity. Insisting on a background independent nonperturbative renormalization group (RG) flow the coarse graining operation must be defined in terms of an unspecified variable metric since no rigid metric of a fixed background spacetime is available. This leads to an extra field dependence in the functional RG equation and a significantly different RG ow in comparison to the standard flow equation with a rigid metric in the mode cutoff. The background independent RG flow can possess a non-Gaussian fixed point, for instance, even though the corresponding standard one does not. We demonstrate the importance of this universal, essentially kinematical effect by computing the RG flow of Quantum Einstein Gravity (QEG) in the ''conformally reduced'' theory which discards all degrees of freedom contained in the metric except the conformal one. The conformally reduced Einstein-Hilbert approximation has exactly the same qualitative properties as in the full Einstein-Hilbert truncation. In particular it possesses the non-Gaussian fixed point which is necessary for asymptotic safety. Without the extra field dependence the resulting RG flow is that of a simple {phi}{sup 4}-theory. We employ the Local Potential Approximation for the conformal factor to generalize the RG flow on an infinite dimensional theory space. Again we find a Gaussian as well as a non-Gaussian fixed point which provides further evidence for the viability of the asymptotic safety scenario. The analog of the invariant cubic in the curvature which spoils perturbative renormalizability is seen to be unproblematic for the asymptotic safety of the conformally reduced theory. The scaling fields and dimensions of both fixed points are obtained explicitly and possible implications for the predictivity of the theory are discussed. Since the RG flow depends on the topology of the

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Science.gov (United States)

Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark

2011-01-01

The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.

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

International Nuclear Information System (INIS)

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

1980-01-01

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

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.

Disposal and close of major non-conformity of crack of concrete baseplate

International Nuclear Information System (INIS)

Zhang Zhihua; Liu Hangan; Qian Dazhi; Huang Hongwen; Deng Yue; Zhou Wei; Yang Guoqing

2009-01-01

In terms of the quality assurance and control for nuclear engineering construction, this paper introduced the determination, origin analysis, remediation, disposal and close of the major non conformity of crack of concrete baseplate. (authors)

Non-local Effects of Conformal Anomaly

Science.gov (United States)

Meissner, Krzysztof A.; Nicolai, Hermann

2018-03-01

It is shown that the nonlocal anomalous effective actions corresponding to the quantum breaking of the conformal symmetry can lead to observable modifications of Einstein's equations. The fact that Einstein's general relativity is in perfect agreement with all observations including cosmological or recently observed gravitational waves imposes strong restrictions on the field content of possible extensions of Einstein's theory: all viable theories should have vanishing conformal anomalies. It is shown that a complete cancellation of conformal anomalies in D=4 for both the C^2 invariant and the Euler (Gauss-Bonnet) invariant can only be achieved for N-extended supergravity multiplets with N ≥ 5.

Extended SL(2,R)/U(1) characters, or modular properties of a simple non-rational conformal field theory

International Nuclear Information System (INIS)

Israel, D.; Pakman, A.; Troost, J.

2004-01-01

We define extended SL(2,R)/U(1) characters which include a sum over winding sectors. By embedding these characters into similarly extended characters of N=2 algebras, we show that they have nice modular transformation properties. We calculate the modular matrices of this simple but non-trivial non-rational conformal field theory explicitly. As a result, we show that discrete SL(2,R) representations mix with continuous SL(2,R) representations under modular transformations in the coset conformal field theory. We comment upon the significance of our results for a general theory of non-rational conformal field theories. (author)

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 ...

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.

Non-perturbative scalar potential inspired by type IIA strings on rigid CY

Energy Technology Data Exchange (ETDEWEB)

Alexandrov, Sergei [Laboratoire Charles Coulomb (L2C), UMR 5221, CNRS-Université de Montpellier,F-34095, Montpellier (France); Ketov, Sergei V. [Department of Physics, Tokyo Metropolitan University,1-1 Minami-ohsawa, Hachioji-shi, Tokyo 192-0397 (Japan); Kavli Institute for the Physics and Mathematics of the Universe (IPMU), The University of Tokyo,Chiba 277-8568 (Japan); Institute of Physics and Technology, Tomsk Polytechnic University,30 Lenin Ave., Tomsk 634050 (Russian Federation); Wakimoto, Yuki [Department of Physics, Tokyo Metropolitan University,1-1 Minami-ohsawa, Hachioji-shi, Tokyo 192-0397 (Japan)

2016-11-10

Motivated by a class of flux compactifications of type IIA strings on rigid Calabi-Yau manifolds, preserving N=2 local supersymmetry in four dimensions, we derive a non-perturbative potential of all scalar fields from the exact D-instanton corrected metric on the hypermultiplet moduli space. Applying this potential to moduli stabilization, we find a discrete set of exact vacua for axions. At these critical points, the stability problem is decoupled into two subspaces spanned by the axions and the other fields (dilaton and Kähler moduli), respectively. Whereas the stability of the axions is easily achieved, numerical analysis shows instabilities in the second subspace.

Non-rigid registration of breast surfaces using the laplace and diffusion equations

Directory of Open Access Journals (Sweden)

Ou Jao J

2010-02-01

Full Text Available Abstract A semi-automated, non-rigid breast surface registration method is presented that involves solving the Laplace or diffusion equations over undeformed and deformed breast surfaces. The resulting potential energy fields and isocontours are used to establish surface correspondence. This novel surface-based method, which does not require intensity images, anatomical landmarks, or fiducials, is compared to a gold standard of thin-plate spline (TPS interpolation. Realistic finite element simulations of breast compression and further testing against a tissue-mimicking phantom demonstrate that this method is capable of registering surfaces experiencing 6 - 36 mm compression to within a mean error of 0.5 - 5.7 mm.

Non-conformity of the goods for which the seller is not liable

Directory of Open Access Journals (Sweden)

Fišer-Šobot Sandra

2011-01-01

Full Text Available Seller is liable for the conformity of delivered goods. However, there are cases where the seller's liability is excluded despite the lack of conformity of the goods. First, pursuant to Art. 478(3 of Serbian Law on Obligations an insignificant material defect of the goods should not be taken into account. In other words, minor difference in quantity or quality will not be taken into consideration where it is not material. In international trade, in principle, the seller is liable for minor defects of the goods. However, in practice seller's liability for immaterial lack of conformity will be excluded on the basis of relevant trade usages and previous bussines dealings of the parties. Second, it is commonly accepted in international and domestic trade, as concretization of the principle of good faith, that the seller is not liable for any lack of conformity of goods if at the time of conclusion of a contract the buyer knew or could not have been unaware of such lack of conformity. Seller's liability for the lack of conformity of the goods is excluded when the following requirements are fulfilled. The first requirement is that the buyer had positive knowledge of the defects or that he could not have been unaware of their existence. It is considered that the buyer could not have been unaware of the non-conformity if he acted with gross negligence. Furthermore, buyer's knowledge of the lack of conformity should exist at the time of conclusion of the contract. Finally, the exclusion of seller's liability is not possible when he acts in bad faith.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

Science.gov (United States)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

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

the binding capacity, but no correlation was found between their effect and their alpha-helical, beta-sheet, or beta-turn conformational propensity as calculated by the Chou and Fasman algorithm. In summary, all the data presented herein suggest that, at least in the case of OVA 323-336 and IAd......, the propensity of the antigen molecule to form secondary structures such as alpha-helices, beta-sheets, or beta-turns does not correlate with its capacity to bind MHC molecules....

Water-mediated influence of a crowded environment on internal vibrations of a protein molecule.

Science.gov (United States)

Kuffel, Anna; Zielkiewicz, Jan

2016-02-14

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules.

Homogenized approach for the non linear dynamic analysis of entire masonry buildings by means of rigid plate elements and damaging interfaces

Science.gov (United States)

Bertolesi, Elisa; Milani, Gabriele

2017-07-01

The present paper is devoted to the analysis of entire 3D masonry structures adopting a Rigid Body and Spring-Mass (HRBSM) model. A series of non linear static and dynamic analyses are conducted with respect to two structures with technical relevance. The elementary cell is discretized by means of three-noded plane stress elements and non-linear interfaces. At a structural level, the non-linear analyses are performed replacing the homogenized orthotropic continuum with a rigid element and non-linear spring assemblage (RBSM) by means of which both in and out of plane mechanisms are allowed. In order to validate the proposed model for the analyses of full scale structures subjected to seismic actions, two different examples are critically discussed, namely a church façade and an in-scale masonry building, both subjected to dynamic excitation. The results obtained are compared with experimental or numerical results available in literature.

Role of non-equilibrium conformations on driven polymer translocation.

Science.gov (United States)

Katkar, H H; Muthukumar, M

2018-01-14

One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/N K , is longer than the relaxation time τ 0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations. We have studied the role of initial conformations of a polyelectrolyte chain (which were artificially generated with a flow field) on the kinetics of its translocation across a nanopore under the action of an externally applied transmembrane voltage V (in the absence of the initial flow field). Stretched (out-of-equilibrium) polyelectrolyte chain conformations are deliberately and systematically generated and used as initial conformations in translocation simulations. Independent simulations are performed to study the relaxation behavior of these stretched chains, and a comparison is made between the relaxation time scale and the mean translocation time (⟨τ⟩). For such artificially stretched initial states, ⟨τ⟩/N K polymers including single stranded DNA (ssDNA), double stranded DNA (dsDNA), and synthetic polymers. Even when these data are rescaled assuming a constant effective velocity of translocation, it is found that for flexible (ssDNA and synthetic) polymers with N K Kuhn segments, the condition ⟨τ⟩/N K polymers such as ssDNA, a crossover from quasi-equilibrium to non-equilibrium behavior would occur at N K ∼ O(1000).

Electromagnetic complementary media with arbitrary geometries and non-conformal boundaries

Science.gov (United States)

Liu, Guochang; Li, Chao; Chen, Chao; Fang, Guangyou

2014-06-01

A generalized folded transformation procedure is presented for the space with arbitrary shapes. General expressions for the constitute parameters of complementary media are deduced, which can be readily applied to design complementary media based transformation optics devices (CMTOD) with arbitrary shapes. It's no longer limited to the situation when the inner and outer boundaries of the CMTOD are conformal or similar shapes, and can be available for the non-conformal situations. Three kinds of CMTOD are designed and studied, which involves a super-lens, an external cloak that hides object outside the cloaking shell, and an illusion optics device that transforms one object to another. Full-wave simulations are carried out to validate the proposed approach. The generalization introduced here makes a step forward for the flexible design of CMTOD with arbitrary geometries.

Physicochemical and nanotechnological approaches to the design of 'rigid' spatial structures of DNA

International Nuclear Information System (INIS)

Yevdokimov, Yu M; Salyanov, V I; Skuridin, S G; Shtykova, E V; Khlebtsov, N G; Kats, E I

2015-01-01

This review focuses on physicochemical and nanotechnological approaches to the design of 'rigid' particles based on double-stranded DNA molecules. The physicochemical methods imply cross-linking of adjacent DNA molecules ordered in quasinematic layers of liquid-crystalline dispersion particles by synthetic nanobridges consisting of alternating molecules of an antibiotic (daunomycin) and divalent copper ions, as well as cross-linking of these molecules as a result of their salting-out in quasinematic layers of liquid-crystalline dispersion particles under the action of lanthanide cations. The nanotechnological approach is based on the insertion of gold nanoparticles into the free space between double-stranded DNA molecules that form quasinematic layers of liquid-crystalline dispersion particles. This gives rise to extended clusters of gold nanoparticles and is accompanied by an enhancement of the interaction between the DNA molecules through gold nanoparticles and by a decrease in the solubility of dispersion particles. These approaches produce integrated 'rigid' DNA-containing spatial structures, which are incompatible with the initial aqueous polymeric solutions and have unique properties. The bibliography includes 116 references

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

Science.gov (United States)

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

2009-09-10

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

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.

Interactions between protein molecules and the virus removal membrane surface: Effects of immunoglobulin G adsorption and conformational changes on filter performance.

Science.gov (United States)

Hamamoto, Ryo; Ito, Hidemi; Hirohara, Makoto; Chang, Ryongsok; Hongo-Hirasaki, Tomoko; Hayashi, Tomohiro

2018-03-01

Membrane fouling commonly occurs in all filter types during virus filtration in protein-based biopharmaceutical manufacturing. Mechanisms of decline in virus filter performance due to membrane fouling were investigated using a cellulose-based virus filter as a model membrane. Filter performance was critically dependent on solution conditions; specifically, ionic strength. To understand the interaction between immunoglobulin G (IgG) and cellulose, sensors coated with cellulose were fabricated for surface plasmon resonance and quartz crystal microbalance with energy dissipation measurements. The primary cause of flux decline appeared to be irreversible IgG adsorption on the surface of the virus filter membrane. In particular, post-adsorption conformational changes in the IgG molecules promoted further irreversible IgG adsorption, a finding that could not be adequately explained by DLVO theory. Analyses of adsorption and desorption and conformational changes in IgG molecules on cellulose surfaces mimicking cellulose-based virus removal membranes provide an effective approach for identifying ways of optimizing solution conditions to maximize virus filter performance. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:379-386, 2018. © 2017 American Institute of Chemical Engineers.

DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.

Science.gov (United States)

Lagorce, David; Pencheva, Tania; Villoutreix, Bruno O; Miteva, Maria A

2009-11-13

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. 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. 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.

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...

Toward a general mixed quantum/classical method for the calculation of the vibronic ECD of a flexible dye molecule with different stable conformers: Revisiting the case of 2,2,2-trifluoro-anthrylethanol.

Science.gov (United States)

Cerezo, Javier; Aranda, Daniel; Avila Ferrer, Francisco J; Prampolini, Giacomo; Mazzeo, Giuseppe; Longhi, Giovanna; Abbate, Sergio; Santoro, Fabrizio

2018-06-01

We extend a recently proposed mixed quantum/classical method for computing the vibronic electronic circular dichroism (ECD) spectrum of molecules with different conformers, to cases where more than one hindered rotation is present. The method generalizes the standard procedure, based on the simple Boltzmann average of the vibronic spectra of the stable conformers, and includes the contribution of structures that sample all the accessible conformational space. It is applied to the simulation of the ECD spectrum of (S)-2,2,2-trifluoroanthrylethanol, a molecule with easily interconvertible conformers, whose spectrum exhibits a pattern of alternating positive and negative vibronic peaks. Results are in very good agreement with experiment and show that spectra averaged over all the sampled conformational space can deviate significantly from the simple average of the contributions of the stable conformers. The present mixed quantum/classical method is able to capture the effect of the nonlinear dependence of the rotatory strength on the molecular structure and of the anharmonic couplings among the modes responsible for molecular flexibility. Despite its computational cost, the procedure is still affordable and promises to be useful in all cases where the ECD shape arises from a subtle balance between vibronic effects and conformational variety. © 2018 Wiley Periodicals, Inc.

Accumulation of Tax-Loss Carryforwards : The Role of Book-Tax Non-Conformity

NARCIS (Netherlands)

S. Kohlhase (Saskia)

2016-01-01

textabstractUsing confidential corporate income tax return data, this paper investigates the association between book-tax non-conformity (measured as book-tax differences) and tax-loss carryforwards (TLCFs). I find that TLCFs are positively associated with temporary and permanent book-tax

Correction for non-rigid movement artefacts in calcium imaging using local-global optical flow and PCA-based templates

DEFF Research Database (Denmark)

Brazhe, A.; Fordsmann, J.; Lauritzen, M.

2017-01-01

correction of calcium timelapse imaging data is accurate, can represent non-rigid image distortions, robust to noisy data and allows for fast registration of large videos. The implementation is open-source and is programmed in Python, which provides for easy access and merging into downstream image...

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.

Conserved linear dynamics of single-molecule Brownian motion

Science.gov (United States)

Serag, Maged F.; Habuchi, Satoshi

2017-06-01

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.

Conserved linear dynamics of single-molecule Brownian motion

KAUST Repository

Serag, Maged F.; Habuchi, Satoshi

2017-01-01

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.

Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening

Energy Technology Data Exchange (ETDEWEB)

Begley, Darren W.; Davies, Douglas R.; Hartley, Robert C.; Hewitt, Stephen N.; Rychel, Amanda L.; Myler, Peter J.; Van Voorhis, Wesley C.; Staker, Bart L.; Stewart, Lance J. (Emerald)

2014-10-02

Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.

Science.gov (United States)

Okumura, Hisashi; Itoh, Satoru G; Okamoto, Yuko

2007-02-28

The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5-2 fs which are used by the conventional nonsymplectic algorithms.

"Mind the trap": mindfulness practice reduces cognitive rigidity.

Directory of Open Access Journals (Sweden)

Jonathan Greenberg

Full Text Available Two experiments examined the relation between mindfulness practice and cognitive rigidity by using a variation of the Einstellung water jar task. Participants were required to use three hypothetical jars to obtain a specific amount of water. Initial problems were solvable by the same complex formula, but in later problems ("critical" or "trap" problems solving was possible by an additional much simpler formula. A rigidity score was compiled through perseverance of the complex formula. In Experiment 1, experienced mindfulness meditators received significantly lower rigidity scores than non-meditators who had registered for their first meditation retreat. Similar results were obtained in randomized controlled Experiment 2 comparing non-meditators who underwent an eight meeting mindfulness program with a waiting list group. The authors conclude that mindfulness meditation reduces cognitive rigidity via the tendency to be "blinded" by experience. Results are discussed in light of the benefits of mindfulness practice regarding a reduced tendency to overlook novel and adaptive ways of responding due to past experience, both in and out of the clinical setting.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Virtual and solution conformations of oligosaccharides

International Nuclear Information System (INIS)

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

1987-01-01

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

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.

Memory effects in single-molecule spectroscopy

International Nuclear Information System (INIS)

Schmitt, Daniel T.; Schulz, Michael; Reineker, Peter

2007-01-01

From the time series of LH2 optical single-molecule fluorescence excitation spectra of Rhodospirillum molischianum the memory function of the Mori-Zwanzig equation for the optical intensity is derived numerically. We show that the time dependence of the excited states is determined by at least three different non-Markovian stochastic processes with decay constants for the Mori-Zwanzig kernel on the order of 1-5min -1 . We suggest that this decay stems from the conformational motion of the protein scaffold of LH2

Rigid-plastic seismic design of reinforced concrete structures

DEFF Research Database (Denmark)

Costa, Joao Domingues; Bento, R.; Levtchitch, V.

2007-01-01

structural strength with respect to a pre-defined performance parameter using a rigid-plastic response spectrum, which is characteristic of the ground motion alone. The maximum strength demand at any point is solely dependent on the intensity of the ground motion, which facilitates the task of distributing......In this paper a new seismic design procedure for Reinforced Concrete (R/C) structures is proposed-the Rigid-Plastic Seismic Design (RPSD) method. This is a design procedure based on Non-Linear Time-History Analysis (NLTHA) for systems expected to perform in the non-linear range during a lifetime...... earthquake event. The theoretical background is the Theory of Plasticity (Rigid-Plastic Structures). Firstly, a collapse mechanism is chosen and the corresponding stress field is made safe outside the regions where plastic behaviour takes place. It is shown that this allows the determination of the required...

The C–F bond as a conformational tool in organic and biological chemistry

Directory of Open Access Journals (Sweden)

Luke Hunter

2010-04-01

Full Text Available Organofluorine compounds are widely used in many different applications, ranging from pharmaceuticals and agrochemicals to advanced materials and polymers. It has been recognised for many years that fluorine substitution can confer useful molecular properties such as enhanced stability and hydrophobicity. Another impact of fluorine substitution is to influence the conformations of organic molecules. The stereoselective introduction of fluorine atoms can therefore be exploited as a conformational tool for the synthesis of shape-controlled functional molecules. This review will begin by describing some general aspects of the C–F bond and the various conformational effects associated with C–F bonds (i.e. dipole–dipole interactions, charge–dipole interactions and hyperconjugation. Examples of functional molecules that exploit these conformational effects will then be presented, drawing from a diverse range of molecules including pharmaceuticals, organocatalysts, liquid crystals and peptides.

Soft lubrication: The elastohydrodynamics of nonconforming and conforming contacts

Science.gov (United States)

Skotheim, J. M.; Mahadevan, L.

2005-09-01

We study the lubrication of fluid-immersed soft interfaces and show that elastic deformation couples tangential and normal forces and thus generates lift. We consider materials that deform easily, due to either geometry (e.g., a shell) or constitutive properties (e.g., a gel or a rubber), so that the effects of pressure and temperature on the fluid properties may be neglected. Four different system geometries are considered: a rigid cylinder moving parallel to a soft layer coating a rigid substrate; a soft cylinder moving parallel to a rigid substrate; a cylindrical shell moving parallel to a rigid substrate; and finally a cylindrical conforming journal bearing coated with a thin soft layer. In addition, for the particular case of a soft layer coating a rigid substrate, we consider both elastic and poroelastic material responses. For all these cases, we find the same generic behavior: there is an optimal combination of geometric and material parameters that maximizes the dimensionless normal force as a function of the softness parameter η =hydrodynamicpressure/elasticstiffness=surfacedeflection/gapthickness, which characterizes the fluid-induced deformation of the interface. The corresponding cases for a spherical slider are treated using scaling concepts.

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.

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.

A non-conforming generalization of Raviart-Thomas elements to the spherical harmonic form of the even-parity neutron transport equation

Energy Technology Data Exchange (ETDEWEB)

Van Criekingen, S. [Commissariat a l' energie atomique (CEA-Saclay), DEN/DM2S/SERMA/LENR (Bat 470), 91191 Gif-sur-Yvette Cedex (France)]. E-mail: serge.van-criekingen@cea.fr

2006-05-15

The Raviart-Thomas finite elements provide an appropriate spatial discretization of the mixed-dual form of the diffusion equation. This discretization can then be coupled to an efficient solution method. The high performances achieved by such an approach triggered research on its possible generalization to the transport equation using a spherical harmonic (or P {sub N}) angular approximation. In view of the difficulty of developing a straightforward generalization within the mixed-dual framework, we here consider 2D non-conforming (i.e., allowing interface discontinuities) finite elements coupled to the second-order form of the transport equation. This non-conforming approach keeps the mixed-dual property of the relaxation of the flux interface continuity constraint. We investigate different non-conforming elements and compare them to the well-known Lagrangian conforming elements.

A non-conforming generalization of Raviart-Thomas elements to the spherical harmonic form of the even-parity neutron transport equation

International Nuclear Information System (INIS)

Van Criekingen, S.

2006-01-01

The Raviart-Thomas finite elements provide an appropriate spatial discretization of the mixed-dual form of the diffusion equation. This discretization can then be coupled to an efficient solution method. The high performances achieved by such an approach triggered research on its possible generalization to the transport equation using a spherical harmonic (or P N ) angular approximation. In view of the difficulty of developing a straightforward generalization within the mixed-dual framework, we here consider 2D non-conforming (i.e., allowing interface discontinuities) finite elements coupled to the second-order form of the transport equation. This non-conforming approach keeps the mixed-dual property of the relaxation of the flux interface continuity constraint. We investigate different non-conforming elements and compare them to the well-known Lagrangian conforming elements

Two Phase Non-Rigid Multi-Modal Image Registration Using Weber Local Descriptor-Based Similarity Metrics and Normalized Mutual Information

Directory of Open Access Journals (Sweden)

Feng Yang

2013-06-01

Full Text Available Non-rigid multi-modal image registration plays an important role in medical image processing and analysis. Existing image registration methods based on similarity metrics such as mutual information (MI and sum of squared differences (SSD cannot achieve either high registration accuracy or high registration efficiency. To address this problem, we propose a novel two phase non-rigid multi-modal image registration method by combining Weber local descriptor (WLD based similarity metrics with the normalized mutual information (NMI using the diffeomorphic free-form deformation (FFD model. The first phase aims at recovering the large deformation component using the WLD based non-local SSD (wldNSSD or weighted structural similarity (wldWSSIM. Based on the output of the former phase, the second phase is focused on getting accurate transformation parameters related to the small deformation using the NMI. Extensive experiments on T1, T2 and PD weighted MR images demonstrate that the proposed wldNSSD-NMI or wldWSSIM-NMI method outperforms the registration methods based on the NMI, the conditional mutual information (CMI, the SSD on entropy images (ESSD and the ESSD-NMI in terms of registration accuracy and computation efficiency.

Conformational impact of structural modifications in 2-fluorocyclohexanone

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Francisco A. Martins

2017-08-01

Full Text Available 2-Haloketones are building blocks that combine physical, chemical and biological features of materials and bioactive compounds, while organic fluorine plays a fundamental role in the design of performance organic molecules. Since these features are dependent on the three-dimensional chemical structure of a molecule, simple structural modifications can affect its conformational stability and, consequently, the corresponding physicochemical/biological property of interest. In this work, structural changes in 2-fluorocyclohexanone were theoretically studied with the aim at finding intramolecular interactions that induce the conformational equilibrium towards the axial or equatorial conformer. The interactions evaluated were hydrogen bonding, hyperconjugation, electrostatic and steric effects. While the gauche effect, originated from hyperconjugative interactions, does not appear to cause some preferences for the axial conformation of organofluorine heterocycles, more classical effects indeed rule the conformational equilibrium of the compounds. Spectroscopic parameters (NMR chemical shifts and coupling constants, which can be useful to determine the stereochemistry and the interactions operating in the series of 2-fluorocyclohexanone derivatives, were also calculated.

Classification and handling of non-conformance item of nuclear class equipment during manufacture phase

International Nuclear Information System (INIS)

Wang Ruiping

2001-01-01

Based on inspection experiences in years on nuclear class equipment manufacturing, the author discusses the classification and handling of non-conformance items occurred during equipment manufacturing, and certain technical considerations are presented

Interplay between singlet and triplet excited states in a conformationally locked donor–acceptor dyad

KAUST Repository

Filatov, Mikhail A.

2015-10-13

The synthesis and photophysical characterization of a palladium(II) porphyrin – anthracene dyad bridged via short and conformationally rigid bicyclo[2.2.2]octadiene spacer were achieved. A spectroscopic investigation of the prepared molecule in solution has been undertaken to study electronic energy transfer in excited singlet and triplet states between the anthracene and porphyrin units. By using steady-state and time-resolved photoluminescence spectroscopy it was shown that excitation of the singlet excited state of the anthracene leads to energy transfer to the lower-lying singlet state of porphyrin. Alternatively, excitation of the porphyrin followed by intersystem crossing to the triplet state leads to very fast energy transfer to the triplet state of anthracene. The rate of this energy transfer has been determined by transient absorption spectroscopy. Comparative studies of the dynamics of triplet excited states of the dyad and reference palladium octaethylporphyrin (PdOEP) have been performed.

Interplay between singlet and triplet excited states in a conformationally locked donor–acceptor dyad

KAUST Repository

Filatov, Mikhail A.; Etzold, Fabian; Gehrig, Dominik; Laquai, Fré dé ric; Busko, Dmitri; Landfester, Katharina; Baluschev, Stanislav

2015-01-01

The synthesis and photophysical characterization of a palladium(II) porphyrin – anthracene dyad bridged via short and conformationally rigid bicyclo[2.2.2]octadiene spacer were achieved. A spectroscopic investigation of the prepared molecule in solution has been undertaken to study electronic energy transfer in excited singlet and triplet states between the anthracene and porphyrin units. By using steady-state and time-resolved photoluminescence spectroscopy it was shown that excitation of the singlet excited state of the anthracene leads to energy transfer to the lower-lying singlet state of porphyrin. Alternatively, excitation of the porphyrin followed by intersystem crossing to the triplet state leads to very fast energy transfer to the triplet state of anthracene. The rate of this energy transfer has been determined by transient absorption spectroscopy. Comparative studies of the dynamics of triplet excited states of the dyad and reference palladium octaethylporphyrin (PdOEP) have been performed.

Energy flow in non-equilibrium conformal field theory

Science.gov (United States)

Bernard, Denis; Doyon, Benjamin

2012-09-01

We study the energy current and its fluctuations in quantum gapless 1d systems far from equilibrium modeled by conformal field theory, where two separated halves are prepared at distinct temperatures and glued together at a point contact. We prove that these systems converge towards steady states, and give a general description of such non-equilibrium steady states in terms of quantum field theory data. We compute the large deviation function, also called the full counting statistics, of energy transfer through the contact. These are universal and satisfy fluctuation relations. We provide a simple representation of these quantum fluctuations in terms of classical Poisson processes whose intensities are proportional to Boltzmann weights.

Conformal Ablative Thermal Protection System for Planetary and Human Exploration Missions:An Overview of the Technology Maturation Effort

Science.gov (United States)

Beck, Robin A S.; Arnold, James O.; Gasch, Matthew J.; Stackpoole, Margaret M.; Prabhu, Dinesh K.; Szalai, Christine E.; Wercinski, Paul F.; Venkatapathy, Ethiraj

2013-01-01

The Office of Chief Technologist, NASA identified the need for research and technology development in part from NASAs Strategic Goal 3.3 of the NASA Strategic Plan to develop and demonstrate the critical technologies that will make NASAs exploration, science, and discovery missions more affordable and more capable. Furthermore, the Game Changing Development Program is a primary avenue to achieve the Agencys 2011 strategic goal to Create the innovative new space technologies for our exploration, science, and economic future. The National Research Council (NRC) Space Technology Roadmaps and Priorities report highlights six challenges and they are: Mass to Surface, Surface Access, Precision Landing, Surface Hazard Detection and Avoidance, Safety and Mission Assurance, and Affordability. In order for NASA to meet these challenges, the report recommends immediate focus on Rigid and Flexible Thermal Protection Systems. Rigid TPS systems such as Avcoat or SLA are honeycomb based and PICA is in the form of tiles. The honeycomb systems are manufactured using techniques that require filling of each (38 cell) by hand, and in a limited amount of time all of the cells must be filled and the heatshield must be cured. The tile systems such as PICA pose a different challenge as the low strain-to-failure and manufacturing size limitations require large number of small tiles with gap-fillers between the tiles. Recent investments in flexible ablative systems have given rise to the potential for conformal ablative TPS. A conformal TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials. The high strain-to-failure nature of the conformal ablative materials will allow integration of the TPS with the underlying aeroshell structure much easier and enable monolithic-like configuration and larger segments (or parts) to be used. By reducing the overall part count, the cost of installation (based on cost comparisons between blanket

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change.

Science.gov (United States)

Mandal, Soumit Sankar; Merz, Dale R; Buchsteiner, Maximilian; Dima, Ruxandra I; Rief, Matthias; Žoldák, Gabriel

2017-06-06

Owing to the cooperativity of protein structures, it is often almost impossible to identify independent subunits, flexible regions, or hinges simply by visual inspection of static snapshots. Here, we use single-molecule force experiments and simulations to apply tension across the substrate binding domain (SBD) of heat shock protein 70 (Hsp70) to pinpoint mechanical units and flexible hinges. The SBD consists of two nanomechanical units matching 3D structural parts, called the α- and β-subdomain. We identified a flexible region within the rigid β-subdomain that gives way under load, thus opening up the α/β interface. In exactly this region, structural changes occur in the ATP-induced opening of Hsp70 to allow substrate exchange. Our results show that the SBD's ability to undergo large conformational changes is already encoded by passive mechanics of the individual elements.

Conformal field theory construction for non-Abelian hierarchy wave functions

Science.gov (United States)

Tournois, Yoran; Hermanns, Maria

2017-12-01

The fractional quantum Hall effect is the paradigmatic example of topologically ordered phases. One of its most fascinating aspects is the large variety of different topological orders that may be realized, in particular non-Abelian ones. Here we analyze a class of non-Abelian fractional quantum Hall model states which are generalizations of the Abelian Haldane-Halperin hierarchy. We derive their topological properties and show that the quasiparticles obey non-Abelian fusion rules of type su (q)k . For a subset of these states we are able to derive the conformal field theory description that makes the topological properties—in particular braiding—of the state manifest. The model states we study provide explicit wave functions for a large variety of interesting topological orders, which may be relevant for certain fractional quantum Hall states observed in the first excited Landau level.

A non-conforming 3D spherical harmonic transport solver

Energy Technology Data Exchange (ETDEWEB)

Van Criekingen, S. [Commissariat a l' Energie Atomique CEA-Saclay, DEN/DM2S/SERMA/LENR Bat 470, 91191 Gif-sur-Yvette, Cedex (France)

2006-07-01

A new 3D transport solver for the time-independent Boltzmann transport equation has been developed. This solver is based on the second-order even-parity form of the transport equation. The angular discretization is performed through the expansion of the angular neutron flux in spherical harmonics (PN method). The novelty of this solver is the use of non-conforming finite elements for the spatial discretization. Such elements lead to a discontinuous flux approximation. This interface continuity requirement relaxation property is shared with mixed-dual formulations such as the ones based on Raviart-Thomas finite elements. Encouraging numerical results are presented. (authors)

A non-conforming 3D spherical harmonic transport solver

International Nuclear Information System (INIS)

Van Criekingen, S.

2006-01-01

A new 3D transport solver for the time-independent Boltzmann transport equation has been developed. This solver is based on the second-order even-parity form of the transport equation. The angular discretization is performed through the expansion of the angular neutron flux in spherical harmonics (PN method). The novelty of this solver is the use of non-conforming finite elements for the spatial discretization. Such elements lead to a discontinuous flux approximation. This interface continuity requirement relaxation property is shared with mixed-dual formulations such as the ones based on Raviart-Thomas finite elements. Encouraging numerical results are presented. (authors)

Mitral stenosis due to pannus overgrowth after rigid ring annuloplasty.

Science.gov (United States)

Oda, Takeshi; Kato, Seiya; Tayama, Eiki; Fukunaga, Shuji; Akashi, Hidetoshi; Aoyagi, Shigeaki

2010-03-01

Although mitral stenosis (MS) due to pannus overgrowth after mitral valve repair for rheumatic mitral regurgitation (MR) is not uncommon, it is extremely rare in relation to non-rheumatic mitral regurgitation. Whilst it has been suggested that the rigid annuloplasty ring induces pannus overgrowth in the same manner as the flexible ring, to date only in cases using the flexible ring has pannus formation been confirmed by a pathological examination after redo surgery. The case is described of a woman who had undergone mitral valve repair using a 28 mm rigid ring three years previously because of non-rheumatic MR, and subsequently suffered from MS due to pannus formation over the annuloplasty ring. To the present authors' knowledge, this is the first report of MS due to pannus formation after mitral valve repair using a rigid annuloplasty ring to treat non-rheumatic MR documented at reoperation.

Superplastic flow of two-phase ceramics containing rigid inclusions-zirconia/mullite composites

International Nuclear Information System (INIS)

Yoon, C.K.; Chen, I.W.

1990-01-01

A continuum theory for non-newtonian flow of a two-phase composite containing rigid inclusions is presented. It predicts flow suppression by a factor of (1 - V) q , where V is the volume fraction of the rigid inclusion and q depends on the stress exponent and the inclusion shape. Stress concentrations in the rigid inclusion have also been evaluated. As the stress exponent increases, flow suppression is more pronounced even though stress concentration is less severe. To test this theory, superplastic flow of zirconia/mullite composites, in which zirconia is a soft, non-Newtonian super-plastic matrix and mullite is a rigid phase of various size, shape, and amount, is studied. The continuum theory is found to describe the two-phase superplastic flow reasonably well

Rigid multipodal platforms for metal surfaces

Directory of Open Access Journals (Sweden)

Michal Valášek

2016-03-01

Full Text Available In this review the recent progress in molecular platforms that form rigid and well-defined contact to a metal surface are discussed. Most of the presented examples have at least three anchoring units in order to control the spatial arrangement of the protruding molecular subunit. Another interesting feature is the lateral orientation of these foot structures which, depending on the particular application, is equally important as the spatial arrangement of the molecules. The numerous approaches towards assembling and organizing functional molecules into specific architectures on metal substrates are reviewed here. Particular attention is paid to variations of both, the core structures and the anchoring groups. Furthermore, the analytical methods enabling the investigation of individual molecules as well as monomolecular layers of ordered platform structures are summarized. The presented multipodal platforms bearing several anchoring groups form considerably more stable molecule–metal contacts than corresponding monopodal analogues and exhibit an enlarged separation of the functional molecules due to the increased footprint, as well as restrict tilting of the functional termini with respect to the metal surface. These platforms are thus ideally suited to tune important properties of the molecule–metal interface. On a single-molecule level, several of these platforms enable the control over the arrangement of the protruding rod-type molecular structures (e.g., molecular wires, switches, rotors, sensors with respect to the surface of the substrate.

Small molecules CK-666 and CK-869 inhibit actin-related protein 2/3 complex by blocking an activating conformational change.

Science.gov (United States)

Hetrick, Byron; Han, Min Suk; Helgeson, Luke A; Nolen, Brad J

2013-05-23

Actin-related protein 2/3 (Arp2/3) complex is a seven-subunit assembly that nucleates branched actin filaments. Small molecule inhibitors CK-666 and CK-869 bind to Arp2/3 complex and inhibit nucleation, but their modes of action are unknown. Here, we use biochemical and structural methods to determine the mechanism of each inhibitor. Our data indicate that CK-666 stabilizes the inactive state of the complex, blocking movement of the Arp2 and Arp3 subunits into the activated filament-like (short pitch) conformation, while CK-869 binds to a serendipitous pocket on Arp3 and allosterically destabilizes the short pitch Arp3-Arp2 interface. These results provide key insights into the relationship between conformation and activity in Arp2/3 complex and will be critical for interpreting the influence of the inhibitors on actin filament networks in vivo. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simultaneous PET-MR acquisition and MR-derived motion fields for correction of non-rigid motion in PET

International Nuclear Information System (INIS)

Tsoumpas, C.; Mackewn, J.E.; Halsted, P.; King, A.P.; Buerger, C.; Totman, J.J.; Schaeffter, T.; Marsden, P.K.

2010-01-01

Positron emission tomography (PET) provides an accurate measurement of radiotracer concentration in vivo, but performance can be limited by subject motion which degrades spatial resolution and quantitative accuracy. This effect may become a limiting factor for PET studies in the body as PET scanner technology improves. In this work, we propose a new approach to address this problem by employing motion information from images measured simultaneously using a magnetic resonance (MR) scanner. The approach is demonstrated using an MR-compatible PET scanner and PET-MR acquisition with a purpose-designed phantom capable of non-rigid deformations. Measured, simultaneously acquired MR data were used to correct for motion in PET, and results were compared with those obtained using motion information from PET images alone. Motion artefacts were significantly reduced and the PET image quality and quantification was significantly improved by the use of MR motion fields, whilst the use of PET-only motion information was less successful. Combined PET-MR acquisitions potentially allow PET motion compensation in whole-body acquisitions without prolonging PET acquisition time or increasing radiation dose. This, to the best of our knowledge, is the first study to demonstrate that simultaneously acquired MR data can be used to estimate and correct for the effects of non-rigid motion in PET. (author)

Premutation huntingtin allele adopts a non-B conformation and contains a hot spot for DNA damage

International Nuclear Information System (INIS)

Jarem, Daniel A.; Delaney, Sarah

2011-01-01

Highlights: ► First structural and thermodynamic analysis of premutation allele of HD. ► Premutation allele of HD adopts a stem-loop non-B conformation. ► Healthy and premutation length stem-loops are hyper-susceptible to oxidative damage. ► Stability of stem-loop structures increases linearly with repeat length. ► Thermodynamic stability, not the ability to adopt non-B conformation, distinguishes DNA prone to expansion from stable DNA. -- Abstract: The expansion of a CAG trinucleotide repeat (TNR) sequence has been linked to several neurological disorders, for example, Huntington’s disease (HD). In HD, healthy individuals have 5–35 CAG repeats. Those with 36–39 repeats have the premutation allele, which is known to be prone to expansion. In the disease state, greater than 40 repeats are present. Interestingly, the formation of non-B DNA conformations by the TNR sequence is proposed to contribute to the expansion. Here we provide the first structural and thermodynamic analysis of a premutation length TNR sequence. Using chemical probes of nucleobase accessibility, we found that similar to (CAG) 10 , the premutation length sequence (CAG) 36 forms a stem-loop hairpin and contains a hot spot for DNA damage. Additionally, calorimetric analysis of a series of (CAG) n sequences, that includes repeat tracts in both the healthy and premutation ranges, reveal that thermodynamic stability increases linearly with the number of repeats. Based on these data, we propose that while non-B conformations can be formed by TNR tracts found in both the healthy and premutation allele, only sequences containing at least 36 repeats have sufficient thermodynamic stability to contribute to expansion.

Time asymmetric spacetimes near null and spatial infinity: II. Expansions of developments of initial data sets with non-smooth conformal metrics

International Nuclear Information System (INIS)

Kroon, Juan Antonio Valiente

2005-01-01

This paper uses the conformal Einstein equations and the conformal representation of spatial infinity introduced by Friedrich to analyse the behaviour of the gravitational field near null and spatial infinity for the development of initial data which are, in principle, non-conformally flat and time asymmetric. The paper is the continuation of the investigation started in Class. Quantum Grav. 21 (2004) 5457-92, where only conformally flat initial data sets were considered. For the purposes of this investigation, the conformal metric of the initial hypersurface is assumed to have a very particular type of non-smoothness at infinity in order to allow for the presence of non-Schwarzschildean stationary initial data sets in the class under study. The calculation of asymptotic expansions of the development of these initial data sets reveals-as in the conformally flat case-the existence of a hierarchy of obstructions to the smoothness of null infinity which are expressible in terms of the initial data. This allows for the possibility of having spacetimes where future and past null infinity have different degrees of smoothness. A conjecture regarding the general structure of the hierarchy of obstructions is presented

RIGID AND NON-RIGID KINEMATIC EXCITATION FOR MULTIPLY-SUPPORTED SYSTEM: ONCE MORE ABOUT THE CONTRIBUTION OF DAMPING TO THE DYNAMIC LOADS IN SEISMIC ANALYSIS

Directory of Open Access Journals (Sweden)

Alexander G. Tyapin

2018-03-01

Full Text Available Development of linear equations of motion for seismic analysis is discussed in the paper. The paper continues the discussion: the author does not agree with colleagues putting damping matrix into the right-hand part of the equation of motion describing dynamic loads. This disagreement refers to the most popular case of “rigid” motion of multiple supports. In this paper the author follows the logic of general “non-rigid” support motion and points out a step in the equation development when the transition to “rigid” support motion (as a particular case of “non-rigid” motion is spoiled by the opponents. In the author’s opinion, the mistake is in the implementation of the Rayleigh damping model for the right-hand part of the equation. This is in the contradiction with physical logic, as damping in the Rayleigh model is not really “internal”: due to the participation of mass matrix it works on rigid displacements, which is impossible for internal damping.

Conformable liquid metal printed epidermal electronics for smart physiological monitoring and simulation treatment

Science.gov (United States)

Wang, Xuelin; Zhang, Yuxin; Guo, Rui; Wang, Hongzhang; Yuan, Bo; Liu, Jing

2018-03-01

Conformable epidermal printed electronics enabled from gallium-based liquid metals (LMs), highly conductive and low-melting-point alloys, are proposed as the core to achieving immediate contact between skin surface and electrodes, which can avoid the skin deformation often caused by conventional rigid electrodes. When measuring signals, LMs can eliminate resonance problems with shorter time to reach steady state than Pt and gelled Pt electrodes. By comparing the contact resistance under different working conditions, it is demonstrated that both ex vivo and in vivo LM electrode-skin models have the virtues of direct and immediate contact with skin surface without the deformation encountered with conventional rigid electrodes. In addition, electrocardio electrodes composed of conformable LM printed epidermal electronics are adopted as smart devices to monitor electrocardiogram signals of rabbits. Furthermore, simulation treatment for smart defibrillation offers a feasible way to demonstrate the effect of liquid metal electrodes (LMEs) on the human body with less energy loss. The remarkable features of soft epidermal LMEs such as high conformability, good conductivity, better signal stability, and fine biocompatibility represent a critical step towards accurate medical monitoring and future smart treatments.

Rigidity of Nominal Wages of Non-Production Workers in Industrial Sector

Directory of Open Access Journals (Sweden)

Bambang Sulistiyono

2016-06-01

Full Text Available Excess supply of labor leads to low the levels of nominal wages received by workers. The amount of minimum wage rate exceeds the market wage rate. The determination of minimum wage is a factor manifested in the institutional and regulatory Provincial Minimum Wage or a District Minimum Wage. Unfortunately, it has made nominal wages  difficult to drop below the minimum wage level. High or low level of nominal wages are associated with worker productivity. Further, nominal wages are rigid to go down. If they have increased, they can not be dropped in the future even though the company's performance is declined. Knowing that condition, in designing the remuneration system, an employer should pay attention to the rigidity of nominal wages, so that when  company's performance declines, the company will not be interfered because of the wages burden.  Furthermore, unions and government should consider the rigidity impact of nominal wages that go down. Thus, when macroeconomic conditions deteriorate and company's performance drops, the company will not go bankrupt due to high labor costs. If the company goes bankrupt, the workers will loose their jobs as a result of employment termination, while the government will face the unemployment problem. 

NMR and rotational angles in solution conformation of polypeptides

Science.gov (United States)

Bystrov, V. F.

1985-01-01

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

Conformal symmetry and non-relativistic second-order fluid dynamics

International Nuclear Information System (INIS)

Chao Jingyi; Schäfer, Thomas

2012-01-01

We study the constraints imposed by conformal symmetry on the equations of fluid dynamics at second order in the gradients of the hydrodynamic variables. At zeroth order, conformal symmetry implies a constraint on the equation of state, E 0 =2/3 P, where E 0 is the energy density and P is the pressure. At first order, conformal symmetry implies that the bulk viscosity must vanish. We show that at second order, conformal invariance requires that two-derivative terms in the stress tensor must be traceless, and that it determines the relaxation of dissipative stresses to the Navier–Stokes form. We verify these results by solving the Boltzmann equation at second order in the gradient expansion. We find that only a subset of the terms allowed by conformal symmetry appear. - Highlights: ► We derive conformal constraints for the stress tensor of a scale invariant fluid. ► We determine the relaxation time in kinetic theory. ► We compute the rate of entropy production in second-order fluid dynamics.

A non conforming finite element method for computing eigenmodes of resonant cavities

International Nuclear Information System (INIS)

Touze, F.; Le Meur, G.

1990-06-01

We present here a non conforming finite element in R 3 . This finite element, built on tetrahedrons, is particularly suited for computing eigenmodes. The main advantage of this element is that it preserves some structural properties of the space in which the solutions of the Maxwell's equations are to be found. Numerical results are presented for both two-dimensional and three-dimensional cases

Spectroscopic and electrooptical manifestations of internal rotation of the outer-sphere cation in Li(PO3) molecule

International Nuclear Information System (INIS)

Romanets, A.V.; Sukhanov, L.P.

1997-01-01

Spectroscopic and electrooptical manifestations of internal molecular rotations in LiPO 3 have been studied on the basis of ab initio calculated surface of potential energy and dipole momentum function using the finite element method. It has been ascertained that tunnel splitting of energy levels with number n, available for vibrational spectroscopy of high resolution, apper in the molecule studied only at n≥13. It is shown that internal rotations in the molecule are able to decrease sharply its polarity on vibration-excited levels, sufficiently far from the vertex of potential barrier of intramolecular regroupings. Difficulties of experimental confirmation of predicted electrooptical effect of structural non-rigidity in the molecule studied are discussed

Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications.

Science.gov (United States)

Gilson, Michael K; Irikura, Karl K

2010-12-16

The use of molecular simulations and ab initio calculations to predict thermodynamic properties of molecules has become routine. Such methods rely upon an accurate representation of the molecular partition function or configurational integral, which in turn often includes a rotational symmetry number. However, the reason for including the symmetry number is unclear to many practitioners, and there is also a need for a general prescription for evaluating the symmetry numbers of flexible molecules, i.e., for molecules with thermally active internal degrees of freedom, such as internal rotors. Surprisingly, we have been unable to find any complete and convincing explanations of these important issues in textbooks or the journal literature. The present paper aims to explain why symmetry numbers are needed and how their values should be determined. Both classical and quantum approaches are provided.

Non-rigid molecular group theory and its applications

International Nuclear Information System (INIS)

Balasubramanian, K.

1982-06-01

The use of generalized wreath product groups as representations of symmetry groups of nonrigid molecules is considered. Generating function techniques are outlined for nuclear spin statistics and character tables of the symmetry groups of nonrigid molecules. Several applications of nonrigid molecular group theory to NMR spectroscopy, rovibronic splitting and nuclear spin statistics of nonrigid molecules, molecular beam deflection and electric resonance experiments of weakly bound Van der Waal complexes, isomerization processes, configuration interaction calculations and the symmetry of crystals with structural distortions are described. 81 references

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.

Conformal, planarizing and bridging AZ5214-E layers deposited by a 'draping' technique on non-planar III V substrates

Science.gov (United States)

Eliás, P.; Strichovanec, P.; Kostic, I.; Novák, J.

2006-12-01

A draping technique was tested for the deposition of positive-tone AZ5214-E photo-resist layers on non-planar (1 0 0)-oriented III-V substrates, which had a variety of three-dimensional (3D) topographies micromachined in them that consisted, e.g., of mesa ridges confined to side facets with variable tilt, inverted pyramidal holes and stubs confined to perpendicular side facets. All objects were sharp-edged. In each draping experiment, an AZ5214-E sheet was (1) formed floating on the water surface, (2) lowered onto a non-planar substrate and (3) draped over it during drying to form either self-sustained, or conformal, or planarizing layers over the non-planar substrates. The draping process is based on the depression of the glass transition temperature Tg of AZ5214-E material induced by penetrant water molecules that interact with AZ5214-E. During the process, the molecules are initially trapped under an AZ5214-E sheet and then transported out through the sheet via permeation. The water-AZ5214-E interaction modifies the stiffness κ of the sheet. The magnitude of the effect depends on temperature T and on partial water vapour pressure difference p(T, P, κ): the net effect is that Tg = f(C(T, P), p(T, P, κ)) is lowered as the concentration C of water increases with T and p, where P is the permeability of the sheet. The interaction depressed the Tg of the sheets as low as or lower than 53 °C for 6 µm thick sheets. At room temperature T Tg, the sheet becomes rubbery and mouldable by adhesion and capillary forces. As a result, it can either contour or planarize the topography depending on its geometry and thickness of the sheet.

β-Glucans: Relationships between Modification, Conformation and Functional Activities

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Qiang Wang

2017-02-01

Full Text Available β-glucan is a type of polysaccharide which widely exists in bacteria, fungi, algae, and plants, and has been well known for its biological activities such as enhancing immunity, antitumor, antibacterial, antiviral, and wound healing activities. The conformation of β-glucan plays a crucial role on its biological activities. Therefore, β-glucans obtained from different sources, while sharing the same basic structures, often show different bioactivities. The basic structure and inter-molecular forces of polysaccharides can be changed by modification, which leads to the conformational transformation in solution that can directly affect bioactivity. In this review, we will first determine different ways to modify β-glucan molecules including physical methods, chemical methods, and biological methods, and then reveal the relationship of the flexible helix form of the molecule chain and the helix conformation to their bioactivities. Last, we summarize the scientific challenges to modifying β-glucan’s conformation and functional activity, and discuss its potential future development.

Non-linear realizations of conformal symmetry and effective field theory for the pseudo-conformal universe

International Nuclear Information System (INIS)

Hinterbichler, Kurt; Joyce, Austin; Khoury, Justin

2012-01-01

The pseudo-conformal scenario is an alternative to inflation in which the early universe is described by an approximate conformal field theory on flat, Minkowski space. Some fields acquire a time-dependent expectation value, which breaks the flat space so(4,2) conformal algebra to its so(4,1) de Sitter subalgebra. As a result, weight-0 fields acquire a scale invariant spectrum of perturbations. The scenario is very general, and its essential features are determined by the symmetry breaking pattern, irrespective of the details of the underlying microphysics. In this paper, we apply the well-known coset technique to derive the most general effective lagrangian describing the Goldstone field and matter fields, consistent with the assumed symmetries. The resulting action captures the low energy dynamics of any pseudo-conformal realization, including the U(1)-invariant quartic model and the Galilean Genesis scenario. We also derive this lagrangian using an alternative method of curvature invariants, consisting of writing down geometric scalars in terms of the conformal mode. Using this general effective action, we compute the two-point function for the Goldstone and a fiducial weight-0 field, as well as some sample three-point functions involving these fields

Mixed Messages: Measuring Conformance and Non-Interference in TypeScript (Artifact)

OpenAIRE

Williams, Jack; Morris, J. Garrett; Wadler, Philip; Zalewski, Jakub

2017-01-01

In the paper Mixed Messages: Measuring Conformance and Non-Interference in TypeScript we present our experiences of evaluating gradual typing using our tool TypeScript TPD. The tool, based on the polymorphic blame calculus, monitors JavaScript libraries and TypeScript clients against the corresponding TypeScript definition. Our experiments yield two conclusions. First, TypeScript definitions are prone to error. Second, there are serious technical concerns with the use of the JavaScript proxy ...

Note on non-vacuum conformal family contributions to Rényi entropy in two-dimensional CFT

Science.gov (United States)

Zhang, Jia-ju

2017-06-01

We calculate the contributions of a general non-vacuum conformal family to Rényi entropy in two-dimensional conformal field theory (CFT). The primary operator of the conformal family can be either non-chiral or chiral, and we denote its scaling dimension by Δ. For the case of two short intervals on a complex plane, we expand the Rényi mutual information by the cross ratio x to order x 2Δ+2. For the case of one interval on a torus with low temperature, we expand the Rényi entropy by q=exp(-2πβ/L), with β being the inverse temperature and L being the spatial period, to order q Δ+2. To make the result meaningful, we require that the scaling dimension Δ cannot be too small. For two intervals on a complex plane we need Δ > 1, and for one interval on a torus we need Δ > 2. We work in the small Newton constant limit on the gravity side and so a large central charge limit on the CFT side, and find matches of gravity and CFT results. Supported by ERC Starting Grant 637844-HBQFTNCER

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

Directory of Open Access Journals (Sweden)

Md Zahid Kamal

Full Text Available Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

Kinetics of conformational changes of fibronectin adsorbed onto model surfaces.

Science.gov (United States)

Baujard-Lamotte, L; Noinville, S; Goubard, F; Marque, P; Pauthe, E

2008-05-01

Fibronectin (FN), a large glycoprotein found in body fluids and in the extracellular matrix, plays a key role in numerous cellular behaviours. We investigate FN adsorption onto hydrophilic bare silica and hydrophobic polystyrene (PS) surfaces using Fourier transform infrared spectroscopy-attenuated total reflection (FTIR-ATR) in aqueous medium. Adsorption kinetics using different bulk concentrations of FN were followed for 2h and the surface density of adsorbed FN and its time-dependent conformational changes were determined. When adsorption occurs onto the hydrophilic surface, FN molecules keep their native conformation independent of the adsorption conditions, but the amount of adsorbed FN increases with time and the bulk concentration. Although the protein surface density is the same on the hydrophobic PS surface, this has a strong impact on the average conformation of the adsorbed FN layer. Indeed, interfacial hydration changes induced by adsorption onto the hydrophobic surface lead to a decrease in unhydrated beta-sheet content and cause an increase in hydrated beta-strand and hydrated random domain content of adsorbed FN. This conformational change is mainly dependent on the bulk concentration. Indeed, at low bulk concentrations, the secondary structures of adsorbed FN molecules undergo strong unfolding, allowing an extended and hydrated conformation of the protein. At high bulk concentrations, the molecular packing reduces the unfolding of the stereoregular structures of the FN molecules, preventing stronger spreading of the protein.

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics.

Science.gov (United States)

Smith, Glenna J; Lee, Kang Taek; Qu, Xiaohui; Xie, Zheng; Pesic, Jelena; Sosnick, Tobin R; Pan, Tao; Scherer, Norbert F

2008-05-09

The process of large RNA folding is believed to proceed from many collapsed structures to a unique functional structure requiring precise organization of nucleotides. The diversity of possible structures and stabilities of large RNAs could result in non-exponential folding kinetics (e.g. stretched exponential) under conditions where the molecules have not achieved their native state. We describe a single-molecule fluorescence resonance energy transfer (FRET) study of the collapsed-state region of the free energy landscape of the catalytic domain of RNase P RNA from Bacillus stearothermophilus (C(thermo)). Ensemble measurements have shown that this 260 residue RNA folds cooperatively to its native state at >or=1 mM Mg(2+), but little is known about the conformational dynamics at lower ionic strength. Our measurements of equilibrium conformational fluctuations reveal simple exponential kinetics that reflect a small number of discrete states instead of the expected inhomogeneous dynamics. The distribution of discrete dwell times, collected from an "ensemble" of 300 single molecules at each of a series of Mg(2+) concentrations, fit well to a double exponential, which indicates that the RNA conformational changes can be described as a four-state system. This finding is somewhat unexpected under [Mg(2+)] conditions in which this RNA does not achieve its native state. Observation of discrete well-defined conformations in this large RNA that are stable on the seconds timescale at low [Mg(2+)] (<0.1 mM) suggests that even at low ionic strength, with a tremendous number of possible (weak) interactions, a few critical interactions may produce deep energy wells that allow for rapid averaging of motions within each well, and yield kinetics that are relatively simple.

DNA conformation on surfaces measured by fluorescence self-interference.

Science.gov (United States)

Moiseev, Lev; Unlü, M Selim; Swan, Anna K; Goldberg, Bennett B; Cantor, Charles R

2006-02-21

The conformation of DNA molecules tethered to the surface of a microarray may significantly affect the efficiency of hybridization. Although a number of methods have been applied to determine the structure of the DNA layer, they are not very sensitive to variations in the shape of DNA molecules. Here we describe the application of an interferometric technique called spectral self-interference fluorescence microscopy to the precise measurement of the average location of a fluorescent label in a DNA layer relative to the surface and thus determine specific information on the conformation of the surface-bound DNA molecules. Using spectral self-interference fluorescence microscopy, we have estimated the shape of coiled single-stranded DNA, the average tilt of double-stranded DNA of different lengths, and the amount of hybridization. The data provide important proofs of concept for the capabilities of novel optical surface analytical methods of the molecular disposition of DNA on surfaces. The determination of DNA conformations on surfaces and hybridization behavior provide information required to move DNA interfacial applications forward and thus impact emerging clinical and biotechnological fields.

Full Alignment of Molecules Using Elliptically Polarized Light

DEFF Research Database (Denmark)

Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar

When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...... field can be used to align molecules along their axis of highest polarizability. Here we demonstrate, theoretically and experimentally, that an elliptically polarized laser field can be used to simultaneously force two axes of a molecule into alignment through the same mechanism. Due to the rigidity...

Structure and hydrodynamic properties of plectin molecules.

Science.gov (United States)

Foisner, R; Wiche, G

1987-12-05

Plectin is a cytoskeletal, high molecular weight protein of widespread and abundant occurrence in cultured cells and tissues. To study its molecular structure, the protein was purified from rat glioma C6 cells and subjected to chemical and biophysical analyses. Plectin's polypeptide chains have an apparent molecular weight of 300,000, as shown by one-dimensional sodium dodecyl sulfate/polyacrylamide electrophoresis. Cross-linking of non-denatured plectin in solution with dimethyl suberimidate and electrophoretic analyses on sodium dodecyl sulfate/agarose gels revealed that the predominant soluble plectin species was a molecule of 1200 X 10(3) Mr consisting of four 300 X 10(3) Mr polypeptide chains. Hydrodynamic properties of plectin in solution were obtained by sedimentation velocity centrifugation and high-pressure liquid chromatography analysis yielding a sedimentation coefficient of 10 S and a Stokes radius of 27 nm. The high f/fmin ratio of 4.0 indicated a very elongated shape of plectin molecules and an axial ratio of about 50. Shadowing and negative staining electron microscopy of plectin molecules revealed multiple domains: a rigid rod of 184 nm in length and 2 nm in diameter, and two globular heads of 9 nm diameter at each end of the rod. Circular dichroism spectra suggested a composition of 30% alpha-helix, 9% beta-structure and 61% random coil or aperiodic structure. The rod-like shape, the alpha-helix content as well as the thermal transition within a midpoint of 45 degrees C and the transition enthalpy (168 kJ/mol) of secondary structure suggested a double-stranded, alpha-helical coiled coil rod domain. Based on the available data, we favor a model of native plectin as a dumb-bell-like association of four 300 X 10(3) Mr polypeptide chains. Electron microscopy and turbidity measurements showed that plectin molecules self-associate into various oligomeric states in solutions of nearly physiological ionic strength. These interactions apparently involved

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Directory of Open Access Journals (Sweden)

Bhattacharyya Moitrayee

2010-08-01

Full Text Available Abstract Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in

Conformal symmetry inheritance in null fluid spacetimes

International Nuclear Information System (INIS)

Tupper, B O J; Keane, A J; Hall, G S; Coley, A 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

Immunomodulation of classical and non-classical HLA molecules by ionizing radiation.

Science.gov (United States)

Gallegos, Cristina E; Michelin, Severino; Dubner, Diana; Carosella, Edgardo D

2016-05-01

Radiotherapy has been employed for the treatment of oncological patients for nearly a century, and together with surgery and chemotherapy, radiation oncology constitutes one of the three pillars of cancer therapy. Ionizing radiation has complex effects on neoplastic cells and on tumor microenvironment: beyond its action as a direct cytotoxic agent, tumor irradiation triggers a series of alterations in tumoral cells, which includes the de novo synthesis of particular proteins and the up/down-regulation of cell surface molecules. Additionally, ionizing radiation may induce the release of "danger signals" which may, in turn lead to cellular and molecular responses by the immune system. This immunomodulatory action of ionizing radiation highlights the importance of the combined use (radiotherapy plus immunotherapy) for cancer healing. Major histocompatibility complex antigens (also called Human Leukocyte Antigens, HLA in humans) are one of those molecules whose expression is modulated after irradiation. This review summarizes the modulatory properties of ionizing radiation on the expression of HLA class I (classical and non-classical) and class II molecules, with special emphasis in non-classical HLA-I molecules. Copyright © 2016 Elsevier Inc. All rights reserved.

Benchmarking Commercial Conformer Ensemble Generators.

Science.gov (United States)

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

2017-11-27

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

Cooperative and non-cooperative conformational changes of F-actin induced by cofilin

Energy Technology Data Exchange (ETDEWEB)

Aihara, Tomoki; Oda, Toshiro, E-mail: toda@spring8.or.jp

2013-05-31

Highlights: •Mobility of MTSL attached to C374 in F-actin became high upon addition of cofilin. •Change of motility of MTSL attached to C374 with cofilin-binding was cooperative. •Mobility of MTSL attached to V43C in F-actin became high upon addition of cofilin. •Change of motility of MTSL attached to V43C with cofilin-binding was linear. -- Abstract: Cofilin is an actin-binding protein that promotes F-actin depolymerization. It is well-known that cofilin-coated F-actin is more twisted than naked F-actin, and that the protomer is more tilted. However, the means by which the local changes induced by the binding of individual cofilin proteins proceed to the global conformational changes of the whole F-actin molecule remain unknown. Here we investigated the cofilin-induced changes in several parts of F-actin, through site-directed spin-label electron paramagnetic resonance spectroscopy analyses of recombinant actins containing single reactive cysteines. We found that the global, cooperative conformational changes induced by cofilin-binding, which were detected by the spin-label attached to the Cys374 residue, occurred without the detachment of the D-loop in subdomain 2 from the neighboring protomer. The two processes of local and global changes do not necessarily proceed in sequence.

Spacetime completeness of non-singular black holes in conformal gravity

Energy Technology Data Exchange (ETDEWEB)

Bambi, Cosimo; Rachwał, Lesław [Center for Field Theory and Particle Physics and Department of Physics, Fudan University, 220 Handan Road, 200433 Shanghai (China); Modesto, Leonardo, E-mail: bambi@fudan.edu.cn, E-mail: lmodesto@sustc.edu.cn, E-mail: grzerach@gmail.com [Department of Physics, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055 (China)

2017-05-01

We explicitly prove that the Weyl conformal symmetry solves the black hole singularity problem, otherwise unavoidable in a generally covariant local or non-local gravitational theory. Moreover, we yield explicit examples of local and non-local theories enjoying Weyl and diffeomorphism symmetry (in short co-covariant theories). Following the seminal paper by Narlikar and Kembhavi, we provide an explicit construction of singularity-free spherically symmetric and axi-symmetric exact solutions for black hole spacetimes conformally equivalent to the Schwarzschild or the Kerr spacetime. We first check the absence of divergences in the Kretschmann invariant for the rescaled metrics. Afterwords, we show that the new types of black holes are geodesically complete and linked by a Newman-Janis transformation just as in standard general relativity (based on Einstein-Hilbert action). Furthermore, we argue that no massive or massless particles can reach the former Schwarzschild singularity or touch the former Kerr ring singularity in a finite amount of their proper time or of their affine parameter. Finally, we discuss the Raychaudhuri equation in a co-covariant theory and we show that the expansion parameter for congruences of both types of geodesics (for massless and massive particles) never reaches minus infinity. Actually, the null geodesics become parallel at the r =0 point in the Schwarzschild spacetime (the origin) and the focusing of geodesics is avoided. The arguments of regularity of curvature invariants, geodesic completeness, and finiteness of geodesics' expansion parameter ensure us that we are dealing with singularity-free and geodesically-complete black hole spacetimes.

Analysing the disposal of non-conformance in support and hunger design from the view of quality management

International Nuclear Information System (INIS)

Zhu Jianjun

2008-01-01

A serious non-conformance in the support and hunger design was found during the construction stage in a nuclear power project. In the view of quality management, the origin for the non-conformance is that the design process was not controlled properly and the design result was given without validation. Several experiences are summarized, such as the enhancement of the management level for various leaders and quality consciousness for all staff, the improvement of process management and training scheme, and paying more attention to the communication with the purchaser and the informationization construction in the design work, to ensure the traceability of the design and development. (author)

Molecular conformation, receptor binding, and hormone action of natural and synthetic estrogens and antiestrogens.

Science.gov (United States)

Duax, W L; Griffin, J F; Weeks, C M; Korach, K S

1985-01-01

The X-ray crystallographic structural determinations of synthetic estrogens and antiestrogens provide reliable information on the global minimum energy conformation of these molecules or a local minimum energy conformation that is within 1 or 2 kcal/mole of the global minimum. In favorable cases, state-of-the-art molecular mechanics calculations provide quantitative agreement with X-ray results and information on the relative energy of other local minimum energy conformations not observed crystallographically. Because the conformation of diethylstilbestrol (DES) observed in solvated crystals has an overall conformation and dipole moment more similar to estradiol it is the form more likely to bind to the receptor and produce hormone activity. Either phenol ring of DES can successfully mimic the estradiol A-ring in binding to the receptor. Indenestrol A (INDA) and indenestrol B (INDB) have nearly identical fully extended planar conformations. Either the alpha or gamma rings of these compounds may mimic the A ring of estradiol and compete for the estrogen receptor. Although there are eight distinct ways in which molecules of a racemic mixture of INDA or INDB can bind to the receptor, not all of them may be able to elicit a hormonal response. This may account for the reduced biological activity of the compounds despite their successful competition for receptor binding. The minimum energy conformations of Z-pseudodiethylstilbestrol (ZPD) and E-pseudodiethylstilbestrol (EPD) are bent in a fashion similar to that of indanestrol (INDC). These molecules have good binding affinity suggesting that the receptor does not require a flat molecule. Therefore these conformations would appear to be compatible with receptor binding, but only the Z isomer has an energetically allowed extended conformation that accounts for its observed biological activity relative to DES. PMID:3905370

Full conformational landscape of 3-Methoxyphenol revealed by room temperature mm-wave rotational spectroscopy supported by quantum chemical calculations.

Science.gov (United States)

Roucou, Anthony; Fontanari, Daniele; Dhont, Guillaume; Jabri, Atef; Bray, Cédric; Hindle, Francis; Mouret, Gaël; Bocquet, Robin; Cuisset, Arnaud

2018-03-30

Room temperature millimeter-wave rotational spectroscopy supported by high level of theory calculations have been employed to fully characterise the conformational landscape of 3-Methoxyphenol, a semi-volatile polar oxygenated aromatic compound precursor of secondary organic aerosols in the atmosphere arising from biomass combustion. While previous rotationally-resolved spectroscopic studies in the microwave and in the UV domains failed to observe the complete conformational landscape, the 70 - 330 GHz rotational spectrum measured in this study reveals the ground state rotational signatures of the four stable conformations theoretically predicted. Moreover, rotational transitions in the lowest energy vibrationally excited states were assigned for two conformers. While the inertial defect of methoxyphenol does not signicantly change between conformers and isomers, the excitation of the methoxy out-of-plane bending is the main contribution to the non-planarity of the molecule. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rigid multibody system dynamics with uncertain rigid bodies

Energy Technology Data Exchange (ETDEWEB)

Batou, A., E-mail: anas.batou@univ-paris-est.fr; Soize, C., E-mail: christian.soize@univ-paris-est.fr [Universite Paris-Est, Laboratoire Modelisation et Simulation Multi Echelle, MSME UMR 8208 CNRS (France)

2012-03-15

This paper is devoted to the construction of a probabilistic model of uncertain rigid bodies for multibody system dynamics. We first construct a stochastic model of an uncertain rigid body by replacing the mass, the center of mass, and the tensor of inertia by random variables. The prior probability distributions of the stochastic model are constructed using the maximum entropy principle under the constraints defined by the available information. The generators of independent realizations corresponding to the prior probability distribution of these random quantities are further developed. Then several uncertain rigid bodies can be linked to each other in order to calculate the random response of a multibody dynamical system. An application is proposed to illustrate the theoretical development.

Thioflavin T templates amyloid β(1-40) conformation and aggregation pathway

DEFF Research Database (Denmark)

Di Carlo, Maria Giovanna; Minicozzi, Velia; Foderà, Vito

2015-01-01

Aβ(1-40) peptide supramolecular assembly and fibril formation processes are widely recognized to have direct implications in the progression of Alzheimer's disease. The molecular basis of this biological process is still unknown and there is a strong need of developing effective strategies...... in turn rests on the reliability of the probe/labels involved. Here we present evidences of the effect of Thioflavin T (ThT), a worldwide used fluorescent dye to monitor amyloid growth, on the Aβ(1-40) conformation, stability and aggregation. By combining experimental information and Molecular Dynamics...... simulation results, we show that the presence of ThT in solution affects peptide conformation inducing peculiar supramolecular association. In particular ThT interactions with specific Aβ(1-40) residues promote a rigid partially-folded conformation which shifts the balance between different species...

Quantum Conformal Algebras and Closed Conformal Field Theory

CERN Document Server

Anselmi, D

1999-01-01

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

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

2015-07-28

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

On non-conformal limit of the AGT relations

International Nuclear Information System (INIS)

Marshakov, A.; Mironov, A.; Morozov, A.

2009-01-01

The Seiberg-Witten prepotentials for N=2 SUSY gauge theories with N f c fundamental multiplets are obtained from conformal N f =2N c theory by decoupling 2N c -N f multiplets of heavy matter. This procedure can be lifted to the level of Nekrasov functions with arbitrary background parameters ε 1 and ε 2 . The AGT relations imply that similar limit exists for conformal blocks (or, for generic N c >2, for the blocks in conformal theories with W N c chiral algebra). We consider the limit of the four-point function explicitly in the Virasoro case of N c =2, by bringing the dimensions of external states to infinity. The calculation is performed entirely in terms of representation theory for the Virasoro algebra and reproduces the answers conjectured in [D. Gaiotto, (arXiv:0908.0307)] with the help of the brane-compactification analysis and computer simulations. In this limit, the conformal block involving four external primaries, corresponding to the theory with vanishing beta-function, turns either into a 2-point or 3-point function, with certain coherent rather than primary external states.

Molecular Design of Branched and Binary Molecules at Ordered Interfaces

Energy Technology Data Exchange (ETDEWEB)

Genson, Kirsten Larson [Iowa State Univ., Ames, IA (United States)

2005-01-01

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Science.gov (United States)

Mirzaei, Hanieh; Beglov, Dmitri; Paschalidis, Ioannis Ch; Vajda, Sandor; Vakili, Pirooz; Kozakov, Dima

2012-11-13

Virtually all docking methods include some local continuous minimization of an energy/scoring function in order to remove steric clashes and obtain more reliable energy values. In this paper, we describe an efficient rigid-body optimization algorithm that, compared to the most widely used algorithms, converges approximately an order of magnitude faster to conformations with equal or slightly lower energy. The space of rigid body transformations is a nonlinear manifold, namely, a space which locally resembles a Euclidean space. We use a canonical parametrization of the manifold, called the exponential parametrization, to map the Euclidean tangent space of the manifold onto the manifold itself. Thus, we locally transform the rigid body optimization to an optimization over a Euclidean space where basic optimization algorithms are applicable. Compared to commonly used methods, this formulation substantially reduces the dimension of the search space. As a result, it requires far fewer costly function and gradient evaluations and leads to a more efficient algorithm. We have selected the LBFGS quasi-Newton method for local optimization since it uses only gradient information to obtain second order information about the energy function and avoids the far more costly direct Hessian evaluations. Two applications, one in protein-protein docking, and the other in protein-small molecular interactions, as part of macromolecular docking protocols are presented. The code is available to the community under open source license, and with minimal effort can be incorporated into any molecular modeling package.

Conformal Killing vectors in Robertson-Walker spacetimes

International Nuclear Information System (INIS)

Maartens, R.; Maharaj, S.d.

1986-01-01

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

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...

3D non-rigid surface-based MR-TRUS registration for image-guided prostate biopsy

Science.gov (United States)

Sun, Yue; Qiu, Wu; Romagnoli, Cesare; Fenster, Aaron

2014-03-01

Two dimensional (2D) transrectal ultrasound (TRUS) guided prostate biopsy is the standard approach for definitive diagnosis of prostate cancer (PCa). However, due to the lack of image contrast of prostate tumors needed to clearly visualize early-stage PCa, prostate biopsy often results in false negatives, requiring repeat biopsies. Magnetic Resonance Imaging (MRI) has been considered to be a promising imaging modality for noninvasive identification of PCa, since it can provide a high sensitivity and specificity for the detection of early stage PCa. Our main objective is to develop and validate a registration method of 3D MR-TRUS images, allowing generation of volumetric 3D maps of targets identified in 3D MR images to be biopsied using 3D TRUS images. Our registration method first makes use of an initial rigid registration of 3D MR images to 3D TRUS images using 6 manually placed approximately corresponding landmarks in each image. Following the manual initialization, two prostate surfaces are segmented from 3D MR and TRUS images and then non-rigidly registered using a thin-plate spline (TPS) algorithm. The registration accuracy was evaluated using 4 patient images by measuring target registration error (TRE) of manually identified corresponding intrinsic fiducials (calcifications and/or cysts) in the prostates. Experimental results show that the proposed method yielded an overall mean TRE of 2.05 mm, which is favorably comparable to a clinical requirement for an error of less than 2.5 mm.

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.

Botulinum toxin in myotonia congenita: it does not help against rigidity and pain.

Science.gov (United States)

Dressler, Dirk; Adib Saberi, Fereshte

2014-05-01

Botulinum toxin (BT) is a potent local muscle relaxant with analgetic properties. Myotonia congenita (MC) is a genetic disorder producing muscle rigidity and pain. BT injected into the trapezius produced mild paresis, but no effect on rigidity and pain. There were no signs of systemic effects. Lack of BT efficacy on MC rigidity confirms its origin from muscle membrane dysfunction rather than from inappropriate neuromuscular activation. Lack of BT efficacy on pain could be caused by lack of anti-rigidity effect. It could also be due to separate non-muscular pain mechanisms unresponsive to BT.

Deformed conformal and super-Poincare symmetries in the non- (anti-) commutative spaces

International Nuclear Information System (INIS)

Banerjee, R.; Lee, C.; Siwach, S.

2006-01-01

Generators of the super-Poincare algebra in the non- (anti-) commutative superspace are represented using appropriate higher derivative operators defined in this quantum superspace. Also discussed are the analogous representations of the conformal and superconformal symmetry generators in the deformed spaces. This construction is obtained by generalizing the recent work of Wess et al. on the Poincare generators in the θ-deformed Minkowski space, or by using the substitution rules we derived on the basis of the phase-space structures of non- (anti-) commutative-space variables. Even with the non-zero deformation parameters the algebras remain unchanged although the comultiplication rules are deformed. The transformation of the fields under deformed symmetry is also discussed. Our construction can be used for systematic development of field theories in the deformed spaces. (orig.)

A geometrical approach to two-dimensional Conformal Field Theory

Science.gov (United States)

Dijkgraaf, Robertus Henricus

1989-09-01

This thesis is organized in the following way. In Chapter 2 we will give a brief introduction to conformal field theory along the lines of standard quantum field theory, without any claims to originality. We introduce the important concepts of the stress-energy tensor, the Virasoro algebra, and primary fields. The general principles are demonstrated by fermionic and bosonic free field theories. This also allows us to discuss some general aspects of moduli spaces of CFT's. In particular, we describe in some detail the space of iiiequivalent toroidal comi)actificalions, giving examples of the quantum equivalences that we already mentioned. In Chapter 3 we will reconsider general quantum field theory from a more geometrical point of view, along the lines of the so-called operator formalism. Crucial to this approach will be the consideration of topology changing amplitudes. After a simple application to 2d topological theories, we proceed to give our second introduction to CFT, stressing the geometry behind it. In Chapter 4 the so-called rational conformal field theories are our object of study. These special CFT's have extended symmetries with only a finite number of representations. If an interpretation as non-linear sigma model exists, this extra symmetry can be seen as a kind of resonance effect due to the commensurability of the size of the string and the target space-time. The structure of rational CFT's is extremely rigid, and one of our results will be that the operator content of these models is—up to some discrete choices—completely determined by the symmetry algebra. The study of rational models is in its rigidity very analogous to finite group theory. In Chapter 5 this analogy is further pursued and substantiated. We will show how one can construct from general grounds rational conformal field theories from finite groups. These models are abstract versions of non-linear o-models describing string propagation on 'orbifoids.' An orbifold is a singular

Topological classification of the Goryachev integrable case in rigid body dynamics

International Nuclear Information System (INIS)

Nikolaenko, S S

2016-01-01

A topological analysis of the Goryachev integrable case in rigid body dynamics is made on the basis of the Fomenko-Zieschang theory. The invariants (marked molecules) which are obtained give a complete description, from the standpoint of Liouville classification, of the systems of Goryachev type on various level sets of the energy. It turns out that on appropriate energy levels the Goryachev case is Liouville equivalent to many classical integrable systems and, in particular, the Joukowski, Clebsch, Sokolov and Kovalevskaya-Yehia cases in rigid body dynamics, as well as to some integrable billiards in plane domains bounded by confocal quadrics -- in other words, the foliations given by the closures of generic solutions of these systems have the same structure. Bibliography: 15 titles

Astrophysical evidence for the non-Hermitian but PT-symmetric Hamiltonian of conformal gravity

International Nuclear Information System (INIS)

Mannheim, P.D.

2013-01-01

In this review we discuss the connection between two seemingly disparate topics, macroscopic gravity on astrophysical scales and Hamiltonians that are not Hermitian but PT symmetric on microscopic ones. In particular we show that the quantum-mechanical unitarity problem of the fourth-order derivative conformal gravity theory is resolved by recognizing that the scalar product appropriate to the theory is not the Dirac norm associated with a Hermitian Hamiltonian but is instead the norm associated with a non-Hermitian but PT-symmetric Hamiltonian. Moreover, the fourth-order theory Hamiltonian is not only not Hermitian, it is not even diagonalizable, being of Jordan-block form. With PT symmetry we establish that conformal gravity is consistent at the quantum-mechanical level. In consequence, we can apply the theory to data, to find that the theory is capable of naturally accounting for the systematics of the rotation curves of a large and varied sample of 138 spiral galaxies without any need for dark matter. The success of the fits provides evidence for the relevance of non-diagonalizable but PT-symmetric Hamiltonians to physics. (Copyright copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Oscillations of rigid bar in the special relativity

International Nuclear Information System (INIS)

Paiva, F.M.; Teixeira, A.F.F.

2011-12-01

In the special relativity, a rigid bar slides on herself, with a extreme oscillating harmonically. We have discovered at the movement amplitude and in the bar length, indispensable for the elimination of non physical solutions

Non-adiabatic rotational excitation of dipolar molecule under the ...

Indian Academy of Sciences (India)

J. Chem. Sci. Vol. 125, No. 5, September 2013, pp. 1213–1221. c Indian Academy of Sciences. ... The rotational wave packets of LiCl molecule excited non-adiabatically by half cycle pulse. (HCP) is .... pared to the intensities required for the ionization of ..... out and with delayed ultrashort HCP at different initial pulse dura-.

Prediction of RNA secondary structures: from theory to models and real molecules

International Nuclear Information System (INIS)

Schuster, Peter

2006-01-01

RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA

New 3-D coordination polymers based on semi-rigid V-shape tetracarboxylates

International Nuclear Information System (INIS)

Huang, Jing-Jing; Xu, Wei; Wang, Yan-Ning; Yu, Jie-Hui; Zhang, Ping; Xu, Ji-Qing

2015-01-01

Under the hydrothermal conditions, the reactions of transition-metal salts, tetracarboxylic acids and N,N′-donor ligands yielded three new coordination polymers as [Cu 4 (fph) 2 (bpe) 3 (H 2 O) 2 ]·2H 2 O (fph=4,4′-(hexafluoroisopropylidene)diphthalate, bpe=1,2-bis(pyridyl)ethylene) 1, [Co 2 (fph)(bpa) 2 (H 2 O) 2 ]·3H 2 O (bpa=1,2-bis(pyridyl)ethylane) 2, and [Ni(H 2 O)(H 2 oph)(bpa)] (oph=4,4′-oxydiphthalate) 3. X-ray single-crystal diffraction analysis revealed that the title three compounds all possess the three-dimensional (3-D) network structures. For compound 1, the fph molecules first link the Cu 2+ ions into a two-dimensional (2-D) wave-like layer with a (4,4) topology. The bpe molecules act as the second linkers, extending the 2-D layers into a 3-D network. For compound 2, the fph molecules still serve as the first connectors, linking the Co 2+ ions into a one-dimensional (1-D) tube-like chain. Then the bpa molecules propagate the chains into a 3-D (4,4,4)-connected network. In the formation of the 3-D network of compound 3, the oph molecule does not play a role. The bpa molecules as well as the water molecules act as a mixed bridge. Only a kind of 4-connected metal node is observed in compound 3. The magnetic properties of compounds 1–3 were investigated and all exhibit the predominant antiferromegnetic magnetic behaviors. - Graphical abstract: Structures of three semi-rigid V-shape tetracarboxylate-based coordination polymers were reported, and their magnetic properties were investigated. - Highlights: • Structures of three tetracarboxylate-based coordination polymers were reported. • Role of organic bases in metal–tetracarboxylate compounds was discussed. • Characters of V-shape and semi-rigidity for tetracarboxylate play a key role in crystal growth. • Their magnetic properties were investigated

New 3-D coordination polymers based on semi-rigid V-shape tetracarboxylates

Energy Technology Data Exchange (ETDEWEB)

Huang, Jing-Jing; Xu, Wei; Wang, Yan-Ning [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Road 2699, Changchun 130012, Jilin (China); Yu, Jie-Hui, E-mail: jhyu@jlu.edu.cn [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Road 2699, Changchun 130012, Jilin (China); Zhang, Ping, E-mail: zhangping@jlu.edu.cn [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); Xu, Ji-Qing [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Road 2699, Changchun 130012, Jilin (China)

2015-03-15

Under the hydrothermal conditions, the reactions of transition-metal salts, tetracarboxylic acids and N,N′-donor ligands yielded three new coordination polymers as [Cu{sub 4}(fph){sub 2}(bpe){sub 3}(H{sub 2}O){sub 2}]·2H{sub 2}O (fph=4,4′-(hexafluoroisopropylidene)diphthalate, bpe=1,2-bis(pyridyl)ethylene) 1, [Co{sub 2}(fph)(bpa){sub 2}(H{sub 2}O){sub 2}]·3H{sub 2}O (bpa=1,2-bis(pyridyl)ethylane) 2, and [Ni(H{sub 2}O)(H{sub 2}oph)(bpa)] (oph=4,4′-oxydiphthalate) 3. X-ray single-crystal diffraction analysis revealed that the title three compounds all possess the three-dimensional (3-D) network structures. For compound 1, the fph molecules first link the Cu{sup 2+} ions into a two-dimensional (2-D) wave-like layer with a (4,4) topology. The bpe molecules act as the second linkers, extending the 2-D layers into a 3-D network. For compound 2, the fph molecules still serve as the first connectors, linking the Co{sup 2+} ions into a one-dimensional (1-D) tube-like chain. Then the bpa molecules propagate the chains into a 3-D (4,4,4)-connected network. In the formation of the 3-D network of compound 3, the oph molecule does not play a role. The bpa molecules as well as the water molecules act as a mixed bridge. Only a kind of 4-connected metal node is observed in compound 3. The magnetic properties of compounds 1–3 were investigated and all exhibit the predominant antiferromegnetic magnetic behaviors. - Graphical abstract: Structures of three semi-rigid V-shape tetracarboxylate-based coordination polymers were reported, and their magnetic properties were investigated. - Highlights: • Structures of three tetracarboxylate-based coordination polymers were reported. • Role of organic bases in metal–tetracarboxylate compounds was discussed. • Characters of V-shape and semi-rigidity for tetracarboxylate play a key role in crystal growth. • Their magnetic properties were investigated.

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.

The consequences of translational and rotational entropy lost by small molecules on binding to proteins

Science.gov (United States)

Murray, Christopher W.; Verdonk, Marcel L.

2002-10-01

When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.

Studies of G-quadruplex DNA structures at the single molecule level

DEFF Research Database (Denmark)

Kragh, Sofie Louise

2015-01-01

Folding of G-quaduplex structures adopted by the human telomeric repeat is here studied by single molecule FRET microscopy. This method allows for the investigation of G-quadruplex structures and their conformational dynamic. Telomeres are located at the ends of our chromosomes and end in a single...... with human telomeric repeat adopt several different G-quadruplex conformations in the presence of K+ ions. G-quadruplexes inhibit telomerase activity and are therefore potential targets for anti-cancer drugs, which can be small molecule ligands capable of stabilizing G-quadruplex structures. Understanding...... range. FRET spectroscopy can be performed on an ensemble of molecules, or on the single molecule level. In single molecule FRET experiments it is possible to follow the behaviour in time for each molecule independently, allowing insight into both dynamically and statistically heterogeneous molecular...

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

Conformally-flat, non-singular static metric in infinite derivative gravity

Science.gov (United States)

Buoninfante, Luca; Koshelev, Alexey S.; Lambiase, Gaetano; Marto, João; Mazumdar, Anupam

2018-06-01

In Einstein's theory of general relativity the vacuum solution yields a blackhole with a curvature singularity, where there exists a point-like source with a Dirac delta distribution which is introduced as a boundary condition in the static case. It has been known for a while that ghost-free infinite derivative theory of gravity can ameliorate such a singularity at least at the level of linear perturbation around the Minkowski background. In this paper, we will show that the Schwarzschild metric does not satisfy the boundary condition at the origin within infinite derivative theory of gravity, since a Dirac delta source is smeared out by non-local gravitational interaction. We will also show that the spacetime metric becomes conformally-flat and singularity-free within the non-local region, which can be also made devoid of an event horizon. Furthermore, the scale of non-locality ought to be as large as that of the Schwarzschild radius, in such a way that the gravitational potential in any metric has to be always bounded by one, implying that gravity remains weak from the infrared all the way up to the ultraviolet regime, in concurrence with the results obtained in [arXiv:1707.00273]. The singular Schwarzschild blackhole can now be potentially replaced by a non-singular compact object, whose core is governed by the mass and the effective scale of non-locality.

Non-singular cosmologies in the conformally invariant gravitation theory

International Nuclear Information System (INIS)

Kembhavi, A.K.

1976-01-01

It is shown that in the framework of a conformally invariant gravitation theory, the singularity which is present in some anisotropic universes in general relativity is due to a wrong choice of conformal frame. Frames exist in which these models can be made singularity free. (author)

Vision based tunnel inspection using non-rigid registration

Science.gov (United States)

Badshah, Amir; Ullah, Shan; Shahzad, Danish

2015-04-01

Growing numbers of long tunnels across the globe has increased the need for safety measurements and inspections of tunnels in these days. To avoid serious damages, tunnel inspection is highly recommended at regular intervals of time to find any deformations or cracks at the right time. While following the stringent safety and tunnel accessibility standards, conventional geodetic surveying using techniques of civil engineering and other manual and mechanical methods are time consuming and results in troublesome of routine life. An automatic tunnel inspection by image processing techniques using non rigid registration has been proposed. There are many other image processing methods used for image registration purposes. Most of the processes are operation of images in its spatial domain like finding edges and corners by Harris edge detection method. These methods are quite time consuming and fail for some or other reasons like for blurred or images with noise. Due to use of image features directly by these methods in the process, are known by the group, correlation by image features. The other method is featureless correlation, in which the images are converted into its frequency domain and then correlated with each other. The shift in spatial domain is the same as in frequency domain, but the processing is order faster than in spatial domain. In the proposed method modified normalized phase correlation has been used to find any shift between two images. As pre pre-processing the tunnel images i.e. reference and template are divided into small patches. All these relative patches are registered by the proposed modified normalized phase correlation. By the application of the proposed algorithm we get the pixel movement of the images. And then these pixels shifts are converted to measuring units like mm, cm etc. After the complete process if there is any shift in the tunnel at described points are located.

HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations.

Science.gov (United States)

Ma, Xiaochu; Lu, Maolin; Gorman, Jason; Terry, Daniel S; Hong, Xinyu; Zhou, Zhou; Zhao, Hong; Altman, Roger B; Arthos, James; Blanchard, Scott C; Kwong, Peter D; Munro, James B; Mothes, Walther

2018-03-21

HIV-1 entry into cells requires binding of the viral envelope glycoprotein (Env) to receptor CD4 and coreceptor. Imaging of individual Env molecules on native virions shows Env trimers to be dynamic, spontaneously transitioning between three distinct well-populated conformational states: a pre-triggered Env (State 1), a default intermediate (State 2) and a three-CD4-bound conformation (State 3), which can be stabilized by binding of CD4 and coreceptor-surrogate antibody 17b. Here, using single-molecule Fluorescence Resonance Energy Transfer (smFRET), we show the default intermediate configuration to be asymmetric, with individual protomers adopting distinct conformations. During entry, this asymmetric intermediate forms when a single CD4 molecule engages the trimer. The trimer can then transition to State 3 by binding additional CD4 molecules and coreceptor.

A theoretical and spectroscopic study of conformational structures of piroxicam

Science.gov (United States)

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

2010-02-01

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

Conformal bootstrap: non-perturbative QFT's under siege

CERN Multimedia

CERN. Geneva

2016-01-01

[Exceptionally in Council Chamber] Originally formulated in the 70's, the conformal bootstrap is the ambitious idea that one can use internal consistency conditions to carve out, and eventually solve, the space of conformal field theories. In this talk I will review recent developments in the field which have boosted this program to a new level. I will present a method to extract quantitative informations in strongly-interacting theories, such as 3D Ising, O(N) vector model and even systems without a Lagrangian formulation. I will explain how these techniques have led to the world record determination of several critical exponents. Finally, I will review exact analytical results obtained using bootstrap techniques.

Probing the conformational dynamics of photosystem I in unconfined and confined spaces.

Science.gov (United States)

Das, Gaurav; Chattoraj, Shyamtanu; Nandi, Somen; Mondal, Prasenjit; Saha, Abhijit; Bhattacharyya, Kankan; Ghosh, Surajit

2017-12-20

The fluorescence dynamics of Photosystem I (PSI) in bulk water and inside a confined environment like a liposome have been investigated using time resolved confocal microscopy. In bulk water, PSI exhibits a major emission peak at ∼680 nm, while in the liposome it exhibits a markedly blue shifted emission maximum at ∼485 nm. This is indicative of conformational changes due to entrapment and emergence of a stressed conformation of PSI inside the liposome. The observed time constants for the fluorescence lifetime of PSI inside the liposome are significantly high as opposed to PSI in bulk water. More interestingly, the fluorescence intensity of PSI in bulk water exhibits strong fluctuations with many high intensity jumps and these are anti-correlated with the fluorescence lifetime of PSI. In contrast, inside the liposome, no such anti-correlated behaviour is observed. We further demonstrated that PSI exhibits at least two conformational states in bulk water, whereas a single conformation is observed inside the liposome, indicating the conformational rigidity and locking of the PSI complex inside a liposome.

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

Science.gov (United States)

Balachandran, V.; Parimala, K.

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

On flexible and rigid nouns

DEFF Research Database (Denmark)

Rijkhoff, Jan

2008-01-01

Studies in Language 32-3 (2008), 727-752. Special issue: Parts of Speech: Descriptive tools, theoretical constructs Jan Rijkhoff - On flexible and rigid nouns This article argues that in addition to the flexible lexical categories in Hengeveld’s classification of parts-of-speech systems (Contentive......, Non-Verb, Modifier), there are also flexible word classes within the rigid lexical category Noun (Set Noun, Sort Noun, General Noun). Members of flexible word classes are characterized by their vague semantics, which in the case of nouns means that values for the semantic features Shape...... and Homogeneity are either left undetermined or they are specified in such a way that they do not quite match the properties of the kind of entity denoted by the flexible item in the external world. I will then argue that flexible word classes constitute a proper category (i.e. they are not the result of a merger...

Direct Imaging of Deformation and Disorder in Extended-Chain Polymer Fibers

Science.gov (United States)

1991-03-01

conformation. A comparable physical picture of a rigid-rod molecule is that of a stiff strand of "uncooked linguine ". The linguine " analogy is...standing what happens when these " linguine -like" molecules 2 pack together in the solid state. Also, we wished to under- stand how supposedly completely

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

Directory of Open Access Journals (Sweden)

Keskin Ozlem

2007-05-01

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

Gender, Ethnicity, Religiosity, and Same-sex Sexual Attraction and the Acceptance of Same-sex Sexuality and Gender Non-conformity

Science.gov (United States)

Bos, Henny M. W.; Merry, Michael S.; Sandfort, Theo G. M.

2012-01-01

This study explored the role of gender, ethnicity, religiosity, and sexual attraction in adolescents’ acceptance of same-sex sexuality and gender non-conformity. Using an intersectionality perspective, we also tested whether the effects of gender, ethnicity, and religiosity on adolescents’ attitudes would function differently in adolescents with and without same-sex attractions. Data for this study were collected by means of a paper questionnaire completed by 1,518 secondary school students (mean age = 14.56 years, SD = 1.05) in Amsterdam, the Netherlands. The sample was 48.1% female and 51.9% male. Approximately one third of adolescents in the sample were of a non-Western ethnic background (32.3%, n = 491) and 7.5% of the participants (n = 114) reported experiencing same-sex attractions. Results of our analyses showed that adolescents in our sample who were male, of non-Western ethnicity, and who were more religious (as indicated by frequency of religious service attendance), were less accepting of same-sex sexuality and gender non-conformity in comparison to female, Western and less religious peers. We also found a significant interaction effect between religiosity and sexual attractions, but only in relation to evaluation of same-sex attracted, gender nonconforming females. The negative effect of religiosity on acceptance of same-sex attracted, gender non-conforming females was stronger among those adolescents who reported same-sex attractions. PMID:23687403

Diffusion-accomodated rigid-body translations along grain boundaries in nanostructured materials

International Nuclear Information System (INIS)

Bachurin, D.V.; Nazarov, A.A.; Shenderova, O.A.; Brenner, D.W.

2003-01-01

A model for the structural relaxation of grain boundaries (GBs) in nanostructured materials (NSMs) by diffusion-accommodated rigid body translations along GBs is proposed. The model is based on the results of recent computer simulations that have demonstrated that the GBs in NSMs retain a high-energy structure with random translational states due to severe geometrical constraints applied from neighboring grains (J. Appl. Phys. 78 (1995) 847; Scripta Metall. Mater. 33 (1995) 1245). The shear stresses within a GB caused by non-optimized rigid-body translations (RBTs) can be accommodated by diffusive flow of atoms along a GB. This mechanism is particularly important for low-angle and vicinal GBs, the energy of which noticeably depends on the rigid body translations. At moderate and high temperatures the model yields relaxation times that are very short and therefore GBs in NSMs can attain an equilibrium structure with optimized rigid body translations. In contrast, at room temperature the model predicts that in some metals non-equilibrium structures can be preserved for a long time, which may result in the observation of grain boundary structures different from those in coarse grained polycrystals

Laser spectroscopic and theoretical studies of the structures and encapsulation motifs of functional molecules

Energy Technology Data Exchange (ETDEWEB)

Ebata, Takayuki; Kusaka, Ryoji [Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, 739-8526 (Japan); Xantheas, Sotiris S. [Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, WA 99352 (United States)

2015-01-22

Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) 'hosts' interacting with N{sub 2}, acetylene, water, and ammonia 'guest' molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes.

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

Science.gov (United States)

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

2011-06-01

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

Strategy for conformity of non-standard cryogenic equipment

CERN Multimedia

CERN. Geneva

2016-01-01

CERN as an intergovernmental organization establishes its own Safety Rules as necessary for its proper functioning. In particular, the CERN General Safety Instruction for cryogenic equipment requires that cryogenic pressure equipment at CERN shall comply with the European Pressure Equipment Directive (PED). However, due to the particular features of some of the cryogenic equipment required for the accelerators, as well as the existence of international collaborations with in-kind contributions from non-EU countries, full compliance with the PED may not always be achieved. This situation is foreseen in the Safety Rules, where CERN HSE will define the Safety requirements applicable to such equipment as well as any eventual additional compensatory measure as to ensure a commensurate level of Safety for our pressure equipment. Where compliance with PED may not be achieved, CERN HSE will become the de facto Notified Body and therefore be in charge of the assessment of the conformity of the equipment to the applica...

Green waste cooking oil-based rigid polyurethane foam

Science.gov (United States)

Enderus, N. F.; Tahir, S. M.

2017-11-01

Polyurethane is a versatile polymer traditionally prepared using petroleum-based raw material. Petroleum, however, is a non-renewable material and polyurethane produced was found to be non-biodegradable. In quest for a more environmentally friendly alternative, wastecooking oil, a highly abundant domestic waste with easily derivatized structure, is a viable candidate to replace petroleum. In this study,an investigation to determine physical and chemical properties of rigid polyurethane (PU) foam from waste cooking oil (WCO) was carried out. WCO was first adsorbed by using coconut husk activated carbon adsorbent prior to be used for polyol synthesis. The purified WCO was then used to synthesize polyol via transesterification reaction to yield alcohol groups in the WCO chains structure. Finally, the WCO-based polyol was used to prepare rigid PU foam. The optimum formulation for PU formation was found to be 90 polyol: 60 glycerol: 54 water: 40 diethanolamine: 23 diisocyanate. The rigid PU foam has density of 208.4 kg/m3 with maximum compressive strength and capability to receive load at 0.03 MPa and 0.09 kN, respectively. WCO-based PU can potentially be used to replace petroleum-based PU as house construction materials such as insulation panels.

A non-conformal finite element/finite volume scheme for the non-structured grid-based approximation of low Mach number flows; Un schema elements finis non-conformes/volumes finis pour l'approximation en maillages non-structures des ecoulements a faible nombre de Mach

Energy Technology Data Exchange (ETDEWEB)

Ansanay-Alex, G.

2009-06-17

The development of simulation codes aimed at a precise simulation of fires requires a precise approach of flame front phenomena by using very fine grids. The need to take different spatial scale into consideration leads to a local grid refinement and to a discretization with homogeneous grid for computing time and memory purposes. The author reports the approximation of the non-linear convection term, the scalar advection-diffusion in finite volumes, numerical simulations of a flow in a bent tube, of a three-dimensional laminar flame and of a low Mach number an-isotherm flow. Non conformal finite elements are also presented (Rannacher-Turek and Crouzeix-Raviart elements)

Promiscuity and the conformational rearrangement of drug-like molecules: insight from the protein data bank.

Science.gov (United States)

He, Michael W; Lee, Patrick S; Sweeney, Zachary K

2015-02-01

Selectivity is a central aspect of lead optimization in the drug discovery process. Medicinal chemists often try to decrease molecular flexibility to improve selectivity, given the common belief that the two are interdependent. To investigate the relationship between polypharmacology and conformational flexibility, we mined the Protein Data Bank and constructed a dataset of pharmaceutically relevant ligands that crystallized in more than one protein target while binding to each co-crystallized receptor with similar in vitro affinities. After analyzing the molecular conformations of these 100 ligands, we found that 59 ligands bound to different protein targets without significantly changing conformation, suggesting that there is no distinct correlation between conformational flexibility and polypharmacology within our dataset. Ligands crystallized in similar proteins and highly ligand-efficient compounds with five or fewer rotatable bonds were less likely to adjust conformation when binding. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Dipole Correlation of the Electronic Structures of theConformations of Water Molecule Evolving Through theNormal Modes of Vibrations Between Angular (C2v to Linear(D∝h Shapes

Directory of Open Access Journals (Sweden)

Arindam Chakraborty

2006-03-01

Full Text Available In order to settle the issue of equivalence or non-equivalence of the two lone pairsof electrons on oxygen atom in water molecule, a quantum chemical study of the dipolecorrelation of the electronic structure of the molecule as a function of conformationsgenerated following the normal modes of vibrations between the two extremeconformations, C2v (∠HOH at 90o and D∝h (∠HOH at 180o, including the equilibrium one,has been performed. The study invokes quantum mechanical partitioning of moleculardipoles into bond moment and lone pair moment and localization of delocalized canonicalmolecular orbitals, CMO’s into localized molecular orbitals, LMO’s. An earlier suggestion,on the basis of photoelectron spectroscopy, that one lone pair is in p-type and the other is ins-type orbital of O atom of water molecule at its equilibrium shape, and also the qualitative“Squirrel Ears” structure are brought under serious scrutiny. A large number ofconformations are generated and the charge density matrix, dipole moment of eachconformation is computed in terms of the generated canonical molecular orbitals, CMO’sand then Sinanoğlu’s localization method is invoked to localize the CMO’s of eachconformation and the quantum mechanical hybridizations of all the bonds and lone pairs onO center are evaluated in terms of the localized molecular orbitals. Computed datademonstrate that the electronic structures i.e. two bond pairs and two lone pairs and itshybridization status of all conformations of water molecule are straightforward in terms ofthe LMO’s. It is further revealed that the pattern of orbital hybridization changescontinuously as a function of evolution of molecular shape. The close analysis of thegenerated LMO’s reveals that one lone pair is accommodated in a pure p orbital and anotherlone pair is in a hybrid

Local conformal symmetry in non-Riemannian geometry and the origin of physical scales

Energy Technology Data Exchange (ETDEWEB)

De Cesare, Marco [King' s College London, Theoretical Particle Physics and Cosmology Group, Department of Physics, London (United Kingdom); Moffat, John W. [Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada); Sakellariadou, Mairi [King' s College London, Theoretical Particle Physics and Cosmology Group, Department of Physics, London (United Kingdom); Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada)

2017-09-15

We introduce an extension of the Standard Model and General Relativity built upon the principle of local conformal invariance, which represents a generalization of a previous work by Bars, Steinhardt and Turok. This is naturally realized by adopting as a geometric framework a particular class of non-Riemannian geometries, first studied by Weyl. The gravitational sector is enriched by a scalar and a vector field. The latter has a geometric origin and represents the novel feature of our approach. We argue that physical scales could emerge from a theory with no dimensionful parameters, as a result of the spontaneous breakdown of conformal and electroweak symmetries. We study the dynamics of matter fields in this modified gravity theory and show that test particles follow geodesics of the Levi-Civita connection, thus resolving an old criticism raised by Einstein against Weyl's original proposal. (orig.)

Analysis of conformations and ESR spectra of free radicals in carbohydrates

International Nuclear Information System (INIS)

Abaghyan, G.V.; Abaghyan, A.G.; Apresyan, A.S.

1998-01-01

The conformations of free radicals arising when the unpaired electron is localized on carbon atoms in pyranose ring of carbohydrate molecule are considered. On the base of the analysis of expected conformations of radicals a possible contribution of β-protons in hyperfine structure of ESP spectra is predicted. The results of conformational analysis for different types of free radicals are in satisfactory agreement with the corresponding experimental data for the liquid phase. 17 refs

Non vertical vibronic transitions in atom molecule collisions

International Nuclear Information System (INIS)

Klomp, U.C.

1982-01-01

This thesis is mainly devoted to an experimental and theoretical study on vibronic transitions which occur in collisions between an alkali atom and several diatomic molecules. An experimental study on electron and ion production in repulsive Cs-CO and Cs-N 2 collisions, and in Cs-NO and Cs-O 2 non-repulsive collisions is presented. The experimental data are discussed in terms of some existing models. It is clear that a new consistent theory on vibronic transitions is needed to explain the experimental data. Such a theory is presented, and it is shown that some existing models are limiting cases of this theory. An experimental study on the relative probabilities for ion and electron production in collisions between a Na, K or Cs atom and an O 2 or NO molecule is also described. These experiments suggest that the incident velocity of the alkali atoms has a predominant influence on the relative probabilities for ion and electron production in these collisions. (Auth.)

Modular design of synthetic protein mimics. Characterization of the helical conformation of a 13-residue peptide in crystals

International Nuclear Information System (INIS)

Karle, I.L.; Flippen-Anderson, J.L.; Uma, K.; Balaram, P.

1989-01-01

The incorporation of α-aminoisobutyryl (Aib) residues into peptide sequences facilitates helical folding. Aib-containing sequences have been chosen for the design of rigid helical segments in a modular approach to the construction of a synthetic protein mimic. The helical conformation of the synthetic peptide Boc-Aib-(Val-Ala-Leu-Aib) 3 -OMe in crystals is established by X-ray diffraction. The 13-residue apolar peptide adopts a helical form in the crystal with seven α-type hydrogen bonds in the middle and 3 10 -type hydrogen bonds at either end. The helices stack in columns, zigzag rather than linear, by means of direct NH hor-ellipsis OC head to tail hydrogen bonds. Leucyl side chains are extended on one side of the helix and valyl side chains on the other side. Water molecules form hydrogen bonds with several backbone carbonyl oxygens that also participate in α-helix hydrogen bonds. There is no apparent distortion of the helix caused by hydration

Single Molecule Conductance of Oligothiophene Derivatives

Science.gov (United States)

Dell, Emma J.

This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

Molecular Wring Resonances in Chain Molecules

DEFF Research Database (Denmark)

Bohr, Henrik; Brunak, Søren; Bohr, Jakob

1997-01-01

It is shown that the eigenfrequency of collective twist excitations in chain molecules can be in the megahertz and gigahertz range. Accordingly, resonance states can be obtained at specific frequencies, and phenomena that involve structural properties can take place. Chain molecules can alter the...... their conformation and their ability to function, and a breaking of the chain can result. It is suggested that this phenomenon forms the basis for effects caused by the interaction of microwaves and biomolecules, e.g. microwave assisted hydrolysis of chain molecules....

Therapeutic effect analysis of three dimensional conformal radiotherapy non-small cell lung cancer

International Nuclear Information System (INIS)

Yao Zhijun; Cao Yongzhen; Zhang Wenxue; Liang Feng

2012-01-01

Objective: To analyse the treatment effect of non-small cell lung cancer of three dimensional conformal radiotherapy (3D-CRT) and to study the effect of patient survival related factors. Methods: Retrospective analysis was mack for 136 cases of non-small cell lung cancer, all accept 3D-CRT, through the case data collection and long-term follow-up, using the single factor and multiple factor analysis survival time and its influencing factors. Results: The recent curative effects of 136 cases of patients with three dimensional conformal radiotherapy: Complete response (CR) 14.7% (20/136), partial response (PR) 60.3 (82/136), stable disease(SD) 19.9% (27/136), progression disease (PD) 5.1% (7/136), total effective rate is 75% (102/136). One, two, three, five year survival rate is 79.4%, 45.4%, 22.1%, 12.5%. Side effects: Class 1 radiated esophagitis 35 cases, Class 2 radiated esophagitis 16 cases, Class 3 and above radiated esophagitis 0 case. Class I radiated pneumonia 20 cases, Class 2 radiated pneumonia 9 cases, Class 3 radiated pneumonia 0 case. Single factor analysis shows the influence of gender, age, pathology, phase, dose, and first-phase curative effect to the survival time are of a statistical significance, Multiple factor analysis showed KPS score, phase, dose, first-phase curative effect are the survival time independent factors. Conclusion: 3D-CRT for patients with non-small cell lung carcinoma is a safe, effective treatment method, Side effects are relatively low, and the patients survival time is long after radiotherapy. (authors)

Equilibrium and non-equilibrium conformations of peptides in lipid bilayers.

Science.gov (United States)

Boden, N; Cheng, Y; Knowles, P F

1997-04-22

A synthetic, hydrophobic, 27-amino-acid-residue peptide 'K27', modelled on the trans-membrane domain of the slow voltage-gated potassium channel, IsK, has been incorporated into a lipid bilayer and its conformational properties studied using FT-IR spectroscopy. The conformation following reconstitution is found to be dependent on the nature of the solvent employed. When the reconstitution is conducted by solvent evaporation from a methanol solution, aggregates comprised of beta-strands are stabilised and their concentration is essentially invariant with time. By contrast, when trifluoroethanol is used, the initial conformation of the peptide is alpha-helical. This then relaxes to an equilibrium state between alpha-helices and beta-strands. The alpha-helix-to beta-strand conversion rate is relatively slow, and this allows the kinetics to be studied by FT-IR spectroscopy. The reverse process is much slower but again can be demonstrated by FT-IR. Thus, it appears that a true equilibrium structure can only be achieved by starting with peptide in the alpha-helical conformation. We believe this result should be of general validity for hydrophobic peptide reconstitution. The implications for conformational changes in membrane proteins are discussed.

Flexibility and conformational change of IgG molecule

International Nuclear Information System (INIS)

Alpert, Y.; Ostanevich, Yu.M.

1982-12-01

The dynamic behaviour of pig anti-Dnp-immunoglobulin (IgG) investigated by the neutron spin echo technique gave evidence of internal motion of a biological macromolecule. It is suggested that this motion belongs to the wobbling of the Fab parts of the investigated IgG molecule around its so called hinge region. (author)

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

International Nuclear Information System (INIS)

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

2016-01-01

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

The conformal method and the conformal thin-sandwich method are the same

International Nuclear Information System (INIS)

Maxwell, David

2014-01-01

The conformal method developed in the 1970s and the more recent Lagrangian and Hamiltonian conformal thin-sandwich methods are techniques for finding solutions of the Einstein constraint equations. We show that they are manifestations of a single conformal method: there is a straightforward way to convert back and forth between the parameters for these methods so that the corresponding solutions of the Einstein constraint equations agree. The unifying idea is the need to clearly distinguish tangent and cotangent vectors to the space of conformal classes on a manifold, and we introduce a vocabulary for working with these objects without reference to a particular representative background metric. As a consequence of these conceptual advantages, we demonstrate how to strengthen previous near-CMC (constant mean curvature) existence and non-existence theorems for the original conformal method to include metrics with scalar curvatures that change sign. (paper)

Identification of potential small molecule binding pockets on Rho family GTPases.

Directory of Open Access Journals (Sweden)

Juan Manuel Ortiz-Sanchez

Full Text Available Rho GTPases are conformational switches that control a wide variety of signaling pathways critical for eukaryotic cell development and proliferation. They represent attractive targets for drug design as their aberrant function and deregulated activity is associated with many human diseases including cancer. Extensive high-resolution structures (>100 and recent mutagenesis studies have laid the foundation for the design of new structure-based chemotherapeutic strategies. Although the inhibition of Rho signaling with drug-like compounds is an active area of current research, very little attention has been devoted to directly inhibiting Rho by targeting potential allosteric non-nucleotide binding sites. By avoiding the nucleotide binding site, compounds may minimize the potential for undesirable off-target interactions with other ubiquitous GTP and ATP binding proteins. Here we describe the application of molecular dynamics simulations, principal component analysis, sequence conservation analysis, and ensemble small-molecule fragment mapping to provide an extensive mapping of potential small-molecule binding pockets on Rho family members. Characterized sites include novel pockets in the vicinity of the conformationaly responsive switch regions as well as distal sites that appear to be related to the conformations of the nucleotide binding region. Furthermore the use of accelerated molecular dynamics simulation, an advanced sampling method that extends the accessible time-scale of conventional simulations, is found to enhance the characterization of novel binding sites when conformational changes are important for the protein mechanism.

Conformational flexibility of aspartame.

Science.gov (United States)

Toniolo, Claudio; Temussi, Pierandrea

2016-05-01

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

Conformal algebra of Riemann surfaces

International Nuclear Information System (INIS)

Vafa, C.

1988-01-01

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

Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins.

Science.gov (United States)

Säwén, Elin; Massad, Tariq; Landersjö, Clas; Damberg, Peter; Widmalm, Göran

2010-08-21

The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted

Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

Science.gov (United States)

Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

2016-08-01

Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view.

Induced quantum conformal gravity

International Nuclear Information System (INIS)

Novozhilov, Y.V.; Vassilevich, D.V.

1988-11-01

Quantum gravity is considered as induced by matter degrees of freedom and related to the symmetry breakdown in the low energy region of a non-Abelian gauge theory of fundamental fields. An effective action for quantum conformal gravity is derived where both the gravitational constant and conformal kinetic term are positive. Relation with induced classical gravity is established. (author). 15 refs

Could 3-D conformal radiotherapy improve the overall survival for non-small cell lung cancer?

International Nuclear Information System (INIS)

Giraud, P.; Helfre, S.; Lavole, A.; Rosenwald, J.C.; Cosset, J.M.

2002-01-01

The conformal radiotherapy approach, three-dimensional conformal radiotherapy (3DCRT) and intensity-modulated radiotherapy (IMRT), is based on modern imaging modalities, efficient 3-D treatment planning systems, sophisticated immobilization devices and demanding quality assurance and treatment verification. The main goal of conformal radiotherapy is to ensure a high dose distribution tailored to the limits of the target volume while reducing exposure of healthy tissues. These techniques would then allow a further dose escalation increasing local control and survival. Non-small cell lung cancer (NSCLC) is one of the most difficult malignant tumors to be treated. It combines geometrical difficulties due to respiratory motion, and number of low tolerance neighboring organs, and dosimetric difficulties because of the presence of huge inhomogeneities. This localization is an attractive and ambitious example for the evaluation of new techniques. However, the published clinical reports in the last years described very heterogeneous techniques and, in the absence of prospective randomized trials, it is somewhat difficult at present to evaluate the real benefits drawn from those conformal radiotherapy techniques. After reviewing the rationale for 3DCRT for NSCLC, this paper will describe the main studies of 3DCRT, in order to evaluate its impact on lung cancer treatment Then the current state-of-the-art of IMRT and the last technical and therapeutic innovations in NSCL will be discussed. (authors)

Self-objectification, feminist activism and conformity to feminine norms among female vegetarians, semi-vegetarians, and non-vegetarians.

Science.gov (United States)

Brinkman, Britney G; Khan, Aliya; Edner, Benjamin; Rosén, Lee A

2014-01-01

Recent research has suggested that vegetarians may be at an increased risk for developing disordered eating or body image issues when compared to non-vegetarians. However, the results of such studies are mixed, and no research has explored potential connections between vegetarianism and self-objectification. In the current study, the authors examine factors that predicted body surveillance, body shame, and appearance control beliefs; three aspects of self-objectification. Surveys were completed by 386 women from the United States who were categorized as vegetarian, semi-vegetarian, or non-vegetarian. The three groups differed regarding dietary motivations, levels of feminist activism, and body shame, but did not differ on their conformity to feminine norms. While conformity to feminine norms predicted body surveillance and body shame levels among all three groups of women, feminist activism predicted appearance control beliefs among non-vegetarians only. These findings suggest that it is important for researchers and clinicians to distinguish among these three groups when examining the relationship between vegetarianism and self-objectification. Copyright © 2013 Elsevier Ltd. All rights reserved.

Confab - Systematic generation of diverse low-energy conformers

Directory of Open Access Journals (Sweden)

O'Boyle Noel M

2011-03-01

Full Text Available Abstract Background Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. Results Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 Å at a diversity level of 1.5 Å and an energy cutoff of 50 kcal/mol. Conclusions Confab is available from http://confab.googlecode.com.

A New Theoretical Approach to Single-Molecule Fluorescence Optical Studies of RNA Dynamics

International Nuclear Information System (INIS)

Zhao Xinghai; Shan Guangcun; Bao Shuying

2011-01-01

Single-molecule fluorescence spectroscopy in condensed phases has many important chemical and biological applications. The single-molecule fluorescence measurements contain information about conformational dynamics on a vast range of time scales. Based on the data analysis protocols methodology proposed by X. Sunney Xie, the theoretical study here mainly focuses on the single-molecule studies of single RNA with interconversions among different conformational states, to with a single FRET pair attached. We obtain analytical expressions for fluorescence lifetime correlation functions that relate changes in fluorescence lifetime to the distance-dependent FRET mechanism within the context of the Smoluchowski diffusion model. The present work establishes useful guideline for the single-molecule studies of biomolecules to reveal the complicated folding dynamics of single RNA molecules at nanometer scale.

Real-time monitoring and manipulation of single bio-molecules in free solution

Energy Technology Data Exchange (ETDEWEB)

Li, Hung-Wing [Iowa State Univ., Ames, IA (United States)

2005-01-01

The observation and manipulation of single biomolecules allow their dynamic behaviors to be studied to provide insight into molecular genetics, biochip assembly, biosensor design, DNA biophysics. In a PDMS/glass microchannel, a nonuniform electroosmotic flow (EOF) was created. By using a scanning confocal fluorescence microscope and total internal-reflection fluorescence microscope (TIRFM), we demonstrated that negatively charged DNA molecules were focused by the nonuniform EOF into a thin layer at the glass surface. This phenomenon was applied to selectively detect target DNA molecules without requiring the separation of excessive probes and can be applied continuously to achieve high throughput. A variable-angle-TIRFM was constructed for imaging single DNA molecule dynamics at a solid/liquid interface. Implications we have are that the measured intensities cannot be used directly to determine the distances of molecules from the surface and the experimental counting results depict the distance-dependent dynamics of molecules near the surface; Molecules at low ionic strengths experience electrostatic repulsion at distances much further away from the surface than the calculated thickness of the electrical double layer. {delta}-DNA was employed as a nanoprobe for different functionalized surfaces to elucidate adsorption in chromatography. The 12-base unpaired ends of this DNA provide exposed purine and pyrimidine groups for adsorption. Patterns of self-assembled monolayers (SAMs) and patterns of metal oxides are generated. By recording the real-time dynamic motion of DNA molecules at the SAMs/aqueous interface, the various parameters governing the retention of an analyte during chromatographic separation can be studied. Even subtle differences among adsorptive forces can be revealed. Dynamic conformational changes of the prosthetic group, flavin adenine dinucleotide (FAD), in flavoprotein NADH peroxidase, in thioredoxin reductase, and in free solution were monitored

Conformational Effects of UV Light on DNA Origami.

Science.gov (United States)

Chen, Haorong; Li, Ruixin; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

2017-02-01

The responses of DNA origami conformation to UV radiation of different wavelengths and doses are investigated. Short- and medium-wavelength UV light can cause photo-lesions in DNA origami. At moderate doses, the lesions do not cause any visible defects in the origami, nor do they significantly affect the hybridization capability. Instead, they help relieve the internal stress in the origami structure and restore it to the designed conformation. At high doses, staple dissociation increases which causes structural disintegration. Long-wavelength UV does not show any effect on origami conformation by itself. We show that this UV range can be used in conjunction with photoactive molecules for photo-reconfiguration, while avoiding any damage to the DNA structures.

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

Paper based Flexible and Conformal SERS Substrate for Rapid Trace Detection on Real-world Surfaces

Science.gov (United States)

Singamaneni, Srikanth; Lee, Chang; Tian, Limei

2011-03-01

One of the important but often overlooked considerations in the design of surface enhanced Raman scattering (SERS) substrates for trace detection is the efficiency of sample collection. Conventional designs based on rigid substrates such as silicon, alumina, and glass resist conformal contact with the surface under investigation, making the sample collection inefficient. We demonstrate a novel SERS substrate based on common filter paper adsorbed with gold nanorods, which allows conformal contact with real-world surfaces, thus dramatically enhancing the sample collection efficiency compared to conventional rigid substrates. We demonstrate the detection of trace amounts of analyte (140 pg spread over 4 cm2) by simply swabbing the surface under investigation with the novel SERS substrate. The hierarchical fibrous structure of paper serves as a 3D vasculature for easy uptake and transport of the analytes to the electromagnetic hot spots in the paper. Simple yet highly efficient and cost effective SERS substrate demonstrated here brings SERS based trace detection closer to real-world applications. We acknowledge the financial support from Center for Materials Innovation at Washington University.

Conformational Fluctuations in G-Protein-Coupled Receptors

Science.gov (United States)

Brown, Michael F.

2014-03-01

G-protein-coupled receptors (GPCRs) comprise almost 50% of pharmaceutical drug targets, where rhodopsin is an important prototype and occurs naturally in a lipid membrane. Rhodopsin photoactivation entails 11-cis to all-trans isomerization of the retinal cofactor, yielding an equilibrium between inactive Meta-I and active Meta-II states. Two important questions are: (1) Is rhodopsin is a simple two-state switch? Or (2) does isomerization of retinal unlock an activated conformational ensemble? For an ensemble-based activation mechanism (EAM) a role for conformational fluctuations is clearly indicated. Solid-state NMR data together with theoretical molecular dynamics (MD) simulations detect increased local mobility of retinal after light activation. Resultant changes in local dynamics of the cofactor initiate large-scale fluctuations of transmembrane helices that expose recognition sites for the signal-transducing G-protein. Time-resolved FTIR studies and electronic spectroscopy further show the conformational ensemble is strongly biased by the membrane lipid composition, as well as pH and osmotic pressure. A new flexible surface model (FSM) describes how the curvature stress field of the membrane governs the energetics of active rhodopsin, due to the spontaneous monolayer curvature of the lipids. Furthermore, influences of osmotic pressure dictate that a large number of bulk water molecules are implicated in rhodopsin activation. Around 60 bulk water molecules activate rhodopsin, which is much larger than the number of structural waters seen in X-ray crystallography, or inferred from studies of bulk hydrostatic pressure. Conformational selection and promoting vibrational motions of rhodopsin lead to activation of the G-protein (transducin). Our biophysical data give a paradigm shift in understanding GPCR activation. The new view is: dynamics and conformational fluctuations involve an ensemble of substates that activate the cognate G-protein in the amplified visual

Molecular Origin of Model Membrane Bending Rigidity

International Nuclear Information System (INIS)

Kurtisovski, Erol; Taulier, Nicolas; Waks, Marcel; Ober, Raymond; Urbach, Wladimir

2007-01-01

The behavior of the bending modulus κ of bilayers in lamellar phases was studied by Small Angle X-ray Scattering technique for various nonionic C i E j surfactants. The bilayers are either unswollen and dispersed in water or swollen by water and dispersed in dodecane. For unswollen bilayers, the values of κ decrease with both an increase in the area per surfactant molecule and in the polar head length. They increase when the aliphatic chain length increases at constant area per surfactant molecule. Whereas for water-swollen membranes, the values of κ decrease as the content of water increases converging to the value of the single monolayer bending modulus. Such a behavior results from the decoupling of the fluctuations of the two surfactant membrane monolayers. Our results emphasize the determinant contribution of the surfactant conformation to κ

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.)

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...

Utility of semi-rigid thoracoscopy in undiagnosed exudative pleural effusion.

Science.gov (United States)

Nattusamy, Loganathan; Madan, Karan; Mohan, Anant; Hadda, Vijay; Jain, Deepali; Madan, Neha Kawatra; Arava, Sudheer; Khilnani, Gopi C; Guleria, Randeep

2015-01-01

Semi-rigid thoracoscopy is a safe and efficacious procedure in patients with undiagnosed pleural effusion. Literature on its utility from developing countries is limited. We herein describe our initial experience on the utility of semi-rigid thoracoscopy from a tertiary care teaching and referral center in north India. We also perform a systematic review of studies reporting the utility of semi-rigid thoracoscopy from India. The primary objective was to evaluate the diagnostic utility of semi-rigid thoracoscopy in patients with undiagnosed exudative pleural effusion. Semi-rigid thoracoscopy was performed under local anesthesia and conscious sedation in the bronchoscopy suite. A total of 48 patients underwent semi-rigid thoracoscopy between August 2012 and December 2013 for undiagnosed pleural effusion. Mean age was 50.9 ± 14.1 years (range: 17-78 years). Pre-procedure clinico-radiological diagnoses were malignant pleural effusion [36 patients (75%)], tuberculosis (TB) [10 (20.83%) patients], and empyema [2 patients (4.17%)]. Patients with empyema underwent the procedure for pleural biopsy, optimal placement of intercostal tube and adhesiolysis. Thoracoscopic pleural biopsy diagnosed pleural malignancy in 30 (62.5%) patients and TB in 2 (4.17%) patients. Fourteen (29.17%) patients were diagnosed with non-specific pleuritis and normal pleura was diagnosed on a pleural biopsy in 2 (4.17%) patients. Overall, a definitive diagnosis of either pleural malignancy or TB was obtained in 32 (66.7%) patients. Combined overall sensitivity, specificity, positive predictive value and negative predictive value of thoracoscopic pleural biopsy for malignant pleural effusion were 96.77%, 100%, 100% and 66.67%, respectively. There was no procedure-related mortality. On performing a systematic review of literature, four studies on semi-rigid thoracoscopy from India were identified. Semi-rigid thoracoscopy is a safe and efficacious procedure in patients with undiagnosed exudative

A non-conformal finite element/finite volume scheme for the non-structured grid-based approximation of low Mach number flows

International Nuclear Information System (INIS)

Ansanay-Alex, G.

2009-01-01

The development of simulation codes aimed at a precise simulation of fires requires a precise approach of flame front phenomena by using very fine grids. The need to take different spatial scale into consideration leads to a local grid refinement and to a discretization with homogeneous grid for computing time and memory purposes. The author reports the approximation of the non-linear convection term, the scalar advection-diffusion in finite volumes, numerical simulations of a flow in a bent tube, of a three-dimensional laminar flame and of a low Mach number an-isotherm flow. Non conformal finite elements are also presented (Rannacher-Turek and Crouzeix-Raviart elements)

Rigid Body Sampling and Individual Time Stepping for Rigid-Fluid Coupling of Fluid Simulation

Directory of Open Access Journals (Sweden)

Xiaokun Wang

2017-01-01

Full Text Available In this paper, we propose an efficient and simple rigid-fluid coupling scheme with scientific programming algorithms for particle-based fluid simulation and three-dimensional visualization. Our approach samples the surface of rigid bodies with boundary particles that interact with fluids. It contains two procedures, that is, surface sampling and sampling relaxation, which insures uniform distribution of particles with less iterations. Furthermore, we present a rigid-fluid coupling scheme integrating individual time stepping to rigid-fluid coupling, which gains an obvious speedup compared to previous method. The experimental results demonstrate the effectiveness of our approach.

Conformation transitions of blood proteins under influence of physical factors on microwave dielectric method

International Nuclear Information System (INIS)

Gorobchenko, O.A.; Nikolov, O.T.; Gatash, S.V.

2006-01-01

In this article, the influence of γ-irradiation and temperature on albumin and fibrinogen conformation and dielectric properties of protein solutions have been studied by the microwave dielectric method. Both the values of the real part ε' (dielectric permittivity) and the imaginary part ε'' (dielectric losses) of the complex dielectric permittivity of the aqueous solution of bovine serum albumin and human fibrinogen as functions of temperature and γ-irradiation dose have been obtained. The time of dielectric relaxation of water molecules in the protein solutions was calculated. The hydration of the albumin and fibrinogen molecules was determined. The temperature dependencies of hydration are non-monotonous and have a number of characteristic features at the temperatures 30-34 and 44-47 deg. C for serum albumin, and 24 and 32 deg. C for fibrinogen

Semiflexible polymer conformation, distribution and migration in microcapillary flows

Energy Technology Data Exchange (ETDEWEB)

Chelakkot, Raghunath; Gompper, Gerhard [Institut fuer Festkoerperforschung, Forschungszentrum Juelich, 52425 Juelich (Germany); Winkler, Roland G [Institute for Advanced Simulation, Forschungszentrum Juelich, 52425 Juelich (Germany)

2011-05-11

The flow behavior of a semiflexible polymer in microchannels is studied using multiparticle collision dynamics, a particle-based hydrodynamic simulation technique. Conformations, distributions, and radial cross-streamline migration are investigated for various bending rigidities, with persistence lengths L{sub p} in the range 0.5 {<=} L{sub p}/L{sub r} {<=} 30. The flow behavior is governed by the competition between a hydrodynamic lift force and steric repulsion from the wall, which lead to migration away from the wall, and a locally varying flow induced orientation, which drives the polymer away from the channel center and towards the wall. The different dependences of these effects on the polymer bending rigidity and the flow velocity results in a complex dynamical behavior. However, a generic effect is the appearance of a maximum in the monomer and the center-of-mass distributions, which occurs at the channel center for small flow velocities, but moves off-center at higher velocities.

Semiflexible polymer conformation, distribution and migration in microcapillary flows

International Nuclear Information System (INIS)

Chelakkot, Raghunath; Gompper, Gerhard; Winkler, Roland G

2011-01-01

The flow behavior of a semiflexible polymer in microchannels is studied using multiparticle collision dynamics, a particle-based hydrodynamic simulation technique. Conformations, distributions, and radial cross-streamline migration are investigated for various bending rigidities, with persistence lengths L p in the range 0.5 ≤ L p /L r ≤ 30. The flow behavior is governed by the competition between a hydrodynamic lift force and steric repulsion from the wall, which lead to migration away from the wall, and a locally varying flow induced orientation, which drives the polymer away from the channel center and towards the wall. The different dependences of these effects on the polymer bending rigidity and the flow velocity results in a complex dynamical behavior. However, a generic effect is the appearance of a maximum in the monomer and the center-of-mass distributions, which occurs at the channel center for small flow velocities, but moves off-center at higher velocities.

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.

Rigidly foldable origami gadgets and tessellations

Science.gov (United States)

Evans, Thomas A.; Lang, Robert J.; Magleby, Spencer P.; Howell, Larry L.

2015-01-01

Rigidly foldable origami allows for motion where all deflection occurs at the crease lines and facilitates the application of origami in materials other than paper. In this paper, we use a recently discovered method for determining rigid foldability to identify existing flat-foldable rigidly foldable tessellations, which are also categorized. We introduce rigidly foldable origami gadgets which may be used to modify existing tessellations or to create new tessellations. Several modified and new rigidly foldable tessellations are presented. PMID:26473037

Inflationary magnetogenesis and non-local actions: the conformal anomaly

Energy Technology Data Exchange (ETDEWEB)

El-Menoufi, Basem Kamal, E-mail: bmahmoud@physics.umass.edu [Department of Physics, University of Massachusetts Amherst, MA 01003 (United States)

2016-02-01

We discuss the possibility of successful magnetogenesis during inflation by employing the one-loop effective action of massless QED. The action is strictly non-local and results from the long distance fluctuations of massless charged particles present at the inflationary scale. Most importantly, it encodes the conformal anomaly of QED which is crucial to avoid the vacuum preservation in classical electromagnetism. In particular, we find a blue spectrum for the magnetic field with spectral index n{sub B} ≅ 2 − α{sub e} where α{sub e} depends on both the number of e-folds during inflation as well as the coefficient of the one-loop beta function. In particular, the sign of the beta function has important bearing on the final result. A low reheating temperature is required for the present day magnetic field to be consistent with the lower bound inferred on the field in the intergalactic medium.

Transport coefficients in second-order non-conformal viscous hydrodynamics

International Nuclear Information System (INIS)

Ryblewski, Radoslaw

2015-01-01

Based on the exact solution of Boltzmann kinetic equation in the relaxation-time approximation, the precision of the two most recent formulations of relativistic second-order non-conformal viscous hydrodynamics (14-moment approximation and causal Chapman-Enskog method), standard Israel-Stewart theory, and anisotropic hydrodynamics framework, in the simple case of one-dimensional Bjorken expansion, is tested. It is demonstrated that the failure of Israel-Stewart theory in reproducing exact solutions of the Boltzmann kinetic equation occurs due to neglecting and/or choosing wrong forms of some of the second-order transport coefficients. In particular, the importance of shear-bulk couplings in the evolution equations for dissipative quantities is shown. One finds that, in the case of the bulk viscous pressure correction, such coupling terms are as important as the corresponding first-order Navier-Stokes term and must be included in order to obtain, at least qualitative, overall agreement with the kinetic theory. (paper)

Adaptive Particle Swarm Optimizer with Varying Acceleration Coefficients for Finding the Most Stable Conformer of Small Molecules.

Science.gov (United States)

Agrawal, Shikha; Silakari, Sanjay; Agrawal, Jitendra

2015-11-01

A novel parameter automation strategy for Particle Swarm Optimization called APSO (Adaptive PSO) is proposed. The algorithm is designed to efficiently control the local search and convergence to the global optimum solution. Parameters c1 controls the impact of the cognitive component on the particle trajectory and c2 controls the impact of the social component. Instead of fixing the value of c1 and c2 , this paper updates the value of these acceleration coefficients by considering time variation of evaluation function along with varying inertia weight factor in PSO. Here the maximum and minimum value of evaluation function is use to gradually decrease and increase the value of c1 and c2 respectively. Molecular energy minimization is one of the most challenging unsolved problems and it can be formulated as a global optimization problem. The aim of the present paper is to investigate the effect of newly developed APSO on the highly complex molecular potential energy function and to check the efficiency of the proposed algorithm to find the global minimum of the function under consideration. The proposed algorithm APSO is therefore applied in two cases: Firstly, for the minimization of a potential energy of small molecules with up to 100 degrees of freedom and finally for finding the global minimum energy conformation of 1,2,3-trichloro-1-flouro-propane molecule based on a realistic potential energy function. The computational results of all the cases show that the proposed method performs significantly better than the other algorithms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Science.gov (United States)

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

2017-02-06

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

Conformational analysis of g protein-coupled receptor signaling by hydrogen/deuterium exchange mass spectrometry.

Science.gov (United States)

Li, Sheng; Lee, Su Youn; Chung, Ka Young

2015-01-01

Conformational change and protein-protein interactions are two major mechanisms of membrane protein signal transduction, including G protein-coupled receptors (GPCRs). Upon agonist binding, GPCRs change conformation, resulting in interaction with downstream signaling molecules such as G proteins. To understand the precise signaling mechanism, studies have investigated the structural mechanism of GPCR signaling using X-ray crystallography, nuclear magnetic resonance (NMR), or electron paramagnetic resonance. In addition to these techniques, hydrogen/deuterium exchange mass spectrometry (HDX-MS) has recently been used in GPCR studies. HDX-MS measures the rate at which peptide amide hydrogens exchange with deuterium in the solvent. Exposed or flexible regions have higher exchange rates and excluded or ordered regions have lower exchange rates. Therefore, HDX-MS is a useful tool for studying protein-protein interfaces and conformational changes after protein activation or protein-protein interactions. Although HDX-MS does not give high-resolution structures, it analyzes protein conformations that are difficult to study with X-ray crystallography or NMR. Furthermore, conformational information from HDX-MS can help in the crystallization of X-ray crystallography by suggesting highly flexible regions. Interactions between GPCRs and downstream signaling molecules are not easily analyzed by X-ray crystallography or NMR because of the large size of the GPCR-signaling molecule complexes, hydrophobicity, and flexibility of GPCRs. HDX-MS could be useful for analyzing the conformational mechanism of GPCR signaling. In this chapter, we discuss details of HDX-MS for analyzing GPCRs using the β2AR-G protein complex as a model system. © 2015 Elsevier Inc. All rights reserved.

EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

Directory of Open Access Journals (Sweden)

S. Compernolle

2011-09-01

Full Text Available We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects, a method to predict (subcooled liquid pure compound vapour pressure p⁰ of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log₁₀p⁰(T is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA.

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

Science.gov (United States)

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

2018-02-01

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

Clinical Studies on conformal radiotherapy combined with epidermal ...

African Journals Online (AJOL)

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

Rigid cohomology over Laurent series fields

CERN Document Server

Lazda, Christopher

2016-01-01

In this monograph, the authors develop a new theory of p-adic cohomology for varieties over Laurent series fields in positive characteristic, based on Berthelot's theory of rigid cohomology. Many major fundamental properties of these cohomology groups are proven, such as finite dimensionality and cohomological descent, as well as interpretations in terms of Monsky-Washnitzer cohomology and Le Stum's overconvergent site. Applications of this new theory to arithmetic questions, such as l-independence and the weight monodromy conjecture, are also discussed. The construction of these cohomology groups, analogous to the Galois representations associated to varieties over local fields in mixed characteristic, fills a major gap in the study of arithmetic cohomology theories over function fields. By extending the scope of existing methods, the results presented here also serve as a first step towards a more general theory of p-adic cohomology over non-perfect ground fields. Rigid Cohomology over Laurent Series Fields...

Exceptions to the duty to notify the seller of a non-conformity of the delivered goods in international sales law

Directory of Open Access Journals (Sweden)

Fišer-Šobot Sandra

2012-01-01

Full Text Available Breach of the duty to notify the seller of the lack of conformity of the delivered goods is followed by harsh consequences for the buyer. Namely, he loses the right to rely on the non-conformity of the goods if he does not give the notice to the seller in adequate and timely manner. In international sales law the buyer is entitled to rely on the lack of conformity of the goods even when he fails to notify the seller in two specific cases. First, if the lack of conformity relates to the facts of which the seller knew or could not have been unaware and which he did not disclose to the buyer. And secondly, the buyer retains remedies for the nonconforming delivery if he has a reasonable excuse for his failure to give the required notice.

Single-Molecule Nanomagnets

Science.gov (United States)

Friedman, Jonathan R.; Sarachik, Myriam P.

2010-04-01

Single-molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn12-acetate and Fe8: Each behaves as a rigid, spin-10 object and exhibits tunneling between up and down directions. As temperature is lowered, the spin-reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on timescales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are under way to create monolayers and to address and manipulate individual molecules.

Activated barrier crossing dynamics in the non-radiative decay of NADH and NADPH

Energy Technology Data Exchange (ETDEWEB)

Blacker, Thomas S., E-mail: t.blacker@ucl.ac.uk [Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT (United Kingdom); Department of Physics and Astronomy, University College London, London WC1E 6BT (United Kingdom); Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT (United Kingdom); Marsh, Richard J., E-mail: richard.marsh@ucl.ac.uk [Department of Physics and Astronomy, University College London, London WC1E 6BT (United Kingdom); Duchen, Michael R., E-mail: m.duchen@ucl.ac.uk [Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT (United Kingdom); Bain, Angus J., E-mail: a.bain@ucl.ac.uk [Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT (United Kingdom); Department of Physics and Astronomy, University College London, London WC1E 6BT (United Kingdom)

2013-08-30

Highlights: ► NADH and NADPH have a high rate of non-radiative excited state decay. ► Conformational relaxation is shown to be a significant non-radiative pathway. ► The Kramers equation describes the barrier crossing dynamics of the relaxation. ► Conformational restriction upon enzyme binding will alter NAD(P)H lifetimes. - Abstract: In live tissue, alterations in metabolism induce changes in the fluorescence decay of the biological coenzyme NAD(P)H, the mechanism of which is not well understood. In this work, the fluorescence and anisotropy decay dynamics of NADH and NADPH were investigated as a function of viscosity in a range of water–glycerol solutions. The viscosity dependence of the non-radiative decay is well described by Kramers and Kramers–Hubbard models of activated barrier crossing over a wide viscosity range. Our combined lifetime and anisotropy analysis indicates common mechanisms of non-radiative relaxation in the two emitting states (conformations) of both molecules. The low frequencies associated with barrier crossing suggest that non-radiative decay is mediated by small scale motion (e.g. puckering) of the nicotinamide ring. Variations in the fluorescence lifetimes of NADH and NADPH when bound to different enzymes may therefore be attributed to differing levels of conformational restriction upon binding.

Conformational kinetics of aliphatic tails

Science.gov (United States)

Ferrarini, Alberta; Moro, Giorgio; Nordio, Pier Luigi

The master equation describing the random walk between sites identified with the stable conformers of a chain molecule, represents the extension to the time domain of the Rotational Isomeric State model. The asymptotic analysis of the multidimensional diffusion equation in the continuous torsional variables subjected to the configurational potential, provides a rigorous justification for the discrete models, and it supplies, without resorting to phenomenological parameters, molecular definitions of the kinetic rates for the conformational transitions occurring at each segment of the chain. The coupling between the torsional variables is fully taken into account, giving rise to cooperative effects. A complete calculation of the specific correlation functions which describe the time evolution of the angular functions probed by N.M.R. and dielectric relaxation measurements, has been performed for alkyl chains attached to a massive core. The resulting behaviour has been compared with the decay of trans and gauche populations of specific bonds, expressed in terms of suitable correlation functions whose time integrals lead quite naturally to the definition of effective kinetic constants for the conformational transitions.

On the near UV photophysics of a phenylalanine residue: conformation-dependent ππ* state deactivation revealed by laser spectroscopy of isolated neutral dipeptides.

Science.gov (United States)

Loquais, Yohan; Gloaguen, Eric; Alauddin, Mohammad; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel

2014-10-28

The primary step of the near UV photophysics of a phenylalanine residue is investigated in one- and two-color pump-probe R2PI nanosecond experiments carried out on specific conformers of the Ac-Gly-Phe-NH2 molecule and related neutral compounds isolated in a supersonic expansion. Compared to toluene, whose ππ* state photophysics is dominated by intersystem crossing with a lifetime of ∼80 ns at the origin, the first ππ* state of Phe in the peptide environment is systematically found to be shorter-lived. The lifetime at the origin of transition is found to be significantly shortened in the presence of a primary amide (-CONH2) group (20-60 ns, depending on the conformer considered), demonstrating the existence of an additional non-radiative relaxation channel related to this chemical group. The quenching effect induced by the peptide environment is still more remarkable beyond the origin of the ππ* state, since vibronic bands of one of the 4 conformers observed (the 27-ribbon conformation) become barely detectable in the ns R2PI experiment, suggesting a significant conformer-selective lifetime shortening (below 100 ps). These results on dipeptides, which extend previous investigations on shorter Phe-containing molecules (N-Ac-Phe-NH2 and N-Ac-Phe-NH-Me), confirm the existence of conformer-dependent non-radiative deactivation processes, whose characteristic timescales range from tens of ns down to hundreds of ps or below. This dynamics is assigned to two distinct mechanisms: a first one, consistent with an excitation energy transfer from the optically active ππ* state to low-lying amide nπ* excited states accessed through conical intersections, especially in the presence of a C-terminal primary amide group (-CONH2); a second one, responsible for the short lifetimes in 2(7) ribbon structures, would be more specifically triggered by phenyl ring vibrational excitations. Implications in terms of spectroscopic probing of Phe in a peptide environment, especially

Conformation of antifreeze glycoproteins as determined from conformational energy calculations and fully assigned proton NMR spectra

International Nuclear Information System (INIS)

Bush, C.A.; Rao, B.N.N.

1986-01-01

The 1 H NMR spectra of AFGP's ranging in molecular weight from 2600 to 30,000 Daltons isolated from several different species of polar fish have been measured. The spectrum of AFGP 1-4 from Pagothenia borchgrevinki with an average of 30 repeating subunits has a single resonance for each proton of the glycotripeptide repeating unit, (ala-[gal-(β-1→3) galNAc-(α--O-]thr-ala)/sub n/. Its 1 H NMR spectrum including resonances of the amide protons has been completely assigned. Coupling constants and nuclear Overhauser enhancements (n.O.e.) between protons on distant residues imply conformational order. The 2600 dalton molecular weight glycopeptides (AFGP-8) have pro in place of ala at certain specific points in the sequence and AFGP-8R of Eleginus gracilis has arg in place of one thr. The resonances of pro and arg were assigned by decoupling. The resonances of the carboxy and amino terminals have distinct chemical shifts and were assigned in AFGP-8 of Boreogadus saida by titration. n.O.e. between α--protons and amide protons of the adjacent residue (sequential n.O.e.) were used in assignments of additional resonances and to assign the distinctive resonances of thr followed by pro. Conformational energy calculations on the repeating glycotripeptide subunit of AFGP show that the α--glucosidic linkage has a fixed conformation while the β--linkage is less rigid. A conformational model for AFGP 1-4, which is based on the calculations has the peptide in an extended left-handed helix with three residues per turn similar to polyproline II. The model is consistent with CD data, amide proton coupling constants, temperature dependence of amide proton chemical shifts

Tile-based rigidization surface parametric design study

Science.gov (United States)

Giner Munoz, Laura; Luntz, Jonathan; Brei, Diann; Kim, Wonhee

2018-03-01

Inflatable technologies have proven useful in consumer goods as well as in more recent applications including civil structures, aerospace, medical, and robotics. However, inflatable technologies are typically lacking in their ability to provide rigid structural support. Particle jamming improves upon this by providing structures which are normally flexible and moldable but become rigid when air is removed. Because these are based on an airtight bladder filled with loose particles, they always occupy the full volume of its rigid state, even when not rigidized. More recent developments in layer jamming have created thin, compact rigidizing surfaces replacing the loose volume of particles with thinly layered surface materials. Work in this area has been applied to several specific applications with positive results but have not generally provided the broader understanding of the rigidization performance as a function of design parameters required for directly adapting layer rigidization technology to other applications. This paper presents a parametric design study of a new layer jamming vacuum rigidization architecture: tile-based vacuum rigidization. This form of rigidization is based on layers of tiles contained within a thin vacuum bladder which can be bent, rolled, or otherwise compactly stowed, but when deployed flat, can be vacuumed and form a large, flat, rigid plate capable of supporting large forces both localized and distributed over the surface. The general architecture and operation detailing rigidization and compliance mechanisms is introduced. To quantitatively characterize the rigidization behavior, prototypes rigidization surfaces are fabricated and an experimental technique is developed based on a 3-point bending test. Performance evaluation metrics are developed to describe the stiffness, load-bearing capacity, and internal slippage of tested prototypes. A set of experimental parametric studies are performed to better understand the impact of

The Conformational Behaviour of Glucosamine

Science.gov (United States)

Peña, Isabel; Kolesniková, Lucie; Cabezas, Carlos; Bermúdez, Celina; Berdakin, Matías; Simao, Alcides; Alonso, José L.

2014-06-01

A laser ablation method has been successfully used to vaporize the bioactive amino monosaccharide D-glucosamine. Three cyclic α-4C1 pyranose forms have been identified using a combination of CP-FTMW and LA-MB-FTMW spectroscopy. Stereoelectronic hyperconjugative factors, like those associated with anomeric or gauche effects, as well as the cooperative OH\\cdotsO, OH\\cdotsN and NH\\cdotsO chains, extended along the entire molecule, are the main factors driving the conformational behavior. All observed conformers exhibit a counter-clockwise arrangement (cc) of the network of intramolecular hydrogen bonds. The results are compared with those recently obtained for D-glucose. J. L. Alonso, M. A. Lozoya, I. Peña, J. C. López, C. Cabezas, S. Mata, S. Blanco, Chem. Sci. 2014, 5, 515.

Infrared, Raman and laser fluorescence studies on large molecules

International Nuclear Information System (INIS)

Venkateswaran, Sugandhi

2000-01-01

In the present thesis, infrared and Raman spectroscopic studies on large molecules, molecular assemblies and crystalline solids, as a function of temperature, pressure and added materials have been carried out. Spectral changes observed in our studies are interpreted in terms of intermolecular interaction, phase transition and conformational changes taking place in the molecules studied

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....

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.

Conformational targeting of fibrillar polyglutamine proteins in live cells escalates aggregation and cytotoxicity.

Directory of Open Access Journals (Sweden)

Erik Kvam

2009-05-01

Full Text Available Misfolding- and aggregation-prone proteins underlying Parkinson's, Huntington's and Machado-Joseph diseases, namely alpha-synuclein, huntingtin, and ataxin-3 respectively, adopt numerous intracellular conformations during pathogenesis, including globular intermediates and insoluble amyloid-like fibrils. Such conformational diversity has complicated research into amyloid-associated intracellular dysfunction and neurodegeneration. To this end, recombinant single-chain Fv antibodies (scFvs are compelling molecular tools that can be selected against specific protein conformations, and expressed inside cells as intrabodies, for investigative and therapeutic purposes.Using atomic force microscopy (AFM and live-cell fluorescence microscopy, we report that a human scFv selected against the fibrillar form of alpha-synuclein targets isomorphic conformations of misfolded polyglutamine proteins. When expressed in the cytoplasm of striatal cells, this conformation-specific intrabody co-localizes with intracellular aggregates of misfolded ataxin-3 and a pathological fragment of huntingtin, and enhances the aggregation propensity of both disease-linked polyglutamine proteins. Using this intrabody as a tool for modulating the kinetics of amyloidogenesis, we show that escalating aggregate formation of a pathologic huntingtin fragment is not cytoprotective in striatal cells, but rather heightens oxidative stress and cell death as detected by flow cytometry. Instead, cellular protection is achieved by suppressing aggregation using a previously described intrabody that binds to the amyloidogenic N-terminus of huntingtin. Analogous cytotoxic results are observed following conformational targeting of normal or polyglutamine-expanded human ataxin-3, which partially aggregate through non-polyglutamine domains.These findings validate that the rate of aggregation modulates polyglutamine-mediated intracellular dysfunction, and caution that molecules designed to

The effect of equipment efficiency on occurrence of non-conforming products in die casting

Directory of Open Access Journals (Sweden)

S. Borkowski

2010-01-01

Full Text Available This study focuses on determination of the relationships between equipment efficiency in casting machines and the level of quality. The determination was made based on coefficients of Total Productive Maintenance and r correlation coefficient. The degree at which break-downs and downtime affect the occurrence of non-conforming products was also evaluated. The goal of further investigations is to deter-mine the structure of downtime and finding which downtime types have greatest impact on the quality of die-casting products.

Towards ligand docking including explicit interface water molecules.

Directory of Open Access Journals (Sweden)

Gordon Lemmon

Full Text Available Small molecule docking predicts the interaction of a small molecule ligand with a protein at atomic-detail accuracy including position and conformation the ligand but also conformational changes of the protein upon ligand binding. While successful in the majority of cases, docking algorithms including RosettaLigand fail in some cases to predict the correct protein/ligand complex structure. In this study we show that simultaneous docking of explicit interface water molecules greatly improves Rosetta's ability to distinguish correct from incorrect ligand poses. This result holds true for both protein-centric water docking wherein waters are located relative to the protein binding site and ligand-centric water docking wherein waters move with the ligand during docking. Protein-centric docking is used to model 99 HIV-1 protease/protease inhibitor structures. We find protease inhibitor placement improving at a ratio of 9:1 when one critical interface water molecule is included in the docking simulation. Ligand-centric docking is applied to 341 structures from the CSAR benchmark of diverse protein/ligand complexes [1]. Across this diverse dataset we see up to 56% recovery of failed docking studies, when waters are included in the docking simulation.

3D Multi-Level Non-LTE Radiative Transfer for the CO Molecule

Science.gov (United States)

Berkner, A.; Schweitzer, A.; Hauschildt, P. H.

2015-01-01

The photospheres of cool stars are both rich in molecules and an environment where the assumption of LTE can not be upheld under all circumstances. Unfortunately, detailed 3D non-LTE calculations involving molecules are hardly feasible with current computers. For this reason, we present our implementation of the super level technique, in which molecular levels are combined into super levels, to reduce the number of unknowns in the rate equations and, thus, the computational effort and memory requirements involved, and show the results of our first tests against the 1D implementation of the same method.

Factors influencing conformity index in radiotherapy for non-small cell lung cancer.

LENUS (Irish Health Repository)

Brennan, Sinead M

2010-01-01

The radiotherapy conformity index (CI) is a useful tool to quantitatively assess the quality of radiotherapy treatment plans, and represents the relationship between isodose distributions and target volume. A conformity index of unity implies high planning target volume (PTV) coverage and minimal unnecessary irradiation of surrounding tissues. We performed this analysis to describe the CI for lung cancer 3-dimensional conformal radiotherapy (3DCRT) and to identify clinical and technical determinants of CI, as it is not known which factors are associated with good quality 3D conformal radiotherapy treatment planning. Radiotherapy treatment plans from a database of 52 patients with inoperable Stage 1 to 3b lung cancer, on a hypofractionated 3DCRT trial were evaluated. A CI was calculated for all plans using the definition of the ICRU 62:CI = (TV\\/PTV), which is the quotient of the treated volume (TV) and the PTV. Data on patient, tumor, and planning variables, which could influence CI, were recorded and analyzed. Mean CI was 2.01 (range = 1.06-3.8). On univariate analysis, PTV (p = 0.023), number of beams (p = 0.036), medial vs. lateral tumor location (p = 0.016), and increasing tumor stage (p = 0.041) were associated with improved conformity. On multiple regression analysis, factors found to be associated with CI included central vs. peripheral tumor location (p = 0.041) and PTV size (p = 0.058). The term 3DCRT is used routinely in the literature, without any indication of the degree of conformality. We recommend routine reporting of conformity indices. Conformity indices may be affected by both planning variables and tumor factors.

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....

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

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)

Living a Fairy Tale: The Educational Experiences of Transgender and Gender Non-Conforming Youth in Northern Ireland

Science.gov (United States)

McBride, Ruari-Santiago; Schubotz, Dirk

2017-01-01

This article investigates educational experiences of transgender and gender non-conforming (TGNC) youth living in Northern Ireland (NI) through a mixed-methods research design and analytical framework of heteronormativity. It draws on large-scale survey data which, for the first time in NI, captured the experiences of 16 year olds who identify as…

Single-Molecule Sensing with Nanopore Confinement: from Chemical Reactions to Biological Interactions.

Science.gov (United States)

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing which help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this concept, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio Hartree-Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one drug molecule.

Science.gov (United States)

Taşal, Erol; Kumalar, Mustafa

2012-09-01

In this work, the experimental and theoretical spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one molecule (abbreviated as 5CMOT) are studied. The molecular geometry and vibrational frequencies are calculated in the ground state of molecule using ab initio Hartree-Fock (HF) and Density Function Theory (DFT) methods with 6-311++G(d,p), 6-31G++(d,p), 6-31G(d,p), 6-31G(d) and 6-31G basis sets. Three staggered stable conformers were observed on the torsional potential energy surfaces. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters fairly well agree with the theoretically obtained values for the most stable conformer. The theoretical results showed an excellent agreement with the experimental values. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule. Copyright © 2012 Elsevier B.V. All rights reserved.

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

DEFF Research Database (Denmark)

Olsen, Jacob Ingemar

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...... 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...... compounds that could release molecules at a specified change in pH conditions. To investigate this, four hexahydropyridazines were synthesized and investigated for their pH induced conformational change (Chapter 4). Out of the four compounds, one revealed to flip between two conformations depending on pH...

Real-time non-rigid target tracking for ultrasound-guided clinical interventions

Science.gov (United States)

Zachiu, C.; Ries, M.; Ramaekers, P.; Guey, J.-L.; Moonen, C. T. W.; de Senneville, B. Denis

2017-10-01

Biological motion is a problem for non- or mini-invasive interventions when conducted in mobile/deformable organs due to the targeted pathology moving/deforming with the organ. This may lead to high miss rates and/or incomplete treatment of the pathology. Therefore, real-time tracking of the target anatomy during the intervention would be beneficial for such applications. Since the aforementioned interventions are often conducted under B-mode ultrasound (US) guidance, target tracking can be achieved via image registration, by comparing the acquired US images to a separate image established as positional reference. However, such US images are intrinsically altered by speckle noise, introducing incoherent gray-level intensity variations. This may prove problematic for existing intensity-based registration methods. In the current study we address US-based target tracking by employing the recently proposed EVolution registration algorithm. The method is, by construction, robust to transient gray-level intensities. Instead of directly matching image intensities, EVolution aligns similar contrast patterns in the images. Moreover, the displacement is computed by evaluating a matching criterion for image sub-regions rather than on a point-by-point basis, which typically provides more robust motion estimates. However, unlike similar previously published approaches, which assume rigid displacements in the image sub-regions, the EVolution algorithm integrates the matching criterion in a global functional, allowing the estimation of an elastic dense deformation. The approach was validated for soft tissue tracking under free-breathing conditions on the abdomen of seven healthy volunteers. Contact echography was performed on all volunteers, while three of the volunteers also underwent standoff echography. Each of the two modalities is predominantly specific to a particular type of non- or mini-invasive clinical intervention. The method demonstrated on average an accuracy of�

The Incorporation of Ribonucleotides Induces Structural and Conformational Changes in DNA.

Science.gov (United States)

Meroni, Alice; Mentegari, Elisa; Crespan, Emmanuele; Muzi-Falconi, Marco; Lazzaro, Federico; Podestà, Alessandro

2017-10-03

Ribonucleotide incorporation is the most common error occurring during DNA replication. Cells have hence developed mechanisms to remove ribonucleotides from the genome and restore its integrity. Indeed, the persistence of ribonucleotides into DNA leads to severe consequences, such as genome instability and replication stress. Thus, it becomes important to understand the effects of ribonucleotides incorporation, starting from their impact on DNA structure and conformation. Here we present a systematic study of the effects of ribonucleotide incorporation into DNA molecules. We have developed, to our knowledge, a new method to efficiently synthesize long DNA molecules (hundreds of basepairs) containing ribonucleotides, which is based on a modified protocol for the polymerase chain reaction. By means of atomic force microscopy, we could therefore investigate the changes, upon ribonucleotide incorporation, of the structural and conformational properties of numerous DNA populations at the single-molecule level. Specifically, we characterized the scaling of the contour length with the number of basepairs and the scaling of the end-to-end distance with the curvilinear distance, the bending angle distribution, and the persistence length. Our results revealed that ribonucleotides affect DNA structure and conformation on scales that go well beyond the typical dimension of the single ribonucleotide. In particular, the presence of ribonucleotides induces a systematic shortening of the molecules, together with a decrease of the persistence length. Such structural changes are also likely to occur in vivo, where they could directly affect the downstream DNA transactions, as well as interfere with protein binding and recognition. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Scalar perturbations and conformal transformation

International Nuclear Information System (INIS)

Fabris, J.C.; Tossa, J.

1995-11-01

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

Rigidity and symmetry

CERN Document Server

Weiss, Asia; Whiteley, Walter

2014-01-01

This book contains recent contributions to the fields of rigidity and symmetry with two primary focuses: to present the mathematically rigorous treatment of rigidity of structures, and to explore the interaction of geometry, algebra, and combinatorics. Overall, the book shows how researchers from diverse backgrounds explore connections among the various discrete structures with symmetry as the unifying theme.  Contributions present recent trends and advances in discrete geometry, particularly in the theory of polytopes. The rapid development of abstract polytope theory has resulted in a rich theory featuring an attractive interplay of methods and tools from discrete geometry, group theory, classical geometry, hyperbolic geometry and topology.  The volume will also be a valuable source as an introduction to the ideas of both combinatorial and geometric rigidity theory and its applications, incorporating the surprising impact of symmetry. It will appeal to students at both the advanced undergraduate and gradu...

Switching behavior of double-decker single molecule magnets on a metal surface

Energy Technology Data Exchange (ETDEWEB)

Fu, Yingshuang; Schwoebel, Joerg; Hoffmann, Germar; Brede, Jens; Wiesendanger, Roland [University of Hamburg, Hamburg (Germany); Dillulo, Andrew [Ohio University, Athens (United States); Klyatskaya, Svetlana [Karlsruhe Institute of Technology, Karlsruhe (Germany); Ruben, Mario [Karlsruhe Institute of Technology, Karlsruhe (Germany); Universite de Strasbourg, Strasbourg (France)

2011-07-01

Single molecule magnets (SMM) are most promising materials for spin based molecular electronics. Due to their large magnetic anisotropy stabilized by inside chemical bonds, SMM can potentially be used for information storage at the single molecule level. For applications, it is of importance to adsorb the SMM onto surfaces and to study their subsequent conformational, electronic and magnetic properties. We have investigated the adsorption behavior of Tb and Dy based double-decker SMM on an Ir(111) surface with low temperature scanning tunneling microscopy and spectroscopy. It is found that Tb double-decker molecules bind tightly to the Ir(111) surface. By resonantly injecting tunneling electrons into its LUMO or HOMO state, the Tb double-decker molecule can be switched from a four-lobed structure to an eight-lobed structure. After switching, energy positions of the HOMO and LUMO states both shift closer to the Fermi level. Dy double-decker molecules also exhibit the same switching properties on the Ir(111) surface. The switching behavior of the molecules is tentatively attributed to a conformational change of the double-decker molecular frame.

Conformation-independent structural comparison of macromolecules with ProSMART

International Nuclear Information System (INIS)

Nicholls, Robert A.; Fischer, Marcus; McNicholas, Stuart; Murshudov, Garib N.

2014-01-01

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing

Conformation-independent structural comparison of macromolecules with ProSMART

Energy Technology Data Exchange (ETDEWEB)

Nicholls, Robert A., E-mail: nicholls@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Fischer, Marcus [University of California San Francisco, San Francisco, CA 94158 (United States); McNicholas, Stuart [University of York, Heslington, York YO10 5DD (United Kingdom); Murshudov, Garib N. [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom)

2014-09-01

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing

Spacelike conformal Killing vectors and spacelike congruences

International Nuclear Information System (INIS)

Mason, D.P.; Tsamparlis, M.

1985-01-01

Necessary and sufficient conditions are derived for space-time to admit a spacelike conformal motion with symmetry vector parallel to a unit spacelike vector field n/sup a/. These conditions are expressed in terms of the shear and expansion of the spacelike congruence generated by n/sup a/ and in terms of the four-velocity of the observer employed at any given point of the congruence. It is shown that either the expansion or the rotation of this spacelike congruence must vanish if Dn/sup a//dp = 0, where p denotes arc length measured along the integral curves of n/sup a/, and also that there exist no proper spacelike homothetic motions with constant expansion. Propagation equations for the projection tensor and the rotation tensor are derived and it is proved that every isometric spacelike congruence is rigid. Fluid space-times are studied in detail. A relation is established between spacelike conformal motions and material curves in the fluid: if a fluid space-time admits a spacelike conformal Killing vector parallel to n/sup a/ and n/sub a/u/sup a/ = 0, where u/sup a/ is the fluid four-velocity, then the integral curves of n/sup a/ are material curves in an irrotational fluid, while if the fluid vorticity is nonzero, then the integral curves of n/sup a/ are material curves if and only if they are vortex lines. An alternative derivation, based on the theory of spacelike congruences, of some of the results of Collins [J. Math. Phys. 25, 995 (1984)] on conformal Killing vectors parallel to the local vorticity vector in shear-free perfect fluids with zero magnetic Weyl tensor is given

Programmed Switching of Single Polymer Conformation on DNA Origami

DEFF Research Database (Denmark)

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

2016-01-01

-molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern......) 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...

Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography

Energy Technology Data Exchange (ETDEWEB)

Kurpiewska, Katarzyna, E-mail: kurpiews@chemia.uj.edu.pl [Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Protein Crystallography Group, Ingardena 3, 30-060 Kraków (Poland); Dziubek, Kamil; Katrusiak, Andrzej [Adam Mickiewicz University, Faculty of Chemistry, Department of Materials Chemistry, Umultowska 89b, 61-61 Poznań (Poland); Font, Josep [School of Medical Science, University of Sydney, NSW 2006 (Australia); Ribò, Marc; Vilanova, Maria [Universitat de Girona, Laboratorid’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Campus de Montilivi, 17071 Girona (Spain); Lewiński, Krzysztof [Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Protein Crystallography Group, Ingardena 3, 30-060 Kraków (Poland)

2016-04-01

Highlights: • A unique crystallographic studies of wild-type and mutated form of the same protein under high pressure. • Compressibility of RNase A molecule is significantly affected by a single amino acid substitution. • High pressure protein crystallography helps understanding protein flexibility and identify conformational substrates. - Abstract: Hydrostatic pressure in range 0.1–1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. The idea of the presented experiments is to examine the behaviour of RNase A molecule under high pressure before and after introduction of destabilizing mutation. For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. X-ray diffraction experiments at high pressure showed that the secondary structure of RNase A is well preserved even beyond 0.67 GPa at room temperature. Detailed structural analysis of ribonuclease A conformation observed under high pressure revealed that pressure influences hydrogen bonds pattern, cavity size and packing of molecule.

Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography

International Nuclear Information System (INIS)

Kurpiewska, Katarzyna; Dziubek, Kamil; Katrusiak, Andrzej; Font, Josep; Ribò, Marc; Vilanova, Maria; Lewiński, Krzysztof

2016-01-01

Highlights: • A unique crystallographic studies of wild-type and mutated form of the same protein under high pressure. • Compressibility of RNase A molecule is significantly affected by a single amino acid substitution. • High pressure protein crystallography helps understanding protein flexibility and identify conformational substrates. - Abstract: Hydrostatic pressure in range 0.1–1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. The idea of the presented experiments is to examine the behaviour of RNase A molecule under high pressure before and after introduction of destabilizing mutation. For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. X-ray diffraction experiments at high pressure showed that the secondary structure of RNase A is well preserved even beyond 0.67 GPa at room temperature. Detailed structural analysis of ribonuclease A conformation observed under high pressure revealed that pressure influences hydrogen bonds pattern, cavity size and packing of molecule.

Gender, ethnicity, religiosity, and same-sex sexual attraction and the acceptance of same-sex sexuality and gender non-conformity

NARCIS (Netherlands)

Collier, K.L.; Bos, H.M.W.; Merry, M.S.; Sandfort, T.G.M.

2013-01-01

This study explored the role of gender, ethnicity, religiosity, and sexual attraction in adolescents’ acceptance of same-sex sexuality and gender non-conformity. Using an intersectionality perspective, we also tested whether the effects of gender, ethnicity, and religiosity on adolescents’ attitudes

High-order discrete ordinate transport in non-conforming 2D Cartesian meshes

International Nuclear Information System (INIS)

Gastaldo, L.; Le Tellier, R.; Suteau, C.; Fournier, D.; Ruggieri, J. M.

2009-01-01

We present in this paper a numerical scheme for solving the time-independent first-order form of the Boltzmann equation in non-conforming 2D Cartesian meshes. The flux solution technique used here is the discrete ordinate method and the spatial discretization is based on discontinuous finite elements. In order to have p-refinement capability, we have chosen a hierarchical polynomial basis based on Legendre polynomials. The h-refinement capability is also available and the element interface treatment has been simplified by the use of special functions decomposed over the mesh entities of an element. The comparison to a classical S N method using the Diamond Differencing scheme as spatial approximation confirms the good behaviour of the method. (authors)

Surface Design Based on Discrete Conformal Transformations

Science.gov (United States)

Duque, Carlos; Santangelo, Christian; Vouga, Etienne

Conformal transformations are angle-preserving maps from one domain to another. Although angles are preserved, the lengths between arbitrary points are not generally conserved. As a consequence there is always a given amount of distortion associated to any conformal map. Different uses of such transformations can be found in various fields, but have been used by us to program non-uniformly swellable gel sheets to buckle into prescribed three dimensional shapes. In this work we apply circle packings as a kind of discrete conformal map in order to find conformal maps from the sphere to the plane that can be used as nearly uniform swelling patterns to program non-Euclidean sheets to buckle into spheres. We explore the possibility of tuning the area distortion to fit the experimental range of minimum and maximum swelling by modifying the boundary of the planar domain through the introduction of different cutting schemes.

Molecular conformation and liquid structure of 2-propanol through ...

Indian Academy of Sciences (India)

The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to ... 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky ... A Sahoo1 S Sarkar1 P S R Krishna2 R N Joarder1.

Role of residual water hydrogen bonding in sugar/water/biomolecule systems: a possible explanation for trehalose peculiarity

Energy Technology Data Exchange (ETDEWEB)

Cordone, L; Cottone, G; Giuffrida, S [Dipartimento di Scienze Fisiche ed Astronomiche, Universita di Palermo and CNISM (Italy)

2007-05-23

We report on the set of experimental and simulative evidences which enabled us to suggest how biological structures embedded in a non-liquid water-saccharide solvent are anchored to the surrounding matrix via a hydrogen bond network. Such a network, whose rigidity increases by decreasing the sample water content, couples the degrees of freedom of the biostructure to those of the matrix and gives place to protein-saccharide-water structures (protein-solvent conformational substates). In particular, the whole set of data evidences that, while the protein-sugar interaction is well described in terms of a water entrapment hypothesis, the water replacement hypothesis better describes the sugar-membrane interaction; furthermore, it gives a hint towards the understanding of the origin of the trehalose peculiarity since the biomolecule-matrix coupling, specific to each particular sugar, always results in being the tightest for trehalose. In line with the heterogeneous dynamics in supercooled fluids and in carbohydrate glasses of different residual water contents, recent results confirm, at the single molecule level, the existence of protein-solvent conformational substates, spatially heterogeneous and interconverting, whose rigidity increases by lowering the sample hydration.

Intergroup Contact, Attitudes toward Homosexuality, and the Role of Acceptance of Gender Non-Conformity in Young Adolescents

Science.gov (United States)

Collier, Kate L.; Bos, Henny M. W.; Sandfort, Theo G. M.

2012-01-01

This study explored how contact with gay and lesbian persons affects adolescents' attitudes toward them, and whether this association is mediated or moderated by one's acceptance of gender non-conformity. We analyzed survey responses from 456 Dutch adolescents aged 12-15 who reported having no same-sex attractions. Data were collected in 2008 at 8…

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

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

KAUST Repository

Feng, Yitao; Zhang, Lu; Wu, Shaowen; Liu, Zhijun; Gao, Xin; Zhang, Xu; Liu, Maili; Liu, Jianwei; Huang, Xuhui; Wang, Wenning

2016-01-01

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

Influence of the water molecules near surface of viral protein on virus activation process

Energy Technology Data Exchange (ETDEWEB)

O, Shepelenko S; S, Salnikov A; V, Rak S; P, Goncharova E; B, Ryzhikov A, E-mail: shep@vector.nsc.r, E-mail: shep@ngs.r [Federal State Research Institution State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-being (FSRI SRC VB VECTOR) Koltsovo, Novosibirsk Region (Russian Federation)

2009-06-01

The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

Fluorescence quantum yield of thioflavin T in rigid isotropic solution and incorporated into the amyloid fibrils.

Directory of Open Access Journals (Sweden)

Anna I Sulatskaya

Full Text Available In this work, the fluorescence of thioflavin T (ThT was studied in a wide range of viscosity and temperature. It was shown that ThT fluorescence quantum yield varies from 0.0001 in water at room temperature to 0.28 in rigid isotropic solution (T/η→0. The deviation of the fluorescence quantum yield from unity in rigid isotropic solution suggests that fluorescence quantum yield depends not only on the ultra-fast oscillation of ThT fragments relative to each other in an excited state as was suggested earlier, but also depends on the molecular configuration in the ground state. This means that the fluorescence quantum yield of the dye incorporated into amyloid fibrils must depend on its conformation, which, in turn, depends on the ThT environment. Therefore, the fluorescence quantum yield of ThT incorporated into amyloid fibrils can differ from that in the rigid isotropic solution. In particular, the fluorescence quantum yield of ThT incorporated into insulin fibrils was determined to be 0.43. Consequently, the ThT fluorescence quantum yield could be used to characterize the peculiarities of the fibrillar structure, which opens some new possibilities in the ThT use for structural characterization of the amyloid fibrils.

Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET

Science.gov (United States)

Hardin, John W.; Warnasooriya, Chandani; Kondo, Yasushi; Nagai, Kiyoshi; Rueda, David

2015-01-01

In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions as an assembly scaffold as well as a critical catalytic component. Protein binding to the RNA scaffold can induce structural changes, which in turn modulate subsequent binding of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 and U6 snRNAs, Snu13, Prp31, Prp3 and Prp4, seven Sm and seven LSm proteins. We have studied successive binding of all protein components to the snRNA duplex during di-snRNP assembly by electrophoretic mobility shift assay and accompanying conformational changes in the U4/U6 RNA 3-way junction by single-molecule FRET. Stems I and II of the duplex were found to co-axially stack in free RNA and function as a rigid scaffold during the entire assembly, but the U4 snRNA 5′ stem-loop adopts alternative orientations each stabilized by Prp31 and Prp3/4 binding accounting for altered Prp3/4 binding affinities in presence of Prp31. PMID:26503251

Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

Science.gov (United States)

Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

2017-03-01

The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to

Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

Science.gov (United States)

Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

2014-10-01

The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N-H...O=C, type II by a strong O-H...N hydrogen bond, type III by weak N-H...O-H hydrogen bonds, and type IV by a C=O...H-C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O-H...N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm-1, respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG undergoes facile photofragmentation

Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

International Nuclear Information System (INIS)

Borba, Ana; Fausto, Rui; Gómez-Zavaglia, Andrea

2014-01-01

The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N–H···O=C, type II by a strong O–H···N hydrogen bond, type III by weak N–H···O–H hydrogen bonds, and type IV by a C=O···H–C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O–H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N 2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm −1 , respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG

Collective Dynamics of Belief Evolution under Cognitive Coherence and Social Conformity.

Science.gov (United States)

Rodriguez, Nathaniel; Bollen, Johan; Ahn, Yong-Yeol

2016-01-01

Human history has been marked by social instability and conflict, often driven by the irreconcilability of opposing sets of beliefs, ideologies, and religious dogmas. The dynamics of belief systems has been studied mainly from two distinct perspectives, namely how cognitive biases lead to individual belief rigidity and how social influence leads to social conformity. Here we propose a unifying framework that connects cognitive and social forces together in order to study the dynamics of societal belief evolution. Each individual is endowed with a network of interacting beliefs that evolves through interaction with other individuals in a social network. The adoption of beliefs is affected by both internal coherence and social conformity. Our framework may offer explanations for how social transitions can arise in otherwise homogeneous populations, how small numbers of zealots with highly coherent beliefs can overturn societal consensus, and how belief rigidity protects fringe groups and cults against invasion from mainstream beliefs, allowing them to persist and even thrive in larger societies. Our results suggest that strong consensus may be insufficient to guarantee social stability, that the cognitive coherence of belief-systems is vital in determining their ability to spread, and that coherent belief-systems may pose a serious problem for resolving social polarization, due to their ability to prevent consensus even under high levels of social exposure. We argue that the inclusion of cognitive factors into a social model could provide a more complete picture of collective human dynamics.

Intermediate conformation between native β-sheet and non-native α-helix is a precursor of trifluoroethanol-induced aggregation of Human Carbonic Anhydrase-II

International Nuclear Information System (INIS)

Gupta, Preeti; Deep, Shashank

2014-01-01

Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE at which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII

Conformal cosmological model and SNe Ia data

International Nuclear Information System (INIS)

Zakharov, A. F.; Pervushin, V. N.

2012-01-01

Now there is a huge scientific activity in astrophysical studies and cosmological ones in particular. Cosmology transforms from a pure theoretical branch of science into an observational one. All the cosmological models have to pass observational tests. The supernovae type Ia (SNe Ia) test is among the most important ones. If one applies the test to determine parameters of the standard Friedmann-Robertson-Walker cosmological model one can conclude that observations lead to the discovery of the dominance of the Λ term and as a result to an acceleration of the Universe. However, there are big mysteries connected with an origin and an essence of dark matter (DM) and the Λ term or dark energy (DE). Alternative theories of gravitation are treated as a possible solution of DM and DE puzzles. The conformal cosmological approach is one of possible alternatives to the standard ΛCDM model. As it was noted several years ago, in the framework of the conformal cosmological approach an introduction of a rigid matter can explain observational data without Λ term (or dark energy). We confirm the claim with much larger set of observational data.

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.

The amide III vibrational circular dichroism band as a probe to detect conformational preferences of alanine dipeptide in water.

Science.gov (United States)

Mirtič, Andreja; Merzel, Franci; Grdadolnik, Jože

2014-07-01

The conformational preferences of blocked alanine dipeptide (ADP), Ac-Ala-NHMe, in aqueous solution were studied using vibrational circular dichroism (VCD) together with density functional theory (DFT) calculations. DFT calculations of three most representative conformations of ADP surrounded by six explicit water molecules immersed in a dielectric continuum have proven high sensitivity of amide III VCD band shape that is characteristic for each conformation of the peptide backbone. The polyproline II (PII ) and αR conformation of ADP are associated with a positive VCD band while β conformation has a negative VCD band in amide III region. Knowing this spectral characteristic of each conformation allows us to assign the experimental amide III VCD spectrum of ADP. Moreover, the amide III region of the VCD spectrum was used to determine the relative populations of conformations of ADP in water. Based on the interpretation of the amide III region of VCD spectrum we have shown that dominant conformation of ADP in water is PII which is stabilized by hydrogen bonded water molecules between CO and NH groups on the peptide backbone. Copyright © 2014 Wiley Periodicals, Inc.

Entanglement evolution across a conformal interface

Science.gov (United States)

Wen, Xueda; Wang, Yuxuan; Ryu, Shinsei

2018-05-01

For two-dimensional conformal field theories (CFTs) in the ground state, it is known that a conformal interface along the entanglement cut can suppress the entanglement entropy from to , where L is the length of the subsystem A, and is the effective central charge which depends on the transmission property of the conformal interface. In this work, by making use of conformal mappings, we show that a conformal interface has the same effect on entanglement evolution in non-equilibrium cases, including global, local and certain inhomogeneous quantum quenches. I.e. a conformal interface suppresses the time evolution of entanglement entropy by effectively replacing the central charge c with , where is exactly the same as that in the ground state case. We confirm this conclusion by a numerical study on a critical fermion chain. Furthermore, based on the quasi-particle picture, we conjecture that this conclusion holds for an arbitrary quantum quench in CFTs, as long as the initial state can be described by a regularized conformal boundary state.

Irreversibility and higher-spin conformal field theory

Science.gov (United States)

Anselmi, Damiano

2000-08-01

I discuss the properties of the central charges c and a for higher-derivative and higher-spin theories (spin 2 included). Ordinary gravity does not admit a straightforward identification of c and a in the trace anomaly, because it is not conformal. On the other hand, higher-derivative theories can be conformal, but have negative c and a. A third possibility is to consider higher-spin conformal field theories. They are not unitary, but have a variety of interesting properties. Bosonic conformal tensors have a positive-definite action, equal to the square of a field strength, and a higher-derivative gauge invariance. There exists a conserved spin-2 current (not the canonical stress tensor) defining positive central charges c and a. I calculate the values of c and a and study the operator-product structure. Higher-spin conformal spinors have no gauge invariance, admit a standard definition of c and a and can be coupled to Abelian and non-Abelian gauge fields in a renormalizable way. At the quantum level, they contribute to the one-loop beta function with the same sign as ordinary matter, admit a conformal window and non-trivial interacting fixed points. There are composite operators of high spin and low dimension, which violate the Ferrara-Gatto-Grillo theorem. Finally, other theories, such as conformal antisymmetric tensors, exhibit more severe internal problems. This research is motivated by the idea that fundamental quantum field theories should be renormalization-group (RG) interpolations between ultraviolet and infrared conformal fixed points, and quantum irreversibility should be a general principle of nature.

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.

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

The conformational dynamics of the mitochondrial Hsp70 chaperone.

Science.gov (United States)

Mapa, Koyeli; Sikor, Martin; Kudryavtsev, Volodymyr; Waegemann, Karin; Kalinin, Stanislav; Seidel, Claus A M; Neupert, Walter; Lamb, Don C; Mokranjac, Dejana

2010-04-09

Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a plethora of cellular processes. The dynamics of their ATP hydrolysis-driven and cochaperone-regulated conformational cycle are poorly understood. We used fluorescence spectroscopy to analyze, in real time and at single-molecule resolution, the effects of nucleotides and cochaperones on the conformation of Ssc1, a mitochondrial member of the family. We report that the conformation of its ADP state is unexpectedly heterogeneous, in contrast to a uniform ATP state. Substrates are actively involved in determining the conformation of Ssc1. The J protein Mdj1 does not interact transiently with the chaperone, as generally believed, but rather is released slowly upon ATP hydrolysis. Analysis of the major bacterial Hsp70 revealed important differences between highly homologous members of the family, possibly explaining tuning of Hsp70 chaperones to meet specific functions in different organisms and cellular compartments. 2010 Elsevier Inc. All rights reserved.

The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

Science.gov (United States)

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.

2012-01-01

To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the Cα atoms of G60 at switch 2 and G10 at the P-loop and the N-Cα-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition. PMID:22359497

Selective intercalation of six ligands molecules in a self-assembled triple helix

NARCIS (Netherlands)

Mateos timoneda, Miguel; Kerckhoffs, J.M.C.A.; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

The addition of a ligand molecule to an artificial self-assembled triple helix leads to the selective intercalation of two hydrogen-bonded trimers in specific binding pockets. Furthermore, the triple helix suffers large conformational rearrangements in order to accommodate the ligand molecules in a

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.

Body fixed frame, rigid gauge rotations and large N random fields in QCD

International Nuclear Information System (INIS)

Levit, S.

1995-01-01

The ''body fixed frame'' with respect to local gauge transformations is introduced. Rigid gauge ''rotations'' in QCD and their Schroedinger equation are studied for static and dynamic quarks. Possible choices of the rigid gauge field configuration corresponding to a non-vanishing static colormagnetic field in the ''body fixed'' frame are discussed. A gauge invariant variational equation is derived in this frame. For large number N of colors the rigid gauge field configuration is regarded as random with maximally random probability distribution under constraints on macroscopic-like quantities. For the uniform magnetic field the joint probability distribution of the field components is determined by maximizing the appropriate entropy under the area law constraint for the Wilson loop. In the quark sector the gauge invariance requires the rigid gauge field configuration to appear not only as a background but also as inducing an instantaneous quark-quark interaction. Both are random in the large N limit. (orig.)

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

International Nuclear Information System (INIS)

Catikkas, B.

2010-01-01

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

Rigidity of Glasses and Macromolecules

Science.gov (United States)

Thorpe, M. F.

1998-03-01

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

Quantum metamorphosis of conformal symmetry in N=4 super Yang-Mills theory

International Nuclear Information System (INIS)

Kuzenko, S.M.; McArthur, I.N.

2002-01-01

In gauge theories, not all rigid symmetries of the classical action can be maintained manifestly in the quantization procedure, even in the absence of anomalies. If this occurs for an anomaly-free symmetry, the effective action is invariant under a transformation that differs from its classical counterpart by quantum corrections. As shown by Fradkin and Palchik years ago, such a phenomenon occurs for conformal symmetry in quantum Yang-Mills theories with vanishing beta function, such as the N=4 super Yang-Mills theory. More recently, Jevicki et al. demonstrated that the quantum metamorphosis of conformal symmetry sheds light on the nature of the AdS/CFT correspondence. In this paper, we derive the conformal Ward identity for the bosonic sector of the N=4 super Yang-Mills theory using the background field method. We then compute the leading quantum modification of the conformal transformation for a specific Abelian background which is of interest in the context of the AdS/CFT correspondence. In the case of scalar fields, our final result agrees with that of Jevicki et al. The resulting vector and scalar transformations coincide with those which are characteristic of a D3-brane embedded in AdS 5 xS 5 . (author)

Single-Molecule Electronics with Cross- Conjugated Molecules: Quantum Interference, IETS and Non-Equilibrium "Temperatures"

DEFF Research Database (Denmark)

Jørgensen, Jacob Lykkebo

Abstract The idea of using single-molecules as components in electronic devices is fas- cinating. For this idea to come into fruition, a number of technical and theo- retical challenges must be overcome. In this PhD thesis, the electron-phonon interaction is studied for a special class of molecules......, which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......-conjugated molecules. We nd that the vibrational modes that would be expected to dominate, following the propensity, rules are very weak. Instead, other modes are found to be the dominant ones. We study this phenomenon for a number of cross-conjugated molecules, and link these ndings to the anti...

Rigidity-tuning conductive elastomer

Science.gov (United States)

Shan, Wanliang; Diller, Stuart; Tutcuoglu, Abbas; Majidi, Carmel

2015-06-01

We introduce a conductive propylene-based elastomer (cPBE) that rapidly and reversibly changes its mechanical rigidity when powered with electrical current. The elastomer is rigid in its natural state, with an elastic (Young’s) modulus of 175.5 MPa, and softens when electrically activated. By embedding the cPBE in an electrically insulating sheet of polydimethylsiloxane (PDMS), we create a cPBE-PDMS composite that can reversibly change its tensile modulus between 37 and 1.5 MPa. The rigidity change takes ˜6 s and is initiated when a 100 V voltage drop is applied across the two ends of the cPBE film. This magnitude of change in elastic rigidity is similar to that observed in natural skeletal muscle and catch connective tissue. We characterize the tunable load-bearing capability of the cPBE-PDMS composite with a motorized tensile test and deadweight experiment. Lastly, we demonstrate the ability to control the routing of internal forces by embedding several cPBE-PDMS ‘active tendons’ into a soft robotic pneumatic bending actuator. Selectively activating the artificial tendons controls the neutral axis and direction of bending during inflation.

Rigidity-tuning conductive elastomer

International Nuclear Information System (INIS)

Shan, Wanliang; Diller, Stuart; Tutcuoglu, Abbas; Majidi, Carmel

2015-01-01

We introduce a conductive propylene-based elastomer (cPBE) that rapidly and reversibly changes its mechanical rigidity when powered with electrical current. The elastomer is rigid in its natural state, with an elastic (Young’s) modulus of 175.5 MPa, and softens when electrically activated. By embedding the cPBE in an electrically insulating sheet of polydimethylsiloxane (PDMS), we create a cPBE–PDMS composite that can reversibly change its tensile modulus between 37 and 1.5 MPa. The rigidity change takes ∼6 s and is initiated when a 100 V voltage drop is applied across the two ends of the cPBE film. This magnitude of change in elastic rigidity is similar to that observed in natural skeletal muscle and catch connective tissue. We characterize the tunable load-bearing capability of the cPBE–PDMS composite with a motorized tensile test and deadweight experiment. Lastly, we demonstrate the ability to control the routing of internal forces by embedding several cPBE–PDMS ‘active tendons’ into a soft robotic pneumatic bending actuator. Selectively activating the artificial tendons controls the neutral axis and direction of bending during inflation. (paper)

Ultra-thin, conformal, and hydratable color-absorbers using silk protein hydrogel

Science.gov (United States)

Umar, Muhammad; Min, Kyungtaek; Jo, Minsik; Kim, Sunghwan

2018-06-01

Planar and multilayered photonic devices offer unprecedented opportunities in biological and chemical sensing due to strong light-matter interactions. However, uses of rigid substances such as semiconductors and dielectrics confront photonic devices with issues of biocompatibility and a mechanical mismatch for their application on humid, uneven, and soft biological surfaces. Here, we report that favorable material traits of natural silk protein led to the fabrication of an ultra-thin, conformal, and water-permeable (hydratable) metal-insulator-metal (MIM) color absorber that was mapped on soft, curved, and hydrated biological interfaces. Strong absorption was induced in the MIM structure and could be tuned by hydration and tilting of the sample. The transferred MIM color absorbers reached the exhibition of a very strong resonant absorption in the visible and near infra-red ranges. In addition, we demonstrated that the conformal resonator could function as a refractometric glucose sensor applied on a contact lens.

Nonunitary Lagrangians and Unitary Non-Lagrangian Conformal Field Theories

Science.gov (United States)

Buican, Matthew; Laczko, Zoltan

2018-02-01

In various dimensions, we can sometimes compute observables of interacting conformal field theories (CFTs) that are connected to free theories via the renormalization group (RG) flow by computing protected quantities in the free theories. On the other hand, in two dimensions, it is often possible to algebraically construct observables of interacting CFTs using free fields without the need to explicitly construct an underlying RG flow. In this Letter, we begin to extend this idea to higher dimensions by showing that one can compute certain observables of an infinite set of unitary strongly interacting four-dimensional N =2 superconformal field theories (SCFTs) by performing simple calculations involving sets of nonunitary free four-dimensional hypermultiplets. These free fields are distant cousins of the Majorana fermion underlying the two-dimensional Ising model and are not obviously connected to our interacting theories via an RG flow. Rather surprisingly, this construction gives us Lagrangians for particular observables in certain subsectors of many "non-Lagrangian" SCFTs by sacrificing unitarity while preserving the full N =2 superconformal algebra. As a by-product, we find relations between characters in unitary and nonunitary affine Kac-Moody algebras. We conclude by commenting on possible generalizations of our construction.

Nonunitary Lagrangians and Unitary Non-Lagrangian Conformal Field Theories.

Science.gov (United States)

Buican, Matthew; Laczko, Zoltan

2018-02-23

In various dimensions, we can sometimes compute observables of interacting conformal field theories (CFTs) that are connected to free theories via the renormalization group (RG) flow by computing protected quantities in the free theories. On the other hand, in two dimensions, it is often possible to algebraically construct observables of interacting CFTs using free fields without the need to explicitly construct an underlying RG flow. In this Letter, we begin to extend this idea to higher dimensions by showing that one can compute certain observables of an infinite set of unitary strongly interacting four-dimensional N=2 superconformal field theories (SCFTs) by performing simple calculations involving sets of nonunitary free four-dimensional hypermultiplets. These free fields are distant cousins of the Majorana fermion underlying the two-dimensional Ising model and are not obviously connected to our interacting theories via an RG flow. Rather surprisingly, this construction gives us Lagrangians for particular observables in certain subsectors of many "non-Lagrangian" SCFTs by sacrificing unitarity while preserving the full N=2 superconformal algebra. As a by-product, we find relations between characters in unitary and nonunitary affine Kac-Moody algebras. We conclude by commenting on possible generalizations of our construction.

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

International Nuclear Information System (INIS)

Shrestha, Utsab R.; Bhowmik, Debsindhu; Van Delinder, Kurt W.; Mamontov, Eugene; O’Neill, Hugh

2017-01-01

Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. These results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

Energy Technology Data Exchange (ETDEWEB)

Shrestha, Utsab R. [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy; Bhowmik, Debsindhu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Science and Engineering Division; Van Delinder, Kurt W. [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy; Mamontov, Eugene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical and Engineering Materials Division; O’Neill, Hugh [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division; Zhang, Qiu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division; Alatas, Ahmet [Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source; Chu, Xiang-Qiang [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy

2017-01-12

Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. These results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Extracting Models in Single Molecule Experiments

Science.gov (United States)

Presse, Steve

2013-03-01

Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

Importance of the alignment of polar π conjugated molecules inside carbon nanotubes in determining second-order non-linear optical properties.

Science.gov (United States)

Yumura, Takashi; Yamamoto, Wataru

2017-09-20

We employed density functional theory (DFT) calculations with dispersion corrections to investigate energetically preferred alignments of certain p,p'-dimethylaminonitrostilbene (DANS) molecules inside an armchair (m,m) carbon nanotube (n × DANS@(m,m)), where the number of inner molecules (n) is no greater than 3. Here, three types of alignments of DANS are considered: a linear alignment in a parallel fashion and stacking alignments in parallel and antiparallel fashions. According to DFT calculations, a threshold tube diameter for containing DANS molecules in linear or stacking alignments was found to be approximately 1.0 nm. Nanotubes with diameters smaller than 1.0 nm result in the selective formation of linearly aligned DANS molecules due to strong confinement effects within the nanotubes. By contrast, larger diameter nanotubes allow DANS molecules to align in a stacking and linear fashion. The type of alignment adopted by the DANS molecules inside a nanotube is responsible for their second-order non-linear optical properties represented by their static hyperpolarizability (β 0 values). In fact, we computed β 0 values of DANS assemblies taken from optimized n × DANS@(m,m) structures, and their values were compared with those of a single DANS molecule. DFT calculations showed that β 0 values of DANS molecules depend on their alignment, which decrease in the following order: linear alignment > parallel stacking alignment > antiparallel stacking alignment. In particular, a linear alignment has a β 0 value more significant than that of the same number of isolated molecules. Therefore, the linear alignment of DANS molecules, which is only allowed inside smaller diameter nanotubes, can strongly enhance their second-order non-linear optical properties. Since the nanotube confinement determines the alignment of DANS molecules, a restricted nanospace can be utilized to control their second-order non-linear optical properties. These DFT findings can assist in the

Treatment planning evaluation of non-coplanar techniques for conformal radiotherapy of the prostate

International Nuclear Information System (INIS)

Bedford, James L.; Henrys, Anthony J.; Dearnaley, David P.; Khoo, Vincent S.

2005-01-01

Background and purpose: To evaluate the benefit of using non-coplanar treatment plans for irradiation of two different clinical treatment volumes: prostate only (PO) and the prostate plus seminal vesicles (PSV). Material and methods: An inverse planning algorithm was used to produce three-field, four-field, five-field and six-field non-coplanar treatment plans without intensity-modulation in ten patients. These were compared against a three-field coplanar plan. A dose of 74 Gy was prescribed to the isocentre. Plans were compared using the minimum dose to the planning target volume (PTV), maximum dose to the small bowel, and irradiated volumes of rectum, bladder and femoral head. Biological indices were also evaluated. Results: For the PO group, volume of rectum irradiated to 60 Gy (V 60 ) was 22.5±3.7% for the coplanar plan, and 21.5±5.3% for the five-field non-coplanar plan, which was the most beneficial (p=0.3). For the PSV group, the five-field non-coplanar plan was again the most beneficial. Rectal V 60 was in this case reduced from 41.5±10.4% for the coplanar plan to 35.2±9.3% for the non-coplanar plan (p=0.02). Conclusions: The use of non-coplanar beams in conformal prostate radiotherapy provides a small increase in rectal sparing, more significantly with PSV volumes than for PO volumes

Probing the Conformational Landscape of Polyether Building Blocks in Supersonic Jets

Science.gov (United States)

Bocklitz, Sebastian; Hewett, Daniel M.; Zwier, Timothy S.; Suhm, Martin A.

2016-06-01

Polyethylene oxides (Polyethylene glycoles) and their phenoxy-capped analogs represent a prominent class of important polymers that are highly used as precursor molecules in supramolecular reactions. After a detailed study on the simplest representative (1,2-dimethoxyethane) [1], we present results on oligoethylene oxides with increasing chain lengths obtained by spontaneous Raman scattering in a supersonic jet. Through variation of stagnation pressure, carrier gas, nozzle distance and temperature we gain information on the conformational landscape as well as the mutual interconversion of low energy conformers. The obtained results are compared to state-of-the-art quantum chemical calculations. Additionally, we present UV as well as IR-UV and UV-UV double resonance studies on 1-methoxy-2-phenoxyethane in a supersonic jet. These complementary techniques allow for conformationally selective electronic and vibrational spectra in a closely related conformational landscape. [1] S. Bocklitz, M. A. Suhm, Constraining the Conformational Landscape of a Polyether Building Block by Raman Jet Spectroscopy, Z. Phys. Chem. 2015, 229, 1625-1648.

Résistance d'un composite à renforts rigides : le cas d'une matrice de Drucker Prager avec règle d'écoulement plastique non associée

Science.gov (United States)

Dormieux, Luc; Barthélémy, Jean-François; Maghous, Samir

2006-02-01

A rigid plastic behavior characterized by a failure criterion of the Drucker-Prager type and a non associated flow rule is considered. The latter can be viewed formally as the limit of a sequence of viscous behaviors with isotropic prestress. The limit states of a composite made up of such a material reinforced by rigid inclusions are then determined. The latter lie on a Drucker-Prager cone which friction coefficient is greater than that of the matrix and depends on the characteristics of the strength and of the flow rule of the matrix, as well as on the volume fraction of the inclusions. To cite this article: L. Dormieux et al., C. R. Mecanique 334 (2006).

Covalent dye attachment influences the dynamics and conformational properties of flexible peptides.

Directory of Open Access Journals (Sweden)

Manuel P Luitz

Full Text Available Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET and fluorescence correlation spectroscopy (FCS have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET. The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP. Using the intrinsically disordered S-peptide as a model system, we investigate the impact of terminal fluorescence labeling on the molecular properties. We perform extensive molecular dynamics simulations on the labeled and unlabeled peptide and compare the results with in vitro PET-FCS measurements. Experimental and simulated timescales of end-to-end fluctuations were found in excellent agreement. Comparison between simulations with and without labels reveal that the π-stacking interaction between the fluorophore labels traps the conformation of S-peptide in a single dominant state, while the unlabeled peptide undergoes continuous conformational rearrangements. Furthermore, we find that the open to closed transition rate of S-peptide is decreased by at least one order of magnitude by the fluorophore attachment. Our approach combining experimental and in silico methods provides a benchmark for the simulations and reveals the significant effect that fluorescence labeling can have on the conformational dynamics of small biomolecules, at least for inherently flexible short peptides. The presented protocol is not only useful for comparing PET-FCS experiments with simulation results but provides a strategy to minimize the

Conformational analysis of amide extractants by NMR in organic phase

International Nuclear Information System (INIS)

Berthon, C.

1993-08-01

This study deals with nuclear fuel reprocessing. We have essentially used NMR spectroscopy. We want to understand which kind of conformational parameters control selectivity and efficiency of amide extractant. The symmetric monoamides used are DOBA (C 3 H 7 CON (CH 2 CH(C 2 H 5 ) C 4 H 9 ) 2 ), DOiBA ((CH 3 ) 2 CCHON (CH 2 CH(C 2 H 5 )C 4 H 9 ) 2 ) and DOTA ((CH 3 ) 3 CCH 2 CON(CH 2 CH(C 2 H 5 )C 4 H 9 ) 2 ). Each gives two quasi equivalent conformers (cis and trans) in organic phases. The selected malonamide DMDBTDMA ((C 4 H 9 (CH 3 )NCO) 2 CHC 14 H 29 ) has four conformers because of its twice disymmetric amide functions. Weak interactions between monoamides which yield to dimer formation. The malonamide also gives dimers but forms aggregates too. Nitric acid extraction is due to the competitive formation of six species L, L 2 , L 2 (HNO 3 ), L(HNO 3 ), L(HNO 3 ) 2 , L(HNO 3 ) 3 (L: monoamide). Complexation between lanthanides (III) and monoamides yields to the stoichiometries L 3 Ln(NO 3 ) 3 and L 2 Ln(NO 3 ) 3 . Their ratio depend of steric hindrance on the carbonyl and the metal ionic radius. The same thing is observed of Pu 4+ and Th 4+ extraction in non acidic media. L 2 An(NO 3 ) 4 is the main stoichiometric except for the Th 4+ - DOBA system where the species (DOBA) 3 Th(NO 3 ) 4 appear. Exchange rates between the ligand and the complex are pointed out. The monoamide conformations obtained with lanthanide and plutonium nitrate can explain the difference in extracting power of this molecule between An 4+ and Ln 3+ . (author). 162 refs., 87 figs., 44 tabs., 7 annexes

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.

Conformal collineations and anisotropic fluids in general relativity

International Nuclear Information System (INIS)

Duggal, K.L.; Sharma, R.

1986-01-01

Recently, Herrera et al. [L. Herrera, J. Jimenez, L. Leal, J. Ponce de Leon, M. Esculpi, and V. Galino, J. Math. Phys. 25, 3274 (1984)] studied the consequences of the existence of a one-parameter group of conformal motions for anisotropic matter. They concluded that for special conformal motions, the stiff equation of state (p = μ) is singled out in a unique way, provided the generating conformal vector field is orthogonal to the four-velocity. In this paper, the same problem is studied by using conformal collineations (which include conformal motions as subgroups). It is shown that, for a special conformal collineation, the stiff equation of state is not singled out. Non-Einstein Ricci-recurrent spaces are considered as physical models for the fluid matter

On the bioactive conformation of R(+)-8-chloro-2,3,4,5-tetrahydro-3-methyl-5-phenyl-1H-3-benzazepin-7-ol

Science.gov (United States)

Verdonk, M. L.; Voogd, K.; Kanters, J. A.; Kroon, J.; van Duijneveldt, F. B.

1994-07-01

A redetermination of the X-ray structure of the title compound is reported. In this structure a partially occupied position of a water molecule was found that was not observed in an earlier structure determination. This water molecule appears to have an important role in the crystal packing. Molecular mechanics calculations were performed on 12 conformations of the protonated title compound, complexed to a chloride anion. This anion represents the anionic binding site of the receptors at which the title compound exerts its biological activity. Crystal-structure statistics and ab initio calculations were used to generate starting geometries for the molecular mechanics calculations. It appears that the conformation that is assumed to be the active conformation for the D 1 receptor is the lowest-energy conformation. It is concluded that this conformation may, therefore, also be the active conformation for other receptors.

Characterization of conformational dynamics of bistable RNA by equilibrium and non-equilibrium NMR.

Science.gov (United States)

Fürtig, Boris; Reining, Anke; Sochor, Florian; Oberhauser, Eva Marie; Heckel, Alexander; Schwalbe, Harald

2014-12-19

Unlike proteins, a given RNA sequence can adopt more than a single conformation. The two (or more) conformations are long-lived and have similar stabilities, but interconvert only slowly. Such bi- or multistability is often linked to the biological functions of the RNA. This unit describes how nuclear magnetic resonance (NMR) spectroscopy can be used to characterize the conformational dynamics of bistable RNAs. Copyright © 2014 John Wiley & Sons, Inc.

Torsional Rigidity of Minimal Submanifolds

DEFF Research Database (Denmark)

Markvorsen, Steen; Palmer, Vicente

2006-01-01

We prove explicit upper bounds for the torsional rigidity of extrinsic domains of minimal submanifolds $P^m$ in ambient Riemannian manifolds $N^n$ with a pole $p$. The upper bounds are given in terms of the torsional rigidities of corresponding Schwarz symmetrizations of the domains in warped...

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots.

Science.gov (United States)

Hess, H; Ross, Jennifer L

2017-09-18

Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.

Control superstructure of rigid polyelectrolytes in oppositely charged hydrogels via programmed internal stress

Science.gov (United States)

Takahashi, Riku; Wu, Zi Liang; Arifuzzaman, Md; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

2014-08-01

Biomacromolecules usually form complex superstructures in natural biotissues, such as different alignments of collagen fibres in articular cartilages, for multifunctionalities. Inspired by nature, there are efforts towards developing multiscale ordered structures in hydrogels (recognized as one of the best candidates of soft biotissues). However, creating complex superstructures in gels are hardly realized because of the absence of effective approaches to control the localized molecular orientation. Here we introduce a method to create various superstructures of rigid polyanions in polycationic hydrogels. The control of localized orientation of rigid molecules, which are sensitive to the internal stress field of the gel, is achieved by tuning the swelling mismatch between masked and unmasked regions of the photolithographic patterned gel. Furthermore, we develop a double network structure to toughen the hydrogels with programmed superstructures, which deform reversibly under large strain. This work presents a promising pathway to develop superstructures in hydrogels and should shed light on designing biomimetic materials with intricate molecular alignments.

Conformation of flexibly linked triterpene dimers by using RDC-enhanced NMR spectroscopy

Science.gov (United States)

Lakshmi, Jerripothula K.; Pattnaik, Banita; Kavitha, Rachineni; Mallavadhani, Uppuluri V.; Jagadeesh, Bharatam

2018-06-01

Dimers of flexibly linked pentacyclic triterpene ursolic acid (UA) and its related frameworks such as asiatic acid (AA) and oleanolic acid (OA) have recently attracted significant attention due to their enhanced anti-cancer and anti-HCV activity compared to their respective monomers. Determination of conformation/inter-monomer orientation of these molecules is very important to understand their structure-activity relationship and to develop new scaffolds, which, however, is difficult through conventional NOE based solution-state NMR spectroscopy, due to lack of long-range NOEs. In the present work, we report a precise determination of conformation of two 1,2,3-triazole-linked triterpene dimer molecules, UA-AA and UA-OA, by employing one-bond Csbnd H residual dipolar couplings (RDCs) as additional long-range orientational restraints, measured in anisotropic PDMS/CDCl3 solvent medium.

Flexible and rigid cystoscopy in women.

Science.gov (United States)

Gee, Jason R; Waterman, Bradley J; Jarrard, David F; Hedican, Sean P; Bruskewitz, Reginald C; Nakada, Stephen Y

2009-01-01

Previous studies have evaluated the tolerability of rigid versus flexible cystoscopy in men. Similar studies, however, have not been performed in women. We sought to determine whether office-based flexible cystoscopy was better tolerated than rigid cystoscopy in women. Following full IRB approval, women were prospectively randomized in a single-blind manner. Patients were randomized to flexible or rigid cystoscopy and draped in the lithotomy position to maintain blinding of the study. Questionnaires evaluated discomfort before, during, and after cystoscopy. Thirty-six women were randomized to flexible (18) or rigid (18) cystoscopy. Indications were surveillance (16), hematuria (15), recurrent UTIs (2), voiding dysfunction (1), and other (2). All questionnaires were returned by 31/36 women. Using a 10-point visual analog scale (VAS), median discomfort during the procedure for flexible and rigid cystoscopy were 1.4 and 1.8, respectively, in patients perceiving pain. Median recalled pain 1 week later was similar at 0.8 and 1.15, respectively. None of these differences were statistically significant. Flexible and rigid cystoscopy are well tolerated in women. Discomfort during and after the procedure is minimal in both groups. Urologists should perform either procedure in women based on their preference and skill level.

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

NARCIS (Netherlands)

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

2003-01-01

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

Separation and Characterization of DNA Molecules and Intermolecular Interactions in Pressure-Driven Micro Flow

Science.gov (United States)

Friedrich, Sarah; Wang, Tza-Huei

Pressure-driven flow in micron-sized diameter capillaries can be used to separate DNA molecules by size in a technique called Free Solution Hydrodynamic Separation. By coupling this technique with Cylindrical Illumination Confocal Spectroscopy, we have developed a highly sensitive and quantitative platform capable of separating DNA molecules by length over a large dynamic range (25 bp to 48 kbp) in a single run using only picoliters or femtograms of a DNA sample. The optical detection volume completely spans the capillary cross section, enabling highly efficient single molecule detection for enhanced sensitivity and quantification accuracy via single molecule counting. Because each DNA molecule generates its own fluorescent burst, these burst profiles can be further analyzed to individually characterize each DNA molecule's shape as it passes through the detection region. We exploit these burst profiles to visualize fluctuations in conformation under shear flow in microcapillaries, and utilizing combined mobility shift analysis, explore the complex relationship between molecular properties including length and conformation, hydrodynamic mobility, solution conditions including ion species and concentrations, and separation conditions including flow rate and capillary diameter.

Emotional rigidity negatively impacts remission from anxiety and recovery of well-being.

Science.gov (United States)

Wiltgen, Anika; Shepard, Christopher; Smith, Ryan; Fowler, J Christopher

2018-08-15

Emotional rigidity is described in clinical literature as a significant barrier to recovery; however, few there are few empirical measures of the construct. The current study had two aims: Study 1 aimed to identify latent factors that may bear on the construct of emotional rigidity while Study 2 assessed the potential impact of the latent factor(s) on anxiety remission rates and well-being. This study utilized data from 2472 adult inpatients (1176 females and 1296 males) with severe psychopathology. Study 1 utilized exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to identify latent factors of emotional rigidity. Study 2 utilized hierarchical logistic regression analyses to assess the relationships among emotional rigidity factors and anxiety remission and well-being recovery at discharge. Study 1 yielded a two-factor solution identified in EFA was confirmed with CFA. Factor 1 consisted of neuroticism, experiential avoidance, non-acceptance of emotions, impaired goal-directed behavior, impulse control difficulties and limited access to emotion regulation strategies when experiencing negative emotions. Factor 2 consisted of lack of emotional awareness and lack of emotional clarity when experiencing negative emotions. Results of Study 2 indicated higher scores on Factor 1 was associated with lower remission rates from anxiety and poorer well-being upon discharge. Factor 2 was not predictive of outcome. Emotional rigidity appears to be a latent construct that negatively impacts remission rates from anxiety. Limitations of the present study include its retrospective design, and inefficient methods of assessing emotional rigidity. Copyright © 2018. Published by Elsevier B.V.

Conductance mechanism in a linear non-conjugated trimethylsilyl-acetylene molecule: tunneling through localized states

NARCIS (Netherlands)

Petrov, E.G.; Marchenko, A.; Kapitanchuk, O.; Katsonis, Nathalie Hélène; Fichou, D.

2014-01-01

The conductance properties of 1,3-(trimethylsilyl)-1-tridecene-6,12-diyne, a non-conjugated trimethylsil-acetylene molecule have been investigated both experimentally and theoretically. Based on scanning tunnelling spectroscopy experiments, a discussion on the mechanisms controlling the charge

Conformal invariant quantum field theory and composite field operators

International Nuclear Information System (INIS)

Kurak, V.

1976-01-01

The present status of conformal invariance in quantum field theory is reviewed from a non group theoretical point of view. Composite field operators dimensions are computed in some simple models and related to conformal symmetry

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

Science.gov (United States)

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

2018-01-01

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

Thermal Behaviour of a Gypsum Fibre Board Associated with Rigid Polyurethane Foam under Standard Fire Conditions

DEFF Research Database (Denmark)

Dreau, Jerome Le; Jensen, Rasmus Lund; Kolding, Klaus

2015-01-01

Due to its low thermal conductivity (λ ≈ 20 mW/m.K), rigid polyurethane (PUR) foam has the potential to improve the thermal performance of buildings without increasing the thickness of construction elements. Nevertheless, PUR foam has the drawback of having a low resistance to fire: non-flaming t......Due to its low thermal conductivity (λ ≈ 20 mW/m.K), rigid polyurethane (PUR) foam has the potential to improve the thermal performance of buildings without increasing the thickness of construction elements. Nevertheless, PUR foam has the drawback of having a low resistance to fire: non...

Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch

DEFF Research Database (Denmark)

Ning, Yanxiao; Cramer, Jacob Roland; Nuermaimaiti, Ajiguli

2015-01-01

). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure...... conformational states. Together these observations imply selection and adaptation of conformational states upon molecular self-assembly. From DFT modeling and statistical analysis of the molecular conformations, the observed selection of conformational states is attributed to steric interaction between...

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case.

Science.gov (United States)

Mroczyńska, Karina; Kaczorowska, Małgorzata; Kolehmainen, Erkki; Grubecki, Ireneusz; Pietrzak, Marek; Ośmiałowski, Borys

2015-01-01

The association of substituted benzoates and naphthyridine dianions was used to study the complexation of dibutyltriuret. The title molecule is the simplest molecule able to form two intramolecular hydrogen bonds. The naphthyridine salt was used to break two intramolecular hydrogen bonds at a time while with the use of substituted benzoates the systematic approach to study association was achieved. Both, titrations and variable temperature measurements shed the light on the importance of conformational equilibrium and its influence on association in solution. Moreover, the associates were observed by mass spectrometry. The DFT-based computations for complexes and single bond rotational barriers supports experimental data and helps understanding the properties of multiply hydrogen bonded complexes.

Ligand binding turns moth pheromone-binding protein into a pH sensor: effect on the Antheraea polyphemus PBP1 conformation.

Science.gov (United States)

Katre, Uma V; Mazumder, Suman; Prusti, Rabi K; Mohanty, Smita

2009-11-13

In moths, pheromone-binding proteins (PBPs) are responsible for the transport of the hydrophobic pheromones to the membrane-bound receptors across the aqueous sensillar lymph. We report here that recombinant Antheraea polyphemus PBP1 (ApolPBP1) picks up hydrophobic molecule(s) endogenous to the Escherichia coli expression host that keeps the protein in the "open" (bound) conformation at high pH but switches to the "closed" (free) conformation at low pH. This finding has bearing on the solution structures of undelipidated lepidopteran moth PBPs determined thus far. Picking up a hydrophobic molecule from the host expression system could be a common feature for lipid-binding proteins. Thus, delipidation is critical for bacterially expressed lipid-binding proteins. We have shown for the first time that the delipidated ApolPBP1 exists primarily in the closed form at all pH levels. Thus, current views on the pH-induced conformational switch of PBPs hold true only for the ligand-bound open conformation of the protein. Binding of various ligands to delipidated ApolPBP1 studied by solution NMR revealed that the protein in the closed conformation switches to the open conformation only at or above pH 6.0 with a protein to ligand stoichiometry of approximately 1:1. Mutation of His(70) and His(95) to alanine drives the equilibrium toward the open conformation even at low pH for the ligand-bound protein by eliminating the histidine-dependent pH-induced conformational switch. Thus, the delipidated double mutant can bind ligand even at low pH in contrast to the wild type protein as revealed by fluorescence competitive displacement assay using 1-aminoanthracene and solution NMR.

Analysis of Switched-Rigid Floating Oscillator

Directory of Open Access Journals (Sweden)

Prabhakar R. Marur

2009-01-01

Full Text Available In explicit finite element simulations, a technique called deformable-to-rigid (D2R switching is used routinely to reduce the computation time. Using the D2R option, the deformable parts in the model can be switched to rigid and reverted back to deformable when needed during the analysis. The time of activation of D2R however influences the overall dynamics of the system being analyzed. In this paper, a theoretical basis for the selection of time of rigid switching based on system energy is established. A floating oscillator problem is investigated for this purpose and closed-form analytical expressions are derived for different phases in rigid switching. The analytical expressions are validated by comparing the theoretical results with numerical computations.

On the electronic structure of Barrelene-based rigid organic donor-acceptor systems. An INDO model study including solvent effects

International Nuclear Information System (INIS)

Fox, T.; Kotzian, M.; Roesch, N.

1992-01-01

The authors present an INDO/S Molecular-orbital investigation of organic molecules containing a barrelene moiety that provides a rigid link between an aromatic donor and a maleic ester acceptor group. Molecules of this type have recently been synthesized and characterized spectroscopically. The authors discuss the ground state and various excited states both in vacuo and in solution. Solvent effects are incorporated by use of an electrostatic cavity model which is not restricted to a spherical cavity, but allows for a cavity shape that is adapted to the solute molecule. The calculations indicate low-lying charge-transfer (CT) excitations in the region of the first aromatic transitions, even in the gas phase

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

Energy Technology Data Exchange (ETDEWEB)

Justino, Licínia L. G., E-mail: liciniaj@ci.uc.pt; Reva, Igor; Fausto, Rui [CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal)

2016-07-07

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N{sub 2}, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

Science.gov (United States)

Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

2016-07-01

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

International Nuclear Information System (INIS)

Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

2016-01-01

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N 2 , Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

The conformally invariant Laplace-Beltrami operator and factor ordering

International Nuclear Information System (INIS)

Ryan, Michael P.; Turbiner, Alexander V.

2004-01-01

In quantum mechanics the kinetic energy term for a single particle is usually written in the form of the Laplace-Beltrami operator. This operator is a factor ordering of the classical kinetic energy. We investigate other relatively simple factor orderings and show that the only other solution for a conformally flat metric is the conformally invariant Laplace-Beltrami operator. For non-conformally-flat metrics this type of factor ordering fails, by just one term, to give the conformally invariant Laplace-Beltrami operator

Characterizing single-molecule FRET dynamics with probability distribution analysis.

Science.gov (United States)

Santoso, Yusdi; Torella, Joseph P; Kapanidis, Achillefs N

2010-07-12

Probability distribution analysis (PDA) is a recently developed statistical tool for predicting the shapes of single-molecule fluorescence resonance energy transfer (smFRET) histograms, which allows the identification of single or multiple static molecular species within a single histogram. We used a generalized PDA method to predict the shapes of FRET histograms for molecules interconverting dynamically between multiple states. This method is tested on a series of model systems, including both static DNA fragments and dynamic DNA hairpins. By fitting the shape of this expected distribution to experimental data, the timescale of hairpin conformational fluctuations can be recovered, in good agreement with earlier published results obtained using different techniques. This method is also applied to studying the conformational fluctuations in the unliganded Klenow fragment (KF) of Escherichia coli DNA polymerase I, which allows both confirmation of the consistency of a simple, two-state kinetic model with the observed smFRET distribution of unliganded KF and extraction of a millisecond fluctuation timescale, in good agreement with rates reported elsewhere. We expect this method to be useful in extracting rates from processes exhibiting dynamic FRET, and in hypothesis-testing models of conformational dynamics against experimental data.

M-CARS and EFISHG study of the influence of a static electric field on a non-polar molecule

Science.gov (United States)

Capitaine, E.; Louot, C.; Ould-Moussa, N.; Lefort, C.; Kaneyasu, J. F.; Kano, H.; Pagnoux, D.; Couderc, V.; Leproux, P.

2016-03-01

The influence of a static electric field on a non-polar molecule has been studied by means of multiplex coherent anti-Stokes Raman scattering (M-CARS). A parallel measurement of electric field induced second harmonic generation (EFISHG) has also been led. Both techniques suggest a reorientation of the molecule due to the presence of an electric field. This phenomenon can be used to increase the chemical selectivity and the signal to non-resonant background ratio, namely, the sensitivity of the M-CARS spectroscopy.

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

Directory of Open Access Journals (Sweden)

Ruan Jishou

2007-04-01

Full Text Available Abstract Background Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP; the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction. Results The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are

Tensor categories and the mathematics of rational and logarithmic conformal field theory

International Nuclear Information System (INIS)

Huang, Yi-Zhi; Lepowsky, James

2013-01-01

We review the construction of braided tensor categories and modular tensor categories from representations of vertex operator algebras, which correspond to chiral algebras in physics. The extensive and general theory underlying this construction also establishes the operator product expansion for intertwining operators, which correspond to chiral vertex operators, and more generally, it establishes the logarithmic operator product expansion for logarithmic intertwining operators. We review the main ideas in the construction of the tensor product bifunctors and the associativity isomorphisms. For rational and logarithmic conformal field theories, we review the precise results that yield braided tensor categories, and in the rational case, modular tensor categories as well. In the case of rational conformal field theory, we also briefly discuss the construction of the modular tensor categories for the Wess–Zumino–Novikov–Witten models and, especially, a recent discovery concerning the proof of the fundamental rigidity property of the modular tensor categories for this important special case. In the case of logarithmic conformal field theory, we mention suitable categories of modules for the triplet W-algebras as an example of the applications of our general construction of the braided tensor category structure. (review)

24 +24 real scalar multiplet in four dimensional N =2 conformal supergravity

Science.gov (United States)

Hegde, Subramanya; Lodato, Ivano; Sahoo, Bindusar

2018-03-01

Starting from the 48 +48 component multiplet of supercurrents for a rigid N =2 tensor multiplet in four spacetime dimensions, we obtain the transformation of the linearized supergravity multiplet which couples to this supercurrent multiplet. At the linearized level, this 48 +48 component supergravity multiplet decouples into the 24 +24 component linearized standard Weyl multiplet and a 24 +24 component irreducible matter multiplet containing a real scalar field. By a consistent application of the supersymmetry algebra with field-dependent structure constants appropriate to N =2 conformal supergravity, we find the full transformation law for this multiplet in a conformal supergravity background. By performing a suitable field redefinition, we find that the multiplet is a generalization of the flat space multiplet, obtained by Howe et al. in Nucl. Phys. B214, 519 (1983), 10.1016/0550-3213(83)90249-3, to a conformal supergravity background. We also present a set of constraints which can be consistently imposed on this multiplet to obtain a restricted minimal 8 +8 off-shell matter multiplet. We also show, as an example, the precise embedding of the tensor multiplet inside this multiplet.

Broadband Chirped-Pulse Fourier-Transform Microwave Spectroscopic Investigation of the Structures of Three Diethylsilane Conformers

Science.gov (United States)

Steber, Amanda L.; Obenchain, Daniel A.; Peebles, Rebecca A.; Peebles, Sean A.; Neill, Justin L.; Muckle, Matt T.; Pate, Brooks H.; Guirgis, Gamil A.

2009-06-01

The rotational spectrum of diethylsilane has been assigned using broadband chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy. Previously, Fourier-transform microwave rotational spectra were observed using a Balle-Flygare type instrument for the ^{28}Si isotopologues of the gauche-gauche, trans-gauche, and trans-trans conformers. In the present study, a broadband microwave spectrum was obtained at the University of Virginia, taking advantage of the ability to perform deep signal averaging to increase the measurement sensitivity. To obtain a full structural determination of the conformers of this molecule, spectra for the ^{29}Si, ^{30}Si, and single ^{13}C substitutions for the gauche-gauche, the trans-gauche, and the trans-trans species were assigned. Substitution (r_s) structures and inertial fit (r_0) structures were determined and a comparison between the experimental and ab initio structures will be presented. For the ^{28}Si isotopologues, the percent differences between the experimental and ab initio rotational constants are less than 1.5% for the trans-trans and trans-gauche and are between 2.0 and 5.0% for the gauche-gauche conformer. The structural parameters will be compared between this molecule, diethylgermane and other silicon containing molecules and the relative abundances of the three conformers will be discussed. S.A. Peebles, M.M. Serafin, R.A. Peebles, G.A. Guirgis, and H.D. Stidham J. Phys. Chem. A, (2009), DOI: 10.1021/jp811049n.

Renormalization, conformal ward identities and the origin of a conformal anomaly pole

Science.gov (United States)

Corianò, Claudio; Maglio, Matteo Maria

2018-06-01

We investigate the emergence of a conformal anomaly pole in conformal field theories in the case of the TJJ correlator. We show how it comes to be generated in dimensional renormalization, using a basis of 13 form factors (the F-basis), where only one of them requires renormalization (F13), extending previous studies. We then combine recent results on the structure of the non-perturbative solutions of the conformal Ward identities (CWI's) for the TJJ in momentum space, expressed in terms of a minimal set of 4 form factors (A-basis), with the properties of the F-basis, and show how the singular behaviour of the corresponding form factors in both basis can be related. The result proves the centrality of such massless effective interactions induced by the anomaly, which have recently found realization in solid state, in the theory of topological insulators and of Weyl semimetals. This pattern is confirmed in massless abelian and nonabelian theories (QED and QCD) investigated at one-loop.

A kinetic theory description of the viscosity of dense fluids consisting of chain molecules.

Science.gov (United States)

de Wijn, Astrid S; Vesovic, Velisa; Jackson, George; Trusler, J P Martin

2008-05-28

An expression for the viscosity of a dense fluid is presented that includes the effect of molecular shape. The molecules of the fluid are approximated by chains of equal-sized, tangentially jointed, rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions between two rigid spheres belonging to different chains. The approach is thus analogous to that of Enskog for a fluid consisting of rigid spheres. The description is developed in terms of two molecular parameters, the diameter sigma of the spherical segment and the chain length (number of segments) m. It is demonstrated that an analysis of viscosity data of a particular pure fluid alone cannot be used to obtain independently effective values of both sigma and m. Nevertheless, the chain lengths of n-alkanes are determined by assuming that the diameter of each rigid sphere making up the chain can be represented by the diameter of a methane molecule. The effective chain lengths of n-alkanes are found to increase linearly with the number C of carbon atoms present. The dependence can be approximated by a simple relationship m=1+(C-1)3. The same relationship was reported within the context of a statistical associating fluid theory equation of state treatment of the fluid, indicating that both the equilibrium thermodynamic properties and viscosity yield the same value for the chain lengths of n-alkanes.

Non conformance in fittings for critical environmental conditions; Conexoes nao conformes para trabalho em meios criticos