WorldWideScience

Sample records for calculated conformer energies

  1. The calculations of small molecular conformation energy differences by density functional method

    Science.gov (United States)

    Topol, I. A.; Burt, S. K.

    1993-03-01

    The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.

  2. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  3. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    Science.gov (United States)

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  4. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

    NARCIS (Netherlands)

    Hritz, J.; Oostenbrink, C.

    2009-01-01

    Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such

  5. 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

  6. Calculating zeros: Non-equilibrium free energy calculations

    International Nuclear Information System (INIS)

    Oostenbrink, Chris; Gunsteren, Wilfred F. van

    2006-01-01

    Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations

  7. Vibrational spectrum, ab initio calculations, conformational stabilities and assignment of fundamentals of 1,2-dibromopropane

    Science.gov (United States)

    LaPlante, Arthur J.; Stidham, Howard D.

    2009-10-01

    The mid and far infrared and the Raman spectrum of 1,2-dibromopropane is reported in solid, liquid and gas. Several bands reported by earlier workers are not present in the spectrum of the purified material. Ab initio calculations of optimized geometry, energy, dipole moment, molar volume, vibrational spectrum and normal coordinate calculation were performed using the density functional B3LYP/6-311++g(3df,2pd), and the results used to assist a complete assignment of the 81 fundamental modes of vibrations of the three conformers of 1,2-dibromopropane. Relative energies found conformer A the lowest with G and G' at 815.6 and 871.4 cm -1 higher. The temperature dependence of the Raman spectrum of the liquid was investigated in the CCC bending region and the relative energies determined. It was found that the G' and G conformers lie 236 ± 11 and 327 ±11 cm -1, respectively above the A conformer, leading to the room temperature composition of the liquid as A, 65 ± 1; G', 21 ± 1; G, 14 ± 1%. It is apparent that the calculated highest energy conformer G' is stabilized more than the G conformer in the liquid. The G' conformer has the lowest molar volume effectively changing the interaction distance between conformers in the liquid, and enhancing the effect of its dipole moment.

  8. Quantum-chemical calculation of energies and spectral characteristics of conformers in derivatives of phenylphosphine

    International Nuclear Information System (INIS)

    Chuvashev, D.D.; Ratovskii, G.V.; Zakzhevskii, V.G.

    1987-01-01

    The phenylphosphines PhPX 2 calculated by the MNDO method are characterized by two potential minima corresponding to the bisector and gonal conformations. For X = Cl, F, and C=N the bisector conformer predominates considerably, but for X = H and CH 3 the populations of the conformers are approximately the same. The characteristics of the electron transitions of the conformers found, determined by the CNDO/S method, differ substantially, which makes it possible to analyze the conformational compositions of arylphosphines by means of UV spectroscopy. In excited ππ* states the gonal conformation is characterized by a substantial donor effect of the PX 2 group, whereas the bisector conformation gives a certain acceptor effect

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

    Science.gov (United States)

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

    2014-10-01

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

  10. Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties.

    Science.gov (United States)

    Scheraga, H A; Paine, G H

    1986-01-01

    We are using a variety of theoretical and computational techniques to study protein structure, protein folding, and higher-order structures. Our earlier work involved treatments of liquid water and aqueous solutions of nonpolar and polar solutes, computations of the stabilities of the fundamental structures of proteins and their packing arrangements, conformations of small cyclic and open-chain peptides, structures of fibrous proteins (collagen), structures of homologous globular proteins, introduction of special procedures as constraints during energy minimization of globular proteins, and structures of enzyme-substrate complexes. Recently, we presented a new methodology for predicting polypeptide structure (described here); the method is based on the calculation of the probable and average conformation of a polypeptide chain by the application of equilibrium statistical mechanics in conjunction with an adaptive, importance sampling Monte Carlo algorithm. As a test, it was applied to Met-enkephalin.

  11. Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis.

    Science.gov (United States)

    Kamachi, Takashi; Yoshizawa, Kazunari

    2016-02-22

    A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.

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

    OpenAIRE

    Gómez-Zavaglia, Andrea; Fausto, R.

    2003-01-01

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

  13. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

  14. Narrowband NIR-Induced In Situ Generation of the High-Energy Trans Conformer of Trichloroacetic Acid Isolated in Solid Nitrogen and its Spontaneous Decay by Tunneling to the Low-Energy Cis Conformer

    Directory of Open Access Journals (Sweden)

    R. F. G. Apóstolo

    2015-12-01

    Full Text Available The monomeric form of trichloroacetic acid (CCl3COOH; TCA was isolated in a cryogenic nitrogen matrix (15 K and the higher energy trans conformer (O=C–O–H dihedral: 180° was generated in situ by narrowband near-infrared selective excitation the 1st OH stretching overtone of the low-energy cis conformer (O=C–O–H dihedral: 0°. The spontaneous decay, by tunneling, of the generated high-energy conformer into the cis form was then evaluated and compared with those observed previously for the trans conformers of acetic and formic acids in identical experimental conditions. The much faster decay of the high-energy conformer of TCA compared to both formic and acetic acids (by ~35 and ca. 25 times, respectively was found to correlate well with the lower energy barrier for the trans→cis isomerization in the studied compound. The experimental studies received support from quantum chemistry calculations undertaken at the DFT(B3LYP/cc-pVDZ level of approximation, which allowed a detailed characterization of the potential energy surface of the molecule and the detailed assignment of the infrared spectra of the two conformers.

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

    Science.gov (United States)

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

    2017-04-14

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

  16. 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.

  17. Conformational analysis of capsaicin using 13C, 15N MAS NMR, GIAO DFT and GA calculations

    Science.gov (United States)

    Siudem, Paweł; Paradowska, Katarzyna; Bukowicki, Jarosław

    2017-10-01

    Capsaicin produced by plants from genus Capsicum exerts multiple pharmacological effects and has found applications in food and pharmaceutical industry. The alkaloid was studied by a combined approach: solid-state NMR, GA conformational search and GIAO DFT methods. The 13C CPMAS NMR spectra were recorded using variable contact time and dipolar dephasing experiments. The results of cross-polarization (CP) kinetics, such as TCP values and long T1ρH (100-200 ms), indicated that the capsaicin molecule is fairly mobile, especially at the end of the aliphatic chain. The15N MAS NMR spectrum showed one narrow signal at -255 ppm. Genetic algorithm (GA) search with multi modal optimization was used to find low-energy conformations of capsaicin. Theoretical GIAO DFT calculations were performed using different basis sets to characterize five selected conformations. 13C CPMAS NMR was used as a validation method and the experimental chemical shifts were compared with those calculated for selected stable conformers. Conformational analysis suggests that the side chain can be bent or extended. A comparison of the experimental and the calculated chemical shifts indicates that solid capsaicin does not have the same structure as those established by PWXRD.

  18. Conformational and structural analysis of 2-allyl-1,2-benzisothiazol-3(2 H)-one 1,1-dioxide as probed by matrix-isolation spectroscopy and quantum chemical calculations

    Science.gov (United States)

    Gómez-Zavaglia, Andrea; Kaczor, Agnieszka; Coelho, Daniela; Cristiano, M. Lurdes S.; Fausto, Rui

    2009-02-01

    2-Allyl-1,2-benzisothiazol-3(2 H)-one 1,1-dioxide (ABIOD) has been studied by matrix-isolation infrared spectroscopy and quantum chemical calculations. A conformational search on the B3LYP/6 -311++G(3df,3pd) potential energy surface of the molecule demonstrated the existence of three conformers, Sk, Sk' and C, with similar energies, differing in the orientation of the allyl group. The calculations predicted the Sk form as the most stable in the gaseous phase, whereas the Sk' and C conformers have calculated relative energies of ca. 0.6 and 0.8-3.0 kJ mol -1, respectively (depending on the level of theory). In agreement with the relatively large (>6 kJ mol -1) calculated barriers for conformational interconversion, the three conformers could be efficiently trapped in an argon matrix at 10 K, the experimental infrared spectrum of the as-deposited matrix fitting well the simulated spectrum built from the calculated spectra for individual conformers scaled by their predicted populations at the temperature of the vapour of the compound prior to matrix deposition. Upon annealing the matrix at 24 K, however, both Sk and Sk' conformers were found to convert to the more polar C conformer, indicating that this latter form becomes the most stable ABIOD conformer in the argon matrix.

  19. Poly (3, 4-ethylendioxithiophene) (PEDOT) oxidation: activation energy and conformational energy

    International Nuclear Information System (INIS)

    Otero, T F; Romero, M C

    2008-01-01

    The oxidation kinetics of films of the conducting polymer PEDOT-C1O4 after electrochemical reduction by polarization at increasing cathodic potential was studied by potential steps. The response i/t presents a maximum at intermediate oxidation times. At the maximum the reaction occurs under chemical kinetic control following the expected current variations from the Chemical and Electrochemical Kinetics, when reactant concentrations or temperatures are changed. The obtained activation energy of the oxidation present two ranges as a function of the cathodic potential of prepolarization: constant values after prepolarization at low cathodic potentials and a lineal variation after prepolarization at increasing high cathodic potentials. According with the conformational relaxation model during electrochemical reduction the polymer shrinks, closes and packs the conformational structure. The activation energy for the subsequent oxidation includes two terms: the constant chemical activation energy and the conformational energy required to relax the packed polymeric structure. The conformational energy only appears after prepolarization at more cathodic potentials than the closing potential where more packed conformations were obtained. The conformational activation energy accounts the energetic requirements to relax and unfold the polymeric chains generating the required free volume to lodge balancing counterions; meanwhile the chemical activation energy accounts the energetic requirements for the electrochemical reaction to occur.

  20. NMR investigation and theoretical calculations of the solvent effect on the conformation of valsartan

    Science.gov (United States)

    Chashmniam, Saeed; Tafazzoli, Mohsen

    2017-11-01

    Structure and conformational properties of valsartan were studied by advanced NMR techniques and quantum calculation methods. Potential energy scanning using B3LYP/6-311++g** and B3LYP-D3/6-311++g** methods were performed and four conformers (V1-V4) at minimum points of PES diagram were observed. According to the NMR spectra in acetone-d6, there are two conformers (M and m) with m/M = 0.52 ratio simultaneously and energy barriers of the two conformers were predicted from chemical shifts and multiplicities. While, intramolecular hydrogen bond at tetrazole ring and carboxylic groups prevent the free rotation on N6sbnd C11 bond in M-conformer, this bond rotates freely in m-conformer. On the other hand, intramolecular hydrogen bond at carbonyl and carboxylic acid can be observed at m-conformer. So, different intramolecular hydrogen bond is the reason for the stability of both M and m structures. Quite interestingly, 1H NMR spectra in CDCl3 show two distinct conformers (N and n) with unequal ratio which are differ from M-m conformers. Also, intramolecular hydrogen bond seven-member ring involving five-membered tetrazole ring and carboxylic acid group observed in both N and n-conformers Solvent effect, by using a set of polar and non-polar solvents including DMSO-d6, methanol-d4, benzene-d6, THF-d8, nitromethane-d3, methylene chloride-d2 and acetonitrile-d3 were investigated. NMR parameters include chemical shifts and spin-spin coupling constants were obtained from a set of 2D NMR spectra (H-H COSY, HMQC and HMBC). For this purpose, several DFT functionals from LDA, GGA and hybrid categories were used which the hybrid method showed better agreement with experiment values.

  1. Willmore energy estimates in conformal Berger spheres

    International Nuclear Information System (INIS)

    Barros, Manuel; Ferrandez, Angel

    2011-01-01

    Highlights: → The Willmore energy is computed in a wide class of surfaces. → Isoperimetric inequalities for the Willmore energy of Hopf tori are obtained. → The best possible lower bound is achieved on isoareal Hopf tori. - Abstract: We obtain isoperimetric inequalities for the Willmore energy of Hopf tori in a wide class of conformal structures on the three sphere. This class includes, on the one hand, the family of conformal Berger spheres and, on the other hand, a one parameter family of Lorentzian conformal structures. This allows us to give the best possible lower bound of Willmore energies concerning isoareal Hopf tori.

  2. Conformal fields in prostate radiotherapy: A comparison between measurement, calculation and simulation

    Directory of Open Access Journals (Sweden)

    Seied R Mahdavi

    2012-01-01

    Full Text Available Aims: The objective of this study is to evaluate the accuracy of a treatment planning system (TPS for calculating the dose distribution parameters in conformal fields (CF. Dosimetric parameters of CF′s were compared between measurement, Monte Carlo simulation (MCNP4C and TPS calculation. Materials and Methods: Field analyzer water phantom was used for obtaining percentage depth dose (PDD curves and beam profiles (BP of different conformal fields. MCNP4C was used to model conformal fields dose specification factors and head of linear accelerator varian model 2100C/D. Results: Results showed that the distance to agreement (DTA and dose difference (DD of our findings were well within the acceptance criteria of 3 mm and 3%, respectively. Conclusions: According to this study it can be revealed that TPS using equivalent tissue air ratio calculation method is still convenient for dose prediction in non small conformal fields normally used in prostate radiotherapy. It was also showed that, since there is a close correlation with Monte Carlo simulation, measurements and TPS, Monte Carlo can be further confirmed for implementation and calculation dose distribution in non standard and complex conformal irradiation field for treatment planning systems.

  3. 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.

  4. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

    Directory of Open Access Journals (Sweden)

    Qing Wang

    2016-05-01

    Full Text Available Free energy calculations of the potential of mean force (PMF based on the combination of targeted molecular dynamics (TMD simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35. The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.

  5. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

    Science.gov (United States)

    Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2017-06-05

    Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

    OpenAIRE

    Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.

    2002-01-01

    Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...

  7. Conformal Gravity: Dark Matter and Dark Energy

    Directory of Open Access Journals (Sweden)

    Robert K. Nesbet

    2013-01-01

    Full Text Available This short review examines recent progress in understanding dark matter, dark energy, and galactic halos using theory that departs minimally from standard particle physics and cosmology. Strict conformal symmetry (local Weyl scaling covariance, postulated for all elementary massless fields, retains standard fermion and gauge boson theory but modifies Einstein–Hilbert general relativity and the Higgs scalar field model, with no new physical fields. Subgalactic phenomenology is retained. Without invoking dark matter, conformal gravity and a conformal Higgs model fit empirical data on galactic rotational velocities, galactic halos, and Hubble expansion including dark energy.

  8. Conformational Analysis of Contrast Media for X-Ray Diagnostic Radiology

    International Nuclear Information System (INIS)

    Solieman, A.H.M.

    2010-01-01

    The conformational analysis of iodinated non-ionic contrast agent, Iobitridol, was carried out using theoretical calculations to explore its conformational space, and to study different aspects connected with application of different search techniques. Monte Carlo (MC), random search (RS) and molecular dynamics (MD) based conformational search techniques were used to extract a reasonable-size sample that adequately represents and has an average behavior of the entire conformational ensemble.While MC is good for quick search for lowest energy conformer, RS is better in obtaining conformational sample that cover the whole conformational space and MD is the best for investigation of isomeric preferences inside the conformational ensemble at thermal equilibrium. Conformational analysis of the produced gas phase samples reveals that RS and MD methods could sufficiently present the 18 distinct isomeric classes that constitute the total conformational space of the Iobitridol. S samples of conformational space of Iobitridol are extensively studied, as it hypothetically cover the total conformational space. They are used to test the suitability of different methods (charge distribution methods, energy calculation methods) for Iobitridol molecular computations and internal structure forces (steric hindrance, resonance interaction), as well as dependences among the internal coordinates (dihedral angles correlations and coincidences). The atomic partial charge distribution is found to greatly affect the energy calculation for the molecular mechanics based conformational energy distributions. Further energy minimization of conformational sample by the quantum molecular orbital methods is crucial to obtain charge independent as well as energy balanced conformational sample.

  9. 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.

  10. Conformational changes in glycine tri- and hexapeptide

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2006-01-01

    conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods...... also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids....

  11. Energy Landscape of Pentapeptides in a Higher-Order (ϕ,ψ Conformational Subspace

    Directory of Open Access Journals (Sweden)

    Karim M. ElSawy

    2016-01-01

    Full Text Available The potential energy landscape of pentapeptides was mapped in a collective coordinate principal conformational subspace derived from principal component analysis of a nonredundant representative set of protein structures from the PDB. Three pentapeptide sequences that are known to be distinct in terms of their secondary structure characteristics, (Ala5, (Gly5, and Val.Asn.Thr.Phe.Val, were considered. Partitioning the landscapes into different energy valleys allowed for calculation of the relative propensities of the peptide secondary structures in a statistical mechanical framework. The distribution of the observed conformations of pentapeptide data showed good correspondence to the topology of the energy landscape of the (Ala5 sequence where, in accord with reported trends, the α-helix showed a predominant propensity at 298 K. The topography of the landscapes indicates that the stabilization of the α-helix in the (Ala5 sequence is enthalpic in nature while entropic factors are important for stabilization of the β-sheet in the Val.Asn.Thr.Phe.Val sequence. The results indicate that local interactions within small pentapeptide segments can lead to conformational preference of one secondary structure over the other where account of conformational entropy is important in order to reveal such preference. The method, therefore, can provide critical structural information for ab initio protein folding methods.

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

    Directory of Open Access Journals (Sweden)

    Yanwei Li

    2016-08-01

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

  13. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.

    Science.gov (United States)

    Xiang, Zhexin; Soto, Cinque S; Honig, Barry

    2002-05-28

    In this paper, we introduce a method to account for the shape of the potential energy curve in the evaluation of conformational free energies. The method is based on a procedure that generates a set of conformations, each with its own force-field energy, but adds a term to this energy that favors conformations that are close in structure (have a low rmsd) to other conformations. The sum of the force-field energy and rmsd-dependent term is defined here as the "colony energy" of a given conformation, because each conformation that is generated is viewed as representing a colony of points. The use of the colony energy tends to select conformations that are located in broad energy basins. The approach is applied to the ab initio prediction of the conformations of all of the loops in a dataset of 135 nonredundant proteins. By using an rmsd from a native criterion based on the superposition of loop stems, the average rmsd of 5-, 6-, 7-, and 8-residue long loops is 0.85, 0.92, 1.23, and 1.45 A, respectively. For 8-residue loops, 60 of 61 predictions have an rmsd of less than 3.0 A. The use of the colony energy is found to improve significantly the results obtained from the potential function alone. (The loop prediction program, "Loopy," can be downloaded at http://trantor.bioc.columbia.edu.)

  14. Using the fast fourier transform in binding free energy calculations.

    Science.gov (United States)

    Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L

    2018-04-30

    According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. 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.

  16. Spectroscopic and DFT studies of calix[4]arene: time-dependent DFT calculations for elucidating the variation in the excitation energies with geometry

    Energy Technology Data Exchange (ETDEWEB)

    Boo, Bong Hyun; Kwak, Hae Ran; Hong, Seung Ki [Chungnam National University, Daejeon (Korea, Republic of); Park, Chan Jo [Korea Research Institute of Chemical Technology, Daejeon (Korea, Republic of); No, Kwang Hyun [Sookmyung Womens University, Seoul (Korea, Republic of)

    2010-08-15

    We have searched low-lying conformers of calix[4]arene and found one global minimum having a cone shape, together with three conformers such as partial cone-shape conformers. We then elucidated the thermodynamics for the conformational changes by performing density-functional theory (DFT) calculations. The time-dependent DFT calculation enabled us to assign the absorption spectrum and to reveal a variation of the excitation energies with geometry.

  17. Conformational locking by design: relating strain energy with luminescence and stability in rigid metal-organic frameworks.

    Science.gov (United States)

    Shustova, Natalia B; Cozzolino, Anthony F; Dincă, Mircea

    2012-12-05

    Minimization of the torsional barrier for phenyl ring flipping in a metal-organic framework (MOF) based on the new ethynyl-extended octacarboxylate ligand H(8)TDPEPE leads to a fluorescent material with a near-dark state. Immobilization of the ligand in the rigid structure also unexpectedly causes significant strain. We used DFT calculations to estimate the ligand strain energies in our and all other topologically related materials and correlated these with empirical structural descriptors to derive general rules for trapping molecules in high-energy conformations within MOFs. These studies portend possible applications of MOFs for studying fundamental concepts related to conformational locking and its effects on molecular reactivity and chromophore photophysics.

  18. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.

    Directory of Open Access Journals (Sweden)

    Lili X Peng

    2014-02-01

    Full Text Available αβ-tubulin dimers need to convert between a 'bent' conformation observed for free dimers in solution and a 'straight' conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αβ-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αβ-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.

  19. 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...

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

  2. Assignment of Side-Chain Conformation Using Adiabatic Energy Mapping, Free Energy Perturbation, and Molecular Dynamic Simulations

    DEFF Research Database (Denmark)

    Frimurer, Thomas M.; Günther, Peter H.; Sørensen, Morten Dahl

    1999-01-01

    adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)......adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)...

  3. Ab initio calculation of conformation and vibrational spectrum for the pyrosulfate ion

    DEFF Research Database (Denmark)

    Dyekjær, Jane Dannow; Berg, Rolf W.; Johansen, Helge

    2003-01-01

    Theoretical calculations have been performed and applied to determine the most likely geometry for the pyrosulfate ion. The main question was to determine as to whether the system has C-2 or C-2, conformation. The present study favors C-2 symmetry. Bond lengths and angles have been calculated for...

  4. Independent dose calculation of the Tps Iplan in radiotherapy conformed with MLC

    International Nuclear Information System (INIS)

    Adrada, A.; Tello, Z.; Medina, L.; Garrigo, E.; Venencia, D.

    2014-08-01

    The systems utilization of independent dose calculation in three dimensional-Conformal Radiation Therapy (3D-Crt) treatments allows a direct verification of the treatments times. The utilization of these systems allows diminishing the probability of errors occurrence generated by the treatment planning system (Tps), allowing a detailed analysis of the dose to delivering and review of the normalization point (Np) or prescription. The independent dose calculation is realized across the knowledge of dosimetric parameters of the treatment machine and particular characteristics of every individual field. The aim of this work is develops a calculation system of punctual doses for isocentric fields conformed with multi-leaf collimation systems (MLC), where the dose calculation is in conformity with the suggested ones by ICRU Report No. 42, 1987. Calculation software was realized in C ++ under a free platform of programming (Code::Blocks). The system uses files in format Rtp, exported from the Tps to systems of record and verification (Lantis). This file contains detailed information of the dose, Um, position of the MLC sheets and collimators for every field of treatment. The size of equivalent field is obtained from the positions of every sheet; the effective depth of calculation can be introduced from the dosimetric report of the Tps or automatically from the DFS of the field. The 3D coordinates of the isocenter and the Np for the treatment plan must be introduced manually. From this information the system looks the dosimetric parameters and calculates the Um. The calculations were realized in two accelerators a NOVALIS Tx (Varian) with 120 sheets of high definition (hd-MLC) and a PRIMUS Optifocus (Siemens) with 82 sheets. 705 patients were analyzed for a total of 1082, in plans made for both equipment s, the average uncertainty with regard to the calculation of the Tps is-0.43% ± 2.42% in a range between [-7.90 %, 7.50 %]. The major uncertainty was in Np near of the

  5. Wormhole supported by dark energy admitting conformal motion

    Energy Technology Data Exchange (ETDEWEB)

    Bhar, Piyali [Government General Degree College, Singur, Department of Mathematics, Hooghly, West Bengal (India); Rahaman, Farook; Banerjee, Ayan [Jadavpur University, Department of Mathematics, Kolkata, West Bengal (India); Manna, Tuhina [St. Xavier' s College, Department of Mathematics and Statistics (Commerce Evening), Kolkata, West Bengal (India)

    2016-12-15

    In this article, we study the possibility of sustaining static and spherically symmetric traversable wormhole geometries admitting conformal motion in Einstein gravity, which presents a more systematic approach to search a relation between matter and geometry. In wormhole physics, the presence of exotic matter is a fundamental ingredient and we show that this exotic source can be dark energy type which support the existence of wormhole spacetimes. In this work we model a wormhole supported by dark energy which admits conformal motion. We also discuss the possibility of the detection of wormholes in the outer regions of galactic halos by means of gravitational lensing. Studies of the total gravitational energy for the exotic matter inside a static wormhole configuration are also performed. (orig.)

  6. Energy of knots and conformal geometry

    CERN Document Server

    O'Hara, Jun

    2003-01-01

    Energy of knots is a theory that was introduced to create a "canonical configuration" of a knot - a beautiful knot which represents its knot type. This book introduces several kinds of energies, and studies the problem of whether or not there is a "canonical configuration" of a knot in each knot type. It also considers this problems in the context of conformal geometry. The energies presented in the book are defined geometrically. They measure the complexity of embeddings and have applications to physical knotting and unknotting through numerical experiments. Contents: In Search of the "Optima

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

    Science.gov (United States)

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

    1997-08-01

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

  8. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    International Nuclear Information System (INIS)

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-01-01

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  9. On gravitational energy in conformal teleparallel gravity

    Science.gov (United States)

    da Silva, J. G.; Ulhoa, S. C.

    2017-07-01

    The paper deals with the definition of gravitational energy in conformal teleparallel gravity. The total energy is defined by means of the field equations which allow a local conservation law. Then such an expression is analyzed for a homogeneous and isotropic Universe. This model is implemented by the Friedmann-Robertson-Walker (FRW) line element. The energy of the Universe in the absence of matter is identified with the dark energy, however it can be expanded for curved models defining such an energy as the difference between the total energy and the energy of the perfect fluid which is the matter field in the FRW model.

  10. Conformational analysis of 9,10-dihydroanthracenes. Molecular mechanics calculations and /sup 13/C NMR

    Energy Technology Data Exchange (ETDEWEB)

    Rabideau, P.W.; Mooney, J.L.; Lipkowitz, K.B.

    1986-12-24

    The conformational analyses of 9, 10-dihydroanthracene and several of its methylated and ethylated derivatives are studied by empirical force field calculations (MM2 and MMPI). The computational results are considered in light of previous and current carbon NMR data. Model compounds are examined which involve fixed, planar, and boat-shaped conformations about the central ring, and these /sup 13/C NMR data are then compared with flexible systems. It is concluded that carbon chemical shifts and carbon-hydrogen coupling constants are consistent with the results of molecular mechanics calculations which indicate a greater tendency for planarity around the central ring than previously considered.

  11. Semiempirical and ab initio calculations versus dynamic NMR on conformational analysis of cyclohexyl-N,N-dimethylcarbamate

    Directory of Open Access Journals (Sweden)

    Basso Ernani A.

    2001-01-01

    Full Text Available Axial-equatorial conformational proportions for cyclohexyl-N,N-dimethyl carbamate have been measured, for the first time, by the Eliel method, ¹H and 13C dynamic nuclear magnetic resonance (DNMR. The results were compared against those determined by theoretical calculations. By the Eliel method at least five experimentally independent measureables were used in CCl4, CDCl3 and CD3CN. The ¹H and 13C low temperature experiments were performed in CF2Br2/CD2Cl2 . Semiempirical methods MNDO, AM1 and PM3 and ab initio molecular orbital calculations at the HF/STO-3G and HF/6-31G(d,p levels have been performed on the axial and equatorial conformers populations. All applied methods correctly predict the equatorial conformer preference over the axial one. The resulting equatorial preferences determined by NMR data and theoretical calculations are in good agreement.

  12. Rotational Spectrum, Conformational Composition, and Quantum Chemical Calculations of Cyanomethyl Formate (HC(O)OCH2C≡N), a Compound of Potential Astrochemical Interest.

    Science.gov (United States)

    Samdal, Svein; Møllendal, Harald; Carles, Sophie

    2015-08-27

    The rotational spectrum of cyanomethyl formate (HC(O)OCH2C≡N) has been recorded in the 12–123 GHz spectral range. The spectra of two conformers were assigned. The rotamer denoted I has a symmetry plane and two out-of plane hydrogen atoms belonging to the cyanomethyl (CH2CN) moiety. In the conformer called II, the cyanomethyl group is rotated 80.3° out of this plane. Conformer I has an energy that is 1.4(6) kJ/mol lower than the energy of II according to relative intensity measurements. A large number of rotational transitions have been assigned for the ground and vibrationally excited states of the two conformers and accurate spectroscopic constants have been obtained. These constants should predict frequencies of transitions outside the investigated spectral range with a very high degree of precision. It is suggested that cyanomethyl formate is a potential interstellar compound. This suggestion is based on the fact that its congener methyl formate (HC(O)OCH3) exists across a large variety of interstellar environments and the fact that cyanides are very prevalent in the Universe. The experimental work has been augmented by high-level quantum chemical calculations. The CCSD/cc-pVQZ calculations are found to predict structures of the two forms that are very close to the Born–Oppenheimer equilibrium structures. MP2/cc-pVTZ predictions of several vibration–rotation interaction constants were generally found to be rather inaccurate. A gas-phase reaction between methyl formate and the cyanomethyl radical CH2CN to produce a hydrogen atom and cyanomethyl formate was mimicked using MP2/cc-pVTZ calculations. It was found that this reaction is not favored thermodynamically. It is also conjectured that the possible formation of cyanomethyl formate might be catalyzed and take place on interstellar particles.

  13. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  14. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

    Science.gov (United States)

    2016-01-01

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  15. Conformational elasticity can facilitate TALE-DNA recognition.

    Science.gov (United States)

    Lei, Hongxing; Sun, Jiya; Baldwin, Enoch P; Segal, David J; Duan, Yong

    2014-01-01

    Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo and bound conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism. © 2014 Elsevier Inc. All rights reserved.

  16. 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

  17. 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.

  18. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

    Science.gov (United States)

    Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

    2015-06-09

    The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

  19. Hawking–Hayward quasi-local energy under conformal transformations

    International Nuclear Information System (INIS)

    Prain, Angus; Faraoni, Valerio; Lapierre-Léonard, Marianne; Vitagliano, Vincenzo

    2016-01-01

    We derive a formula describing the transformation of the Hawking–Hayward quasi-local energy under a conformal rescaling of the spacetime metric. A known formula for the transformation of the Misner–Sharp–Hernandez mass is recovered as a special case. (paper)

  20. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.

    Directory of Open Access Journals (Sweden)

    Giulio Quarta

    Full Text Available Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant "downhill" pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the "new view" of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.

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

    Science.gov (United States)

    Jiménez, Verónica A

    2010-12-27

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

  2. Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis.

    Science.gov (United States)

    Bai, Qifeng; Pérez-Sánchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun

    2014-08-14

    The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive. In this work, molecular dynamics simulations are performed to study the dynamical inactive and active conformational change of β2AR induced by inverse agonist ICI 118,551. Markov state model analysis and free energy calculation are employed to explore the open and close states of the water channel. The simulation results show that inverse agonist ICI 118,551 can induce water channel opening during the conformational transition of β2AR. Markov state model (MSM) analysis proves that the energy contour can be divided into seven states. States S1, S2 and S5, which represent the active conformation of β2AR, show that the water channel is in the closed state, while states S4 and S6, which correspond to the intermediate state conformation of β2AR, indicate the water channel opens gradually. State S7, which represents the inactive structure of β2AR, corresponds to the full open state of the water channel. The opening mechanism of the water channel is involved in the ligand-induced conformational change of β2AR. These results can provide useful information for understanding the opening mechanism of the water channel and will be useful for the rational design of potent inverse agonists of β2AR.

  3. Torsional energy levels of CH3OH+/CH3OD+/CD3OD+ studied by zero-kinetic energy photoelectron spectroscopy and theoretical calculations

    International Nuclear Information System (INIS)

    Dai, Zuyang; Gao, Shuming; Wang, Jia; Mo, Yuxiang

    2014-01-01

    The torsional energy levels of CH 3 OH + , CH 3 OD + , and CD 3 OD + have been determined for the first time using one-photon zero kinetic energy photoelectron spectroscopy. The adiabatic ionization energies for CH 3 OH, CH 3 OD, and CD 3 OD are determined as 10.8396, 10.8455, and 10.8732 eV with uncertainties of 0.0005 eV, respectively. Theoretical calculations have also been performed to obtain the torsional energy levels for the three isotopologues using a one-dimensional model with approximate zero-point energy corrections of the torsional potential energy curves. The calculated values are in good agreement with the experimental data. The barrier height of the torsional potential energy without zero-point energy correction was calculated as 157 cm −1 , which is about half of that of the neutral (340 cm −1 ). The calculations showed that the cation has eclipsed conformation at the energy minimum and staggered one at the saddle point, which is the opposite of what is observed in the neutral molecule. The fundamental C–O stretch vibrational energy level for CD 3 OD + has also been determined. The energy levels for the combinational excitation of the torsional vibration and the fundamental C–O stretch vibration indicate a strong torsion-vibration coupling

  4. Torsional energy levels of CH₃OH⁺/CH₃OD⁺/CD₃OD⁺ studied by zero-kinetic energy photoelectron spectroscopy and theoretical calculations.

    Science.gov (United States)

    Dai, Zuyang; Gao, Shuming; Wang, Jia; Mo, Yuxiang

    2014-10-14

    The torsional energy levels of CH3OH(+), CH3OD(+), and CD3OD(+) have been determined for the first time using one-photon zero kinetic energy photoelectron spectroscopy. The adiabatic ionization energies for CH3OH, CH3OD, and CD3OD are determined as 10.8396, 10.8455, and 10.8732 eV with uncertainties of 0.0005 eV, respectively. Theoretical calculations have also been performed to obtain the torsional energy levels for the three isotopologues using a one-dimensional model with approximate zero-point energy corrections of the torsional potential energy curves. The calculated values are in good agreement with the experimental data. The barrier height of the torsional potential energy without zero-point energy correction was calculated as 157 cm(-1), which is about half of that of the neutral (340 cm(-1)). The calculations showed that the cation has eclipsed conformation at the energy minimum and staggered one at the saddle point, which is the opposite of what is observed in the neutral molecule. The fundamental C-O stretch vibrational energy level for CD3OD(+) has also been determined. The energy levels for the combinational excitation of the torsional vibration and the fundamental C-O stretch vibration indicate a strong torsion-vibration coupling.

  5. mPW1PW91 Calculated Conformational Study of Calix[n]arene (n = 4,5,6): Hydrogen Bond

    International Nuclear Information System (INIS)

    Kim, Kwang Ho; Choe, Jong In

    2009-01-01

    We have performed mPW1PW91 calculations to investigate the conformational characteristics and hydrogen bonds of p-tert-butylcalix[4]arene, p-tert-butylcalix[5]arene, calix[6]arene and p-tertbutylcalix[ 6]arene. The structures of the different conformers of 1-3 were optimized by using mPW1PW91/ 6-31+G(d,p) method. The relative stability of the four conformers of 1 is in the following order: cone (most stable) > partial-cone > 1,2-alternate > 1,3-alternate. The relative stability of the conformers of 2 is in the following order: cone (most stable) > 1,2-alternate > partial-cone > 1,3-alternate. The relative stability of the various conformers of 3 is in the following order: cone (pinched: most stable) > partial-cone > cone (winged) ∼ 1,2-alternate ∼ 1,2,3-alternate > 1,4-alternate > 1,3-alternate > 1,3,5-alternate. The structures of the various conformers of 4 were optimized by using the mPW1PW91/6-31G(d,p) method followed by single point calculation of mPW1PW91/6-31+G(d,p). The relative stability of the conformers of 4 is in the following order: cone (pinched) > 1,2-alternate > cone (winged) > 1,4-alternate ∼ partial-cone > 1,2,3-alternate > 1,3,5-alternate > 1,3-alternate

  6. An automated and efficient conformation search of L-cysteine and L,L-cystine using the scaled hypersphere search method

    Science.gov (United States)

    Kishimoto, Naoki; Waizumi, Hiroki

    2017-10-01

    Stable conformers of L-cysteine and L,L-cystine were explored using an automated and efficient conformational searching method. The Gibbs energies of the stable conformers of L-cysteine and L,L-cystine were calculated with G4 and MP2 methods, respectively, at 450, 298.15, and 150 K. By assuming thermodynamic equilibrium and the barrier energies for the conformational isomerization pathways, the estimated ratios of the stable conformers of L-cysteine were compared with those determined by microwave spectroscopy in a previous study. Equilibrium structures of 1:1 and 2:1 cystine-Fe complexes were also calculated, and the energy of insertion of Fe into the disulfide bond was obtained.

  7. Measurement of conformability and adhesion energy of polymeric ultrathin film to skin model

    Science.gov (United States)

    Sugano, Junki; Fujie, Toshinori; Iwata, Hiroyasu; Iwase, Eiji

    2018-06-01

    We measured the conformability and adhesion energy of a polymeric ultrathin film “nanosheet” with hundreds of nanometer thickness to a skin model with epidermal depressions. To compare the confirmability of the nanosheets with different thicknesses and/or under different attaching conditions, we proposed a measurement method using skin models with the same surface profile and defined the surface strain εS as the quantified value of the conformability. Then, we measured the adhesion energy of the nanosheet at each conformability through a vertical tensile test. Experimental results indicate that the adhesion energy does not depend on the liquid used in wetting the nanosheet before attaching to the skin model and increases monotonously as the surface strain εS increases.

  8. 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.)

  9. 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.)

  10. CONFORMATIONAL SEARCH BY POTENTIAL-ENERGY ANNEALING - ALGORITHM AND APPLICATION TO CYCLOSPORINE-A

    NARCIS (Netherlands)

    VANSCHAIK, RC; VANGUNSTEREN, WF; BERENDSEN, HJC

    A major problem in modelling (biological) macromolecules is the search for low-energy conformations. The complexity of a conformational search problem increases exponentially with the number of degrees of freedom which means that a systematic search can only be performed for very small structures.

  11. Irreversibility and higher-spin conformal field theory

    CERN Document Server

    Anselmi, D

    2000-01-01

    I discuss the idea that quantum irreversibility is a general principle of nature and a related "conformal hypothesis", stating that all fundamental quantum field theories should be renormalization-group (RG) interpolations between ultraviolet and infrared conformal fixed points. In particular, the Newton constant should be viewed as a low-energy effect of the RG scale. This approach leads naturally to consider higher-spin conformal field theories, which are here classified, as candidate high-energy theories. Bosonic conformal tensors have a positive-definite action, equal to the square of a field strength, and a higher-derivative gauge invariance. The central charges c and a are well defined and positive. I calculate their values and study the operator-product structure. Fermionic theories have no gauge invariance 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...

  12. The dependence of the electronic coupling on energy gap and bridge conformation - Towards prediction of the distance dependence of electron transfer reactions

    International Nuclear Information System (INIS)

    Eng, Mattias P.; Albinsson, Bo

    2009-01-01

    The attenuation factor, β, for the distance dependence of electron exchange reactions is a sensitive function of the donor-bridge energy gap and bridge conformation. In this work the electronic coupling for electron and triplet excitation energy transfer has been investigated for five commonly used repeating bridge structures. The investigated bridge structures are OF (oligo fluorene), OP (oligo phenylene), OPE (oligo p-phenyleneethynylene), OPV (oligo phenylenevinylene), and OTP (oligo thiophene). Firstly, the impact of the donor-bridge energy gap was investigated by performing calculations with a variety of donors appended onto bridges that were kept in a planar conformation. This resulted in, to our knowledge, the first presented sets of bridge specific parameters to be inserted into the commonly used McConnell model. Secondly, since at experimental conditions large conformational flexibility is expected, a previously developed model that takes conformational disorder of the bridge into account has been applied to the investigated systems [M.P. Eng, T. Ljungdahl, J. Martensson, B. Albinsson, J. Phys. Chem. B 110 (2006) 6483]. This model is based on Boltzmann averaging and has been shown to describe the temperature dependence of the attenuation factor through OPE-bridges. Together, the parameters describing the donor-bridge energy gap dependence, for planar bridge structures, and the Boltzmann averaging procedure, describing the impact of rotational disorder, have the potential to a priori predict attenuation factors for electron and excitation energy transfer reactions through bridged donor-acceptor systems

  13. Exploring the conformational energy landscape of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Nienhaus, G.U. [Univ. of Illinois, Urbana, IL (United States)]|[Universitaet Ulm (Germany); Mueller, J.D.; McMahon, B.H. [Univ. of Illinois, Urbana, IL (United States)] [and others

    1997-04-01

    Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates.

  14. Extended conformal algebras

    International Nuclear Information System (INIS)

    Goddard, Peter

    1990-01-01

    The algebra of the group of conformal transformations in two dimensions consists of two commuting copies of the Virasoro algebra. In many mathematical and physical contexts, the representations of ν which are relevant satisfy two conditions: they are unitary and they have the ''positive energy'' property that L o is bounded below. In an irreducible unitary representation the central element c takes a fixed real value. In physical contexts, the value of c is a characteristic of a theory. If c < 1, it turns out that the conformal algebra is sufficient to ''solve'' the theory, in the sense of relating the calculation of the infinite set of physically interesting quantities to a finite subset which can be handled in principle. For c ≥ 1, this is no longer the case for the algebra alone and one needs some sort of extended conformal algebra, such as the superconformal algebra. It is these algebras that this paper aims at addressing. (author)

  15. Spectra and structure of silicon containing compounds. XXXII. Raman and infrared spectra, conformational stability, vibrational assignment and ab initio calculations of n-propylsilane-d0 and Si-d3.

    Science.gov (United States)

    Durig, James R; Pan, Chunhua; Guirgis, Gamil A

    2003-03-15

    The infrared (3100-40 cm(-1)) and Raman (3100-20 cm(-1)) spectra of gaseous and solid n-propylsilane, CH(3)CH(2)CH(2)SiH(3) and the Si-d(3) isotopomer, CH(3)CH(2)CH(2)SiD(3), have been recorded. Additionally, the Raman spectra of the liquids have been recorded and qualitative depolarization values obtained. Both the anti and gauche conformers have been identified in the fluid phases but only the anti conformer remains in the solid. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of n-propylsilane dissolved in liquid krypton have been recorded and the enthalpy difference has been determined to be 220+/-22 cm(-1) (2.63+/-0.26 kJ mol(-1)) with the anti conformer the more stable form. A similar value of 234+/-23 cm(-1) (2.80+/-0.28 kJ mol(-1)) was obtained for deltaH for the Si-d(3) isotopomer. At ambient temperature it is estimated that there is 30+/-2% of the gauche conformer present. The potential function governing the conformation interchange has been estimated from the far infrared spectral data, the enthalpy difference, and the dihedral angle of the gauche conformer, which is compared to the one predicted from ab initio MP2/6-31G(d) calculations. The barriers to conformational interchange are: 942, 970 and 716 cm(-1) for the anti to gauche, gauche to gauche, and gauche to anti conformers, respectively. Relatively complete vibrational assignments are proposed for both the n-propylsilane-d(0) and Si-d(3) molecules based on the relative infrared and Raman spectral intensities, infrared band contours, depolarization ratios, and normal coordinate calculations. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities and depolarization ratios, and energy differences have been obtained for the anti and gauche conformers from ab initio MP2/6-31G(d) calculations. Structural parameters and energy differences have also been obtained utilizing the larger 6-311 + G(d,p) and 6-311 + G(2

  16. Spectra and structure of silicon containing compounds. XXXII. Raman and infrared spectra, conformational stability, vibrational assignment and ab initio calculations of n-propylsilane-d 0 and Si-d 3

    Science.gov (United States)

    Durig, James R.; Pan, Chunhua; Guirgis, Gamil A.

    2003-03-01

    The infrared (3100-40 cm -1) and Raman (3100-20 cm -1) spectra of gaseous and solid n-propylsilane, CH 3CH 2CH 2SiH 3 and the Si-d 3 isotopomer, CH 3CH 2CH 2SiD 3, have been recorded. Additionally, the Raman spectra of the liquids have been recorded and qualitative depolarization values obtained. Both the anti and gauche conformers have been identified in the fluid phases but only the anti conformer remains in the solid. Variable temperature (-105 to -150 °C) studies of the infrared spectra of n-propylsilane dissolved in liquid krypton have been recorded and the enthalpy difference has been determined to be 220±22 cm -1 (2.63±0.26 kJ mol -1) with the anti conformer the more stable form. A similar value of 234±23 cm -1 (2.80±0.28 kJ mol -1) was obtained for Δ H for the Si-d 3 isotopomer. At ambient temperature it is estimated that there is 30±2% of the gauche conformer present. The potential function governing the conformation interchange has been estimated from the far infrared spectral data, the enthalpy difference, and the dihedral angle of the gauche conformer, which is compared to the one predicted from ab initio MP2/6-31G(d) calculations. The barriers to conformational interchange are: 942, 970 and 716 cm -1 for the anti to gauche, gauche to gauche, and gauche to anti conformers, respectively. Relatively complete vibrational assignments are proposed for both the n-propylsilane-d 0 and Si-d 3 molecules based on the relative infrared and Raman spectral intensities, infrared band contours, depolarization ratios, and normal coordinate calculations. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities and depolarization ratios, and energy differences have been obtained for the anti and gauche conformers from ab initio MP2/6-31G(d) calculations. Structural parameters and energy differences have also been obtained utilizing the larger 6-311+G(d,p) and 6-311+G(2d,2p) basis sets. From the isolated

  17. Conformal symmetry in two-dimensional space: recursion representation of conformal block

    International Nuclear Information System (INIS)

    Zamolodchikov, A.B.

    1988-01-01

    The four-point conformal block plays an important part in the analysis of the conformally invariant operator algebra in two-dimensional space. The behavior of the conformal block is calculated in the present paper in the limit in which the dimension Δ of the intermediate operator tends to infinity. This makes it possible to construct a recursion relation for this function that connects the conformal block at arbitrary Δ to the blocks corresponding to the dimensions of the zero vectors in the degenerate representations of the Virasoro algebra. The relation is convenient for calculating the expansion of the conformal block in powers of the uniformizing parameters q = i π tau

  18. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    Science.gov (United States)

    Fischer, Marcus; Coleman, Ryan G.; Fraser, James S.; Shoichet, Brian K.

    2014-07-01

    Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.

  19. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    Science.gov (United States)

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-17

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

  1. Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

    Science.gov (United States)

    Hudson, Brian D.; George, Ashley R.; Ford, Martyn G.; Livingstone, David J.

    1992-04-01

    Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

  2. The logarithmic conformal field theories

    International Nuclear Information System (INIS)

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

    1997-01-01

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

  3. Conformational restrictions in ligand binding to the human intestinal di-/tripeptide transporter

    DEFF Research Database (Denmark)

    Våbenø, Jon; Nielsen, Carsten Uhd; Steffansen, Bente

    2005-01-01

    The aim of the present study was to develop a computational method aiding the design of dipeptidomimetic pro-moieties targeting the human intestinal di-/tripeptide transporter hPEPT1. First, the conformation in which substrates bind to hPEPT1 (the bioactive conformation) was identified...... to change the peptide backbone conformation (DeltaE(bbone)) from the global energy minimum conformation to the identified bioactive conformation was calculated for 20 hPEPT1 targeted model prodrugs with known K(i) values. Quantitatively, an inverse linear relationship (r(2)=0.81, q(2)=0.80) was obtained...

  4. Fluorescein isothiocyanate: Molecular characterization by theoretical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Casanovas, Jordi [Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c/Jaume II No 69, Lleida E-25001 (Spain); Jacquemin, Denis [Laboratoire de Chimie Theorique Appliquee, Facultes Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur (Belgium)], E-mail: denis.jacquemin@fundp.ac.be; Perpete, Eric A. [Laboratoire de Chimie Theorique Appliquee, Facultes Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur (Belgium); Aleman, Carlos [Departament d' Enginyeria Quimica, E. T. S. d' Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E-08028 (Spain)], E-mail: carlos.aleman@upc.edu

    2008-12-10

    Quantum mechanical calculations have been used to investigate the conformation, molecular geometry, basicity and spectroscopic properties of fluorescein isothiocyanate in both the gas-phase and aqueous solution. Specifically, calculations have been performed considering the neutral, monoanionic and dianionic forms of this important fluorescent compound. Results reveal that for the neutral form multiple conformational states are possible, all them with significant contributions, and the stability of the different conformers is similar in the gas-phase and aqueous solution. Calculation of the excitation energies revealed that spectroscopic properties are very sensitive to the relaxation effect in solution. A good agreement has been reached obtained between the experimental and theoretical values derived from time-dependent density functional theory methods for the neutral form, whereas for charged species the calculations fail to accurately reproduce the measured trends.

  5. 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.

  6. Conformational Control of Energy Transfer: A Mechanism for Biocompatible Nanocrystal-Based Sensors

    OpenAIRE

    Kay, Euan R.; Lee, Jungmin; Nocera, Daniel; Bawendi, Moungi G.

    2012-01-01

    Fold-up fluorophore: A new paradigm for designing self-referencing fluorescent nanosensors is demonstrated by interfacing a pH-triggered molecular conformational switch with quantum dots. Analytedependent, large-amplitude conformational motion controls the distance between the nanocrystal energy donor and an organic FRET acceptor. The result is a fluorescence signal capable of reporting pH values from individual endosomes in living cells.

  7. Millimeter and Submillimeter Wave Spectroscopy of Higher Energy Conformers of 1,2-PROPANEDIOL

    Science.gov (United States)

    Zakharenko, Olena; Bossa, Jean-Baptiste; Lewen, Frank; Schlemmer, Stephan; Müller, Holger S. P.

    2017-06-01

    We have performed a study of the millimeter/submillimeter wave spectrum of four higher energy conformers of 1,2-propanediol (continuation of the previous study on the three lowest energy conformers. The present analysis of rotational transitions carried out in the frequency range 38 - 400 GHz represents a significant extension of previous microwave work. The new data were combined with previously-measured microwave transitions and fitted using a Watson's S-reduced Hamiltonian. The final fits were within experimental accuracy, and included spectroscopic parameters up to sixth order of angular momentum, for the ground states of the four higher energy conformers following previously studied ones: g'Ga, gG'g', aGg' and g'Gg. The present analysis provides reliable frequency predictions for astrophysical detection of 1,2-propanediol by radio telescope arrays at millimeter wavelengths. J.-B. Bossa, M.H. Ordu, H.S.P. Müller, F. Lewen, S. Schlemmer, A&A 570 (2014) A12)

  8. Conformational Stability, Structural Parameters And Vibrational Assignments of Allantoin

    International Nuclear Information System (INIS)

    Haman, S.

    2008-01-01

    Allantoin 2,5-Dioxo-4-imidazolinyl) urea , the diureide of glyoxylic acid, is a crystallisable oxidation product of uric acid found in allantoic and amniotic fluids, in fetal urine and in many plants. It is a healing, moisturizing, soothing and anti-irritating, keratolytic and non-toxic agent useful in dermatological, cosmetic and veterinary preparation. The optimized geometries and energies of the low-energy conformers of allantoin have been calculated using density functional theory (Daft) method. The calculations were performed with Beck's nonlocal three-parameter hybrid functional in combination with the Lee, Yang, and Parr correlation functional (By-play) using the 6-311++G(d,p) basis set. We calculated the infrared frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The B3LYP/6-311+G(d,p) harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported

  9. 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.

  10. Total energy calculations from self-energy models

    International Nuclear Information System (INIS)

    Sanchez-Friera, P.

    2001-06-01

    Density-functional theory is a powerful method to calculate total energies of large systems of interacting electrons. The usefulness of this method, however, is limited by the fact that an approximation is required for the exchange-correlation energy. Currently used approximations (LDA and GGA) are not sufficiently accurate in many physical problems, as for instance the study of chemical reactions. It has been shown that exchange-correlation effects can be accurately described via the self-energy operator in the context of many-body perturbation theory. This is, however, a computationally very demanding approach. In this thesis a new scheme for calculating total energies is proposed, which combines elements from many-body perturbation theory and density-functional theory. The exchange-correlation energy functional is built from a simplified model of the self-energy, that nevertheless retains the main features of the exact operator. The model is built in such way that the computational effort is not significantly increased with respect to that required in a typical density-functional theory calculation. (author)

  11. Logarithmic conformal field theory through nilpotent conformal dimensions

    International Nuclear Information System (INIS)

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

    2001-01-01

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

  12. 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

  13. 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

  14. Spontaneous Broken Local Conformal Symmetry and Dark Energy Candidate

    International Nuclear Information System (INIS)

    Liu, Lu-Xin

    2013-01-01

    The local conformal symmetry is spontaneously broken down to the Local Lorentz invariance symmetry through the approach of nonlinear realization. The resulting effective Lagrangian, in the unitary gauge, describes a cosmological vector field non-minimally coupling to the gravitational field. As a result of the Higgs mechanism, the vector field absorbs the dilaton and becomes massive, but with an independent energy scale. The Proca type vector field can be modelled as dark energy candidate. The possibility that it further triggers Lorentz symmetry violation is also pointed out

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

    Science.gov (United States)

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

    2015-01-19

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

  16. Theoretical and Spectroscopic investigations of conformations, rotational barriers and scaled vibrations of 2,3-dimethyl hexane

    Directory of Open Access Journals (Sweden)

    Aziz Aboulmouhajir

    2017-01-01

    Full Text Available The 2,3-dimethyl hexane conformational isomerism has been investigated in detail, based on HF, Post-HF and DFT calculations at different basis set. The effect of size of basis, ZPE, thermal contributions, electronic correlation and optimization methods on the conformational stability was discussed. The rotational barriers from the most stable conformer to the lowest energy secondary conformers and their correspondent inversion barriers at both HF and MP2 methods using 6-31G* basis set have also been approached. A normal mode calculation of the most and less-stable conformers using a scaled ab initio force field in terms of non-redundant local symmetry coordinates have been made to elucidate the conformational dependence of the vibrational spectra.

  17. Conformal and Nearly Conformal Theories at Large N

    Science.gov (United States)

    Tarnoplskiy, Grigory M.

    In this thesis we present new results in conformal and nearly conformal field theories in various dimensions. In chapter two, we study different properties of the conformal Quantum Electrodynamics (QED) in continuous dimension d. At first we study conformal QED using large Nf methods, where Nf is the number of massless fermions. We compute its sphere free energy as a function of d, ignoring the terms of order 1/Nf and higher. For finite Nf we use the epsilon-expansion. Next we use a large Nf diagrammatic approach to calculate the leading corrections to CT, the coefficient of the two-point function of the stress-energy tensor, and CJ, the coefficient of the two-point function of the global symmetry current. We present explicit formulae as a function of d and check them versus the expectations in 2 and 4 - epsilon dimensions. In chapter three, we discuss vacuum stability in 1 + 1 dimensional conformal field theories with external background fields. We show that the vacuum decay rate is given by a non-local two-form. This two-form is a boundary term that must be added to the effective in/out Lagrangian. The two-form is expressed in terms of a Riemann-Hilbert decomposition for background gauge fields, and is given by its novel "functional'' version in the gravitational case. In chapter four, we explore Tensor models. Such models possess the large N limit dominated by the melon diagrams. The quantum mechanics of a real anti-commuting rank-3 tensor has a large N limit similar to the Sachdev-Ye-Kitaev (SYK) model. We also discuss the quantum mechanics of a complex 3-index anti-commuting tensor and argue that it is equivalent in the large N limit to a version of SYK model with complex fermions. Finally, we discuss models of a commuting tensor in dimension d. We study the spectrum of the large N quantum field theory of bosonic rank-3 tensors using the Schwinger-Dyson equations. We compare some of these results with the 4 - epsilon expansion, finding perfect agreement. We

  18. Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

    Science.gov (United States)

    Beck, Warren F; Bishop, Michael M; Roscioli, Jerome D; Ghosh, Soumen; Frank, Harry A

    2015-04-15

    A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (1(1)Bu(+)) state. After an initial displacement from the Franck-Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The Sx state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S(∗) state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Interplay of charge distribution and conformation in peptides: comparison of theory and experiment.

    Science.gov (United States)

    Makowska, Joanna; Bagińska, Katarzyna; Kasprzykowski, F; Vila, Jorge A; Jagielska, Anna; Liwo, Adam; Chmurzyński, Lech; Scheraga, Harold A

    2005-01-01

    We assessed the correlation between charge distribution and conformation of flexible peptides by comparing the theoretically calculated potentiometric-titration curves of two model peptides, Ac-Lys5-NHMe (a model of poly-L-lysine) and Ac-Lys-Ala11-Lys-Gly2-Tyr-NH2 (P1) in water and methanol, with the experimental curves. The calculation procedure consisted of three steps: (i) global conformational search of the peptide under study using the electrostatically driven Monte Carlo (EDMC) method with the empirical conformational energy program for peptides (ECEPP)/3 force field plus the surface-hydration (SRFOPT) or the generalized Born surface area (GBSA) solvation model as well as a molecular dynamics method with the assisted model building and energy refinement (AMBER)99/GBSA force field; (ii) reevaluation of the energy in the pH range considered by using the modified Poisson-Boltzmann approach and taking into account all possible protonation microstates of each conformation, and (iii) calculation of the average degree of protonation of the peptide at a given pH value by Boltzmann averaging over conformations. For Ac-Lys5-NHMe, the computed titration curve agrees qualitatively with the experimental curve of poly-L-lysine in 95% methanol. The experimental titration curves of peptide P1 in water and methanol indicate a remarkable downshift of the first pK(a) value compared to the values for reference compounds (n-butylamine and phenol, respectively), suggesting the presence of a hydrogen bond between the tyrosine hydroxyl oxygen and the H(epsilon) proton of a protonated lysine side chain. The theoretical titration curves agree well with the experimental curves, if conformations with such hydrogen bonds constitute a significant part of the ensemble; otherwise, the theory predicts too small a downward pH shift. Copyright 2005 Wiley Periodicals, Inc

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  1. Theoretical calculation of enthalpy of formation of multiconformational molecules: 1,2-ethanediol, propanediols, and glycerol

    Science.gov (United States)

    Dorofeeva, Olga V.; Suchkova, Taisiya A.

    2018-04-01

    The gas-phase enthalpies of formation of four molecules with high flexibility, which leads to the existence of a large number of low-energy conformers, were calculated with the G4 method to see whether the lowest energy conformer is sufficient to achieve high accuracy in the computed values. The calculated values were in good agreement with the experiment, whereas adding the correction for conformer distribution makes the agreement worse. The reason for this effect is a large anharmonicity of low-frequency torsional motions, which is ignored in the calculation of ZPVE and thermal enthalpy. It was shown that the approximate correction for anharmonicity estimated using a free rotor model is of very similar magnitude compared with the conformer correction but has the opposite sign, and thus almost fully compensates for it. Therefore, the common practice of adding only the conformer correction is not without problems.

  2. An extension of the counterion condensation theory to conformational changes of flexible polymers

    International Nuclear Information System (INIS)

    Benegas, J.C.; Cesaro, A.

    1988-01-01

    A full report on a statistical model is presented in which an ionic polymer is taken as an aggregate of linear flexible segments (similar to the spring-bead model). This model is thought to represent fairly well some flexible ionic polymers in solution. The model assumes two factorizable energy contributions, one purely conformational the other electrostatic. The first contribution is calculated from distribution function of the end-to-end distances and can be obtained from numerical Monte Carlo calculations of chain conformations. The second contribution is the excess thermodynamic property and is calculated, by using Manning's theory of linear polyelectrolytes, as a function of the degree of ionization and of a number of physical variables. Procedures to evaluate changes in the chain conformation of polysaccharides and polypeptides bearing ionizable charged groups are presented. The results show excellent quantitative agreement of averaged functions and experimental data. They also show that statistical average over the conformational states is not equivalent to the thermodynamic property of the averaged conformation. (author). 37 refs, 17 figs

  3. Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Matei, Iulia; Ionescu, Sorana [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania); Hillebrand, Mihaela, E-mail: mihh@gw-chimie.math.unibuc.ro [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania)

    2011-08-15

    The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10{sup 5} M{sup -1} was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the {alpha}-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: > Fisetin-BSA system was studied by fluorescence spectroscopy. > Binding parameters, association constant and number of sites were estimated. > Binding site of fisetin was identified by competitive experiments. > Conformational changes in HSA and fisetin were evidenced by circular dichroism. > TDDFT calculated CD spectra supported the experimental data.

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

    Science.gov (United States)

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

    2017-10-01

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

  5. IR-IR Conformation Specific Spectroscopy of Na+(Glucose) Adducts

    Science.gov (United States)

    Voss, Jonathan M.; Kregel, Steven J.; Fischer, Kaitlyn C.; Garand, Etienne

    2018-01-01

    We report an IR-IR double resonance study of the structural landscape present in the Na+(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na+(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctive Na+ coordination. [Figure not available: see fulltext.

  6. Conformational determination of [Leu]enkephalin based on theoretical and experimental VA and VCD spectral analyses

    DEFF Research Database (Denmark)

    Abdali, Salim; Jalkanen, Karl J.; Cao, X.

    2004-01-01

    Conformational determination of [Leu]enkephalin in DMSO-d6 is carried out using VA and VCD spectral analyses. Conformational energies, vibrational frequencies and VA and VCD intensities are calculated using DFT at B3LYP/6-31G* level of theory. Comparison between the measured spectra...

  7. 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.

  8. 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.

  9. Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

    Science.gov (United States)

    Baxa, Michael C.; Haddadian, Esmael J.; Jumper, John M.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is TΔSTotal = 1.4 kcal⋅mol−1 per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding (ΩU/ΩN). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (TΔShelix−sheet = 0.5 kcal⋅mol−1), a property not fully reflected in the amide N-H and carbonyl C=O bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR. PMID:25313044

  10. Conformational explosion: Understanding the complexity of short chain para-dialkylbenzene potential energy surfaces

    Science.gov (United States)

    Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

    2018-05-01

    The single-conformation ultraviolet and infrared spectroscopy of three short-chain para-dialkylbenzenes (para-diethylbenzene, para-dipropylbenzene, and para-dibutylbenzene) is reported for the jet-cooled, isolated molecules. The present study builds off previous work on single-chain n-alkylbenzenes, where an anharmonic local mode Hamiltonian method was developed to account for stretch-bend Fermi resonance in the alkyl CH stretch region [D. P. Tabor et al., J. Chem. Phys. 144, 224310 (2016)]. The jet-cooled molecules are interrogated using laser-induced fluorescence (LIF) excitation, fluorescence dip infrared spectroscopy, and dispersed fluorescence. The LIF spectra in the S1 ← S0 origin region show a dramatic increase in the number of resolved transitions with increasing length of the 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" shaped potential energy surface. A combination of electronic frequency shift and alkyl CH stretch infrared spectra is used to generate a consistent set of conformational assignments. Using these experimental techniques in conjunction with computational methods, subsets of origin transitions in the LIF excitation spectrum can be classified into different conformational families. Two conformations are resolved in para-diethylbenzene, seven in para-dipropylbenzene, and about nineteen in para-dibutylbenzene. These chains are largely independent of each other as there are no new single-chain conformations induced by the presence of a second chain. A cursory LIF excitation scan of para-dioctylbenzene shows a broad congested spectrum at frequencies consistent with interactions of alkyl chains with the phenyl π cloud.

  11. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

    Science.gov (United States)

    Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong

    2018-04-10

    Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.

  12. 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.

  13. Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

    International Nuclear Information System (INIS)

    Matei, Iulia; Ionescu, Sorana; Hillebrand, Mihaela

    2011-01-01

    The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10 5 M -1 was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the α-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: → Fisetin-BSA system was studied by fluorescence spectroscopy. → Binding parameters, association constant and number of sites were estimated. → Binding site of fisetin was identified by competitive experiments. → Conformational changes in HSA and fisetin were evidenced by circular dichroism. → TDDFT calculated CD spectra supported the experimental data.

  14. Landfill Gas Energy Benefits Calculator

    Science.gov (United States)

    This page contains the LFG Energy Benefits Calculator to estimate direct, avoided, and total greenhouse gas reductions, as well as environmental and energy benefits, for a landfill gas energy project.

  15. Rotational Spectrum, Conformational Composition, Intramolecular Hydrogen Bonding, and Quantum Chemical Calculations of Mercaptoacetonitrile (HSCH2C≡N), a Compound of Potential Astrochemical Interest.

    Science.gov (United States)

    Møllendal, Harald; Samdal, Svein; Guillemin, Jean-Claude

    2016-03-31

    The microwave spectra of mercaptoacetonitrile (HSCH2C≡N) and one deuterated species (DSCH2C≡N) were investigated in the 7.5-124 GHz spectral interval. The spectra of two conformers denoted SC and AP were assigned. The H-S-C-C chain of atoms is synclinal in SC and anti-periplanar in AP. The ground state of SC is split into two substates separated by a comparatively small energy difference resulting in closely spaced transitions with equal intensities. Several transitions of the parent species of SC deviate from Watson's Hamiltonian. Only slight improvements were obtained using a Hamiltonian that takes coupling between the two substates into account. Deviations from Watson's Hamiltonian were also observed for the parent species of AP. However, the spectrum of the deuterated species, which was investigated only for the SC conformer, fits satisfactorily to Watson's Hamiltonian. Relative intensity measurements found SC to be lower in energy than AP by 3.8(3) kJ/mol. The strength of the intramolecular hydrogen bond between the thiol and cyano groups was estimated to be ∼2.1 kJ/mol. The microwave work was augmented by quantum chemical calculations at CCSD and MP2 levels using basis sets of minimum triple-ζ quality. Mercaptoacetonitrile has astrochemical interest, and the spectra presented herein should be useful for a potential identification of this compound in the interstellar medium. Three different ways of generating mercaptoacetonitrile from compounds already found in the interstellar medium were explored by quantum chemical calculations.

  16. 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.

  17. Calculation of molecular free energies in classical potentials

    International Nuclear Information System (INIS)

    Farhi, Asaf; Singh, Bipin

    2016-01-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations. (paper)

  18. Quantum chemical calculations in the structural analysis of phloretin

    Science.gov (United States)

    Gómez-Zavaglia, Andrea

    2009-07-01

    In this work, a conformational search on the molecule of phloretin [2',4',6'-Trihydroxy-3-(4-hydroxyphenyl)-propiophenone] has been performed. The molecule of phloretin has eight dihedral angles, four of them taking part in the carbon backbone and the other four, related with the orientation of the hydroxyl groups. A systematic search involving a random variation of the dihedral angles has been used to generate input structures for the quantum chemical calculations. Calculations at the DFT(B3LYP)/6-311++G(d,p) level of theory permitted the identification of 58 local minima belonging to the C 1 symmetry point group. The molecular structures of the conformers have been analyzed using hierarchical cluster analysis. This method allowed us to group conformers according to their similarities, and thus, to correlate the conformers' stability with structural parameters. The dendrogram obtained from the hierarchical cluster analysis depicted two main clusters. Cluster I included all the conformers with relative energies lower than 25 kJ mol -1 and cluster II, the remaining conformers. The possibility of forming intramolecular hydrogen bonds resulted the main factor contributing for the stability. Accordingly, all conformers depicting intramolecular H-bonds belong to cluster I. These conformations are clearly favored when the carbon backbone is as planar as possible. The values of the νC dbnd O and νOH vibrational modes were compared among all the conformers of phloretin. The redshifts associated with intramolecular H-bonds were correlated with the H-bonds distances and energies.

  19. Calculation of the effective chemical shielding anisotropy in L-alanyl-L-alanine, conformational and charge dependence study

    Czech Academy of Sciences Publication Activity Database

    Benda, Ladislav; Bouř, Petr; Buděšínský, Miloš; Müller, N.; Sychrovský, Vladimír

    2007-01-01

    Roč. 14, č. 1 (2007), s. 31-31 ISSN 1211-5894. [Discussions in Structural Molecular Biology /6./. 29.03.2007-31.03.2007, Nové Hrady] Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR cross-correlated relaxations * peptide conformation * ab-initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry

  20. Good Practices in Free-energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher

    2013-01-01

    As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

  1. Hydrogen abstraction from n-butanol by the methyl radical: high level ab initio study of abstraction pathways and the importance of low energy rotational conformers.

    Science.gov (United States)

    Katsikadakos, D; Hardalupas, Y; Taylor, A M K P; Hunt, P A

    2012-07-21

    Hydrogen abstraction reactions by the methyl radical from n-butanol have been investigated at the ROCBS-QB3 level of theory. Reaction energies and product geometries for the most stable conformer of n-butanol (ROH) have been computed, the reaction energies order α channel more stable than the β-channel? Why do the two C(γ)-H H-abstraction TS differ in energy? The method and basis set dependence of the TS barriers is investigated. The Boltzmann probability distribution for the n-butanol conformers suggests that low energy conformers are present in approximately equal proportions to the most stable conformer at combustion temperatures where ĊH(3) radicals are present. Thus, the relative significance of the various H-abstraction channels has been assessed for a selection of higher energy conformers (ROH'). Key results include finding that higher energy n-butanol conformers (E(ROH') > E(ROH)) can generate lower energy product radicals, E(ROH') < E(ROH). Moreover, higher energy conformers can also have a globally competitive TS energy for H-abstraction.

  2. Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

    Science.gov (United States)

    Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

    2016-01-01

    Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

  3. The butane condensed matter conformational problem

    NARCIS (Netherlands)

    Weber, A.C.J.; de Lange, C.A.; Meerts, W.L.; Burnell, E.E.

    2010-01-01

    From the dipolar couplings of orientationally ordered n-butane obtained by NMR spectroscopy we have calculated conformer probabilities using the modified Chord (Cd) and Size-and-Shape (CI) models to estimate the conformational dependence of the order matrix. All calculation methods make use of

  4. 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

  5. Tetrazole acetic acid: Tautomers, conformers, and isomerization

    Energy Technology Data Exchange (ETDEWEB)

    Araujo-Andrade, C. [Unidad Académica de Física de la Universidad Autónoma de Zacatecas, Zacatecas (Mexico); Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Reva, I., E-mail: reva@qui.uc.pt; Fausto, R. [Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal)

    2014-02-14

    Monomers of (tetrazol-5-yl)-acetic acid (TAA) were obtained by sublimation of the crystalline compound and the resulting vapors were isolated in cryogenic nitrogen matrices at 13 K. The conformational and tautomeric composition of TAA in the matrix was characterized by infrared spectroscopy and vibrational calculations carried out at the B3LYP/6-311++G(d,p) level. TAA may adopt two tautomeric modifications, 1H- and 2H-, depending on the position of the annular hydrogen atom. Two-dimensional potential energy surfaces (PESs) of TAA were theoretically calculated at the MP2/6-311++G(d,p) level, for each tautomer. Four and six symmetry-unique minima were located on these PESs, for 1H- and 2H-TAA, respectively. The energetics of the detected minima was subsequently refined by calculations at the QCISD level. Two 1H- and three 2H-conformers fall within the 0–8 kJ mol{sup −1} energy range and should be appreciably populated at the sublimation temperature (∼330 K). Observation of only one conformer for each tautomer (1ccc and 2pcc) is explained in terms of calculated barriers to conformational rearrangements. All conformers with the cis O=COH moiety are separated by low barriers (less than 10 kJ mol{sup −1}) and collapse to the most stable 1ccc (1H-) and 2pcc (2H-) forms during deposition of the matrix. On the trans O=COH surfaces, the relative energies are very high (between 12 and 27 kJ mol{sup −1}). The trans forms are not thermally populated at the sublimation conditions and were not detected in matrices. One high-energy form in each tautomer, 1cct (1H-) and 2pct (2H-), was found to differ from the most stable form only by rotation of the OH group and separated from other forms by high barriers. This opened a perspective for their stabilization in a matrix. 1cct and 2pct were generated in the matrices selectively by means of narrow-band near-infrared (NIR) irradiations of the samples at 6920 and 6937 cm{sup −1}, where the first OH stretching overtone

  6. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  7. Conformational preferences of γ-aminobutyric acid in the gas phase and in water

    Science.gov (United States)

    Song, Il Keun; Kang, Young Kee

    2012-09-01

    The conformational study of γ-aminobutyric acid (GABA) has been carried out at the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water. In the gas phase, the folded conformation gG1 with gauche- and gauche+ conformations for the Cβsbnd Cα and Cγsbnd Cβ bonds, respectively, is found to be lowest in energy and enthalpy, which can be ascribed to the favored hyperconjugative n → π* interaction between the lone electron pair of the amine nitrogen atom and the Cdbnd O bond of the carboxylic group and the favored antiparallel dipole-dipole interaction between the Nsbnd H bond and the Cdbnd O bond. In addition, the intramolecular hydrogen bonds between the carboxylic group and the amine Nsbnd H group have contributed to stabilize some low-energy conformers. However, the most preferred conformation is found to be tG1 and more stable by 0.4 kcal/mol in ΔG than the conformer gG1, in which the favored entropic term due to the conformational flexibility and the other favored n → σ*, σ → σ*, and π → σ* interactions seem to play a role. The conformational preferences of the neutral GABA calculated by ΔG's are reasonably consistent with the populations deduced from FT microwave spectroscopy in supersonic jets combined with laser ablation. In water, the two folded conformers Gg and gG of the zwitterionic GABA are dominantly populated, each of which has the population of 47%, and the hydrogen bond between the ammonium Nsbnd H group and the lone electron pair of the Csbnd O- group seems to be crucial in stabilizing these conformers. Our calculated result that the folded conformers preferentially exist in water is consistent with the 1H NMR experiments in D2O.

  8. 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

  9. Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems.

    Science.gov (United States)

    Isaksen, Geir Villy; Andberg, Tor Arne Heim; Åqvist, Johan; Brandsdal, Bjørn Olav

    2015-07-01

    Structural information and activity data has increased rapidly for many protein targets during the last decades. In this paper, we present a high-throughput interface (Qgui) for automated free energy and empirical valence bond (EVB) calculations that use molecular dynamics (MD) simulations for conformational sampling. Applications to ligand binding using both the linear interaction energy (LIE) method and the free energy perturbation (FEP) technique are given using the estrogen receptor (ERα) as a model system. Examples of free energy profiles obtained using the EVB method for the rate-limiting step of the enzymatic reaction catalyzed by trypsin are also shown. In addition, we present calculation of high-precision Arrhenius plots to obtain the thermodynamic activation enthalpy and entropy with Qgui from running a large number of EVB simulations. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. 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.

  11. Searching for dark matter-dark energy interactions: Going beyond the conformal case

    Science.gov (United States)

    van de Bruck, Carsten; Mifsud, Jurgen

    2018-01-01

    We consider several cosmological models which allow for nongravitational direct couplings between dark matter and dark energy. The distinguishing cosmological features of these couplings can be probed by current cosmological observations, thus enabling us to place constraints on these specific interactions which are composed of the conformal and disformal coupling functions. We perform a global analysis in order to independently constrain the conformal, disformal, and mixed interactions between dark matter and dark energy by combining current data from: Planck observations of the cosmic microwave background radiation anisotropies, a combination of measurements of baryon acoustic oscillations, a supernova type Ia sample, a compilation of Hubble parameter measurements estimated from the cosmic chronometers approach, direct measurements of the expansion rate of the Universe today, and a compilation of growth of structure measurements. We find that in these coupled dark-energy models, the influence of the local value of the Hubble constant does not significantly alter the inferred constraints when we consider joint analyses that include all cosmological probes. Moreover, the parameter constraints are remarkably improved with the inclusion of the growth of structure data set measurements. We find no compelling evidence for an interaction within the dark sector of the Universe.

  12. Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights

    International Nuclear Information System (INIS)

    Goerler, Adrian; Ulyanov, Nikolai B.; James, Thomas L.

    2000-01-01

    A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed for several copies of a molecule simultaneously. The calculations are restrained with dipolar relaxation rates derived from measured NOE intensities via complete relaxation matrix analysis. The novel feature of the algorithm is that the weights of individual conformers are determined in every refinement step, by the quadratic programming algorithm, in such a way that the restraint energy is minimized. Its design ensures that the calculated populations of the individual conformers are based only on experimental restraints. Presence of internally inconsistent restraints is the driving force for determination of distinct multiple conformers. The method is applied to various simulated test systems. Conformational calculations on nucleic acids are carried out using generalized helical parameters with the program DNAminiCarlo. From different mixtures of A- and B-DNA, minor fractions as low as 10% could be determined with restrained energy minimization. For B-DNA with three local conformers (C2'-endo, O4'-exo, C3'-endo), the minor O4'-exo conformer could not be reliably determined using NOE data typically measured for DNA. The other two conformers, C2'-endo and C3'-endo, could be reproduced by Metropolis Monte Carlo simulated annealing. The behavior of the algorithm in various situations is analyzed, and a number of refinement protocols are discussed. Prior to application of this algorithm to each experimental system, it is suggested that the presence of internal inconsistencies in experimental data be ascertained. In addition, because the performance of the algorithm depends on the type of conformers involved and experimental data available, it is advisable to carry out test calculations with simulated data modeling each experimental system studied

  13. NMR investigation and theoretical calculations of the effect of solvent on the conformational analysis of 4',7-di-hydroxy-8-prenylflavan

    Directory of Open Access Journals (Sweden)

    Alcântara Antônio Flávio de Carvalho

    2004-01-01

    Full Text Available The NMR conformational study of 4',7-di-hydroxy-8-prenylflavan 1 was carried out in acetone-d6, DMSO-d6 and CDCl3 which enabled the proposition of three conformations, namely 1a, 1b and 1c, differing in the position of the prenyl group. Geometry optimizations performed using AM1 method showed that 1a (deltaHf = -86.2 kcal/mol is as stable as 1b (deltaHf = -85.1 kcal/mol and 1c (deltaHf = -85.4 kcal/mol. When the solvent was included, the calculations showed that the solute-solvent interactions could be explained either in the light of the electronic intermolecular delocalization or the electrostatic character between solute and solvent. Theoretical calculations (HF/6-31G*, deltaFT/BLYP/6-31G*, and deltaFT/B3LYP/6-31G* showed that the combination of these types of interactions present in each solute-solvent system, dependent on the chemical properties of the solvent, lead to different spatial arrangements of the prenyl group, which in turn determined the conformation of 1.

  14. Conformal field theories near a boundary in general dimensions

    International Nuclear Information System (INIS)

    McAvity, D.M.

    1995-01-01

    The implications of restricted conformal invariance under conformal transformations preserving a plane boundary are discussed for general dimensions d. Calculations of the universal function of a conformal invariant ξ which appears in the two-point function of scalar operators in conformally invariant theories with a plane boundary are undertaken to first order in the ε=4-d expansion for the operator φ 2 in φ 4 theory. The form for the associated functions of ξ for the two-point functions for the basic field φ α and the auxiliary field λ in the N→∞ limit of the O(N) non-linear sigma model for any d in the range 2 α φ β and λλ. Using this method the form of the two-point function for the energy-momentum tensor in the conformal O(N) model with a plane boundary is also found. General results for the sum of the contributions of all derivative operators appearing in the operator product expansion, and also in a corresponding boundary operator expansion, to the two-point functions are also derived making essential use of conformal invariance. (orig.)

  15. Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

    Science.gov (United States)

    König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

    2012-10-09

    One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

  16. Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

    Science.gov (United States)

    Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

    2018-05-10

    Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

  17. Big bounce, slow-roll inflation, and dark energy from conformal gravity

    Science.gov (United States)

    Gegenberg, Jack; Rahmati, Shohreh; Seahra, Sanjeev S.

    2017-02-01

    We examine the cosmological sector of a gauge theory of gravity based on the SO(4,2) conformal group of Minkowski space. We allow for conventional matter coupled to the spacetime metric as well as matter coupled to the field that gauges special conformal transformations. An effective vacuum energy appears as an integration constant, and this allows us to recover the late time acceleration of the Universe. Furthermore, gravitational fields sourced by ordinary cosmological matter (i.e. dust and radiation) are significantly weakened in the very early Universe, which has the effect of replacing the big bang with a big bounce. Finally, we find that this bounce is followed by a period of nearly exponential slow roll inflation that can last long enough to explain the large scale homogeneity of the cosmic microwave background.

  18. Simple and effective procedure for conformational search of macromolecules. Application to Met- and Leu-Enkephalin

    Energy Technology Data Exchange (ETDEWEB)

    Meirovitch, H.; Meirovitch, E. (Florida State Univ., Tallahassee, FL (United States)); Michel, A.G. (Institut de Recherches Serrier, Suresnes (France)); Vasquez, M. (Protein Design Lab., Mountain View, CA (United States))

    1994-06-23

    A simple and efficient method for searching the conformational space of macromolecules is presented. With this method an initial set of relatively low-energy structures is generated, and their energies are further minimized with a procedure that enables escaping from local energy minima. Illustrative calculations are described for Met- and Leu-enkephalin. 37 refs., 1 tab.

  19. Study on fusion energy conformity with global environmental issues

    International Nuclear Information System (INIS)

    Kurihara, Kenichi

    1998-01-01

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

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

    Science.gov (United States)

    Sullivan, David C; Lim, Carmay

    2006-08-24

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

  1. Particles and energy fluxes from a conformal field theory perspective

    International Nuclear Information System (INIS)

    Fabbri, A.; Navarro-Salas, J.; Olmo, G.J.

    2004-01-01

    We analyze the creation of particles in two dimensions under the action of conformal transformations. We focus our attention on Mobius transformations and compare the usual approach, based on the Bogoliubov coefficients, with an alternative but equivalent viewpoint based on correlation functions. In the latter approach the absence of particle production under full Mobius transformations is manifest. Moreover, we give examples, using the moving-mirror analogy, to illustrate the close relation between the production of quanta and energy

  2. On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

    Science.gov (United States)

    Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

    Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

  3. 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.

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

    Science.gov (United States)

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

    1997-01-01

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

  5. Danish Sector Guide for Calculation of the Actual Energy Consumption

    DEFF Research Database (Denmark)

    Mortensen, Lone Hedegaard

    2016-01-01

    , the innovation network for sustainable construction, InnoBYG started work on a Danish sector guide for the calculation of actual energy consumption in relation to upgrading of buildings. The focus was to make a common guide for energy calculations that can be used by consultants performing calculations...... consumption compared with the estimated energy demand by calculation. The paper concludes that the result of an energy calculation should not be given as a single figure but rather as a spread between the best and worst case for the assumed conditions. Finally, a brief update on current actions is given...... related to the sector guide for calculation of actual energy consumption. Keywords – Energy calculations, actual energy consumption, energy perfomance...

  6. Theoretical conformational analysis of the tetrasaccharide repeating units of the O-antigenic polysaccharide of Shigella flexneri

    International Nuclear Information System (INIS)

    Lipkind, G.M.; Kochetkov, N.K.

    1986-01-01

    A theoretical conformational analysis has been made of the four tetrasaccharide repeating units of the polysaccharide of Shigella flexneri, serotype Y. The interdependence of the conformation states of the neighboring disaccharide units and the oligosaccharides has been investigated. The distribution of the tetrasaccharides over the conformations in solution obtained by calculating the free energies of the optimum structures is given. It has been shown that a substantial correction of the results relating to oligosaccharide chains is achieved when the entropy factors is taken into account

  7. Averaged electron collision cross sections for thermal mixtures of β-alanine conformers in the gas phase

    Science.gov (United States)

    Fujimoto, Milton M.; de Lima, Erik V. R.; Tennyson, Jonathan

    2017-10-01

    A theoretical study of elastic electron scattering by gas-phase amino acid molecule β-alanine (NH2-CH2-CH2-COOH) is presented. R-matrix calculations are performed for each of the ten lowest-lying, thermally-accessible conformers of β-alanine. Eigenphase sums, resonance features, differential and integral cross sections are computed for each conformer. The positions of the low-energy shape resonance associated with the unoccupied {π }* orbital of the -COOH group are found to vary from 2.5 to 3.3 eV and the resonance widths from 0.2 to 0.5 eV depending on the conformation. The temperature-dependent population ratios are derived, based on temperature-corrected Gibbs free energies. Averaged cross sections for thermal mixtures of the 10 conformers are presented. A comparison with previous results for the α-alanine isomer is also presented.

  8. SU-E-T-632: Preliminary Study On Treating Nose Skin Using Energy and Intensity Modulated Electron Beams with Monte Carlo Based Dose Calculations

    International Nuclear Information System (INIS)

    Jin, L; Eldib, A; Li, J; Price, R; Ma, C

    2015-01-01

    Purpose: Uneven nose surfaces and air cavities underneath and the use of bolus present complexity and dose uncertainty when using a single electron energy beam to plan treatments of nose skin with a pencil beam-based planning system. This work demonstrates more accurate dose calculation and more optimal planning using energy and intensity modulated electron radiotherapy (MERT) delivered with a pMLC. Methods: An in-house developed Monte Carlo (MC)-based dose calculation/optimization planning system was employed for treatment planning. Phase space data (6, 9, 12 and 15 MeV) were used as an input source for MC dose calculations for the linac. To reduce the scatter-caused penumbra, a short SSD (61 cm) was used. Our previous work demonstrates good agreement in percentage depth dose and off-axis dose between calculations and film measurement for various field sizes. A MERT plan was generated for treating the nose skin using a patient geometry and a dose volume histogram (DVH) was obtained. The work also shows the comparison of 2D dose distributions between a clinically used conventional single electron energy plan and the MERT plan. Results: The MERT plan resulted in improved target dose coverage as compared to the conventional plan, which demonstrated a target dose deficit at the field edge. The conventional plan showed higher dose normal tissue irradiation underneath the nose skin while the MERT plan resulted in improved conformity and thus reduces normal tissue dose. Conclusion: This preliminary work illustrates that MC-based MERT planning is a promising technique in treating nose skin, not only providing more accurate dose calculation, but also offering an improved target dose coverage and conformity. In addition, this technique may eliminate the necessity of bolus, which often produces dose delivery uncertainty due to the air gaps that may exist between the bolus and skin

  9. Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Sinha, Sumona, E-mail: sumona.net.09@gmail.com [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Wang, C.-H. [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China); Mukherjee, M. [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India)

    2017-07-01

    Highlights: • Impact of contact contaminations on the energy level alignment and molecular conformation at rubrene/Ag interfaces. • Adventitious contamination layer was acted as a spacer layer between Ag substrate surface and rubrene molecular layer. • Hole injection barrier height and interface dipole at rubrene/Ag interfaces depend on the cleanliness of Ag substrate. • Molecular conformation as well as orientation controlled by the cleanliness of Ag surface. • Resulted different surface morphology of rubrene thin films on unclean and clean Ag substrate. - Abstract: This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation

  10. 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

  11. Guidelines for the analysis of free energy calculations.

    Science.gov (United States)

    Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

    2015-05-01

    Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.

  12. Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

    OpenAIRE

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

    2006-01-01

    Dimethyl sulfite has three conformers of low energy, GG, GT and GG0, which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG0 conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ molK1, respectively, while the barriers associated with the GG0/GT and GT/GG isomerizations are 1.90 and 9.64 kJ molK1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonst...

  13. Conformal field theories and critical phenomena

    International Nuclear Information System (INIS)

    Xu, Bowei

    1993-01-01

    In this article we present a brief review of the conformal symmetry and the two dimensional conformal quantum field theories. As concrete applications of the conformal theories to the critical phenomena in statistical systems, we calculate the value of central charge and the anomalous scale dimensions of the Z 2 symmetric quantum chain with boundary condition. The results are compatible with the prediction of the conformal field theories

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

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

    2013-03-01

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

  16. Bioactive focus in conformational ensembles: a pluralistic approach

    Science.gov (United States)

    Habgood, Matthew

    2017-12-01

    Computational generation of conformational ensembles is key to contemporary drug design. Selecting the members of the ensemble that will approximate the conformation most likely to bind to a desired target (the bioactive conformation) is difficult, given that the potential energy usually used to generate and rank the ensemble is a notoriously poor discriminator between bioactive and non-bioactive conformations. In this study an approach to generating a focused ensemble is proposed in which each conformation is assigned multiple rankings based not just on potential energy but also on solvation energy, hydrophobic or hydrophilic interaction energy, radius of gyration, and on a statistical potential derived from Cambridge Structural Database data. The best ranked structures derived from each system are then assembled into a new ensemble that is shown to be better focused on bioactive conformations. This pluralistic approach is tested on ensembles generated by the Molecular Operating Environment's Low Mode Molecular Dynamics module, and by the Cambridge Crystallographic Data Centre's conformation generator software.

  17. Holography beyond conformal invariance and AdS isometry?

    CERN Document Server

    Barvinsky, A.O.

    2015-01-01

    We suggest that the principle of holographic duality can be extended beyond conformal invariance and AdS isometry. Such an extension is based on a special relation between functional determinants of the operators acting in the bulk and on its boundary, provided that the boundary operator represents the inverse propagators of the theory induced on the boundary by the Dirichlet boundary value problem from the bulk spacetime. This relation holds for operators of general spin-tensor structure on generic manifolds with boundaries irrespective of their background geometry and conformal invariance, and it apparently underlies numerous $O(N^0)$ tests of AdS/CFT correspondence, based on direct calculation of the bulk and boundary partition functions, Casimir energies and conformal anomalies. The generalized holographic duality is discussed within the concept of the "double-trace" deformation of the boundary theory, which is responsible in the case of large $N$ CFT coupled to the tower of higher spin gauge fields for t...

  18. Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations

    DEFF Research Database (Denmark)

    Abdali, Salim; Jensen, Morten Østergaard; Bohr, Henrik

    2003-01-01

    This paper describes a theoretical and experimental study of [Leu]enkephalin conformations with respect to the quantum estates of the atomic structure of the peptide. Results from vibrational absorption measurements and quantum calculations are used to outline a quantum picture and to assign vibr...

  19. Recent advancements in conformal gravity

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  20. Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

    Science.gov (United States)

    Halder, Ritaban; Manna, Rabindra Nath; Chakraborty, Sandipan; Jana, Biman

    2017-06-15

    Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK. In addition to its conventional open state, Escherichia coli apo-ADK adopts conformations that resemble a closed-like intermediate, the "half-open-half-closed" (HOHC) state, and a π-cation interaction can account for the stability of this HOHC state. Energetics and the electronic properties of this π-cation interaction have been explored using QM/MM calculations. Upon rescinding the π-cation interaction, the conformational landscape of the apo-ADK changes completely. The apo-ADK population is shifted completely toward the open state. This π-cation interaction is highly conserved in bacterial ADK; the cationic guanidinium moiety of a conserved ARG interacts with the delocalized π-electron cloud of either PHE or TYR. Interestingly, this study demonstrates the modulation of a principal protein dynamics by a conserved specific π-cation interaction across different organisms.

  1. SU-F-T-81: Treating Nose Skin Using Energy and Intensity Modulated Electron Beams with Monte Carlo Based Dose Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, L; Fan, J; Eldib, A; Price, R; Ma, C [Fox Chase Cancer Center, Philadelphia, PA (United States)

    2016-06-15

    Purpose: Treating nose skin with an electron beam is of a substantial challenge due to uneven nose surfaces and tissue heterogeneity, and consequently could have a great uncertainty of dose accuracy on the target. This work explored the method using Monte Carlo (MC)-based energy and intensity modulated electron radiotherapy (MERT), which would be delivered with a photon MLC in a standard medical linac (Artiste). Methods: The traditional treatment on the nose skin involves the usage of a bolus, often with a single energy electron beam. This work avoided using the bolus, and utilized mixed energies of electron beams. An in-house developed Monte Carlo (MC)-based dose calculation/optimization planning system was employed for treatment planning. Phase space data (6, 9, 12 and 15 MeV) were used as an input source for MC dose calculations for the linac. To reduce the scatter-caused penumbra, a short SSD (61 cm) was used. A clinical case of the nose skin, which was previously treated with a single 9 MeV electron beam, was replanned with the MERT method. The resultant dose distributions were compared with the plan previously clinically used. The dose volume histogram of the MERT plan is calculated to examine the coverage of the planning target volume (PTV) and critical structure doses. Results: The target coverage and conformality in the MERT plan are improved as compared to the conventional plan. The MERT can provide more sufficient target coverage and less normal tissue dose underneath the nose skin. Conclusion: Compared to the conventional treatment technique, using MERT for the nose skin treatment has shown the dosimetric advantages in the PTV coverage and conformality. In addition, this technique eliminates the necessity of the cutout and bolus, which makes the treatment more efficient and accurate.

  2. Internal rotation for predicting conformational population of 1,2-difluorethane and 1,2-dichloroethane

    Energy Technology Data Exchange (ETDEWEB)

    Venâncio, Mateus F. [Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, 31.270-901 Belo Horizonte, MG (Brazil); Dos Santos, Hélio F. [Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330 (Brazil); De Almeida, Wagner B., E-mail: wbdealmeida@gmail.com [Laboratório de Química Computacional (LQC), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense, Campus do Valonguinho, Centro, Niterói, RJ CEP: 24020-141 (Brazil)

    2016-06-15

    Highlights: • Contribution of internal rotation to Gibbs free energy estimated using the quantum pendulum model. • Theoretical prediction of conformational population of 1,2-difluorethane and 1,2-dichloroethane. • The predicted populations are in excellent agreement with experimental gas phase data available. • QPM model account for low vibrational frequency modes effect on thermodynamic calculation. • Caution is needed when the RR–HO approach has to be used in conformational analysis studies. - Abstract: The contribution of internal rotation to the thermal correction of Gibbs free energy (ΔG) is estimated using the quantum pendulum model (QPM) to solve the characteristic Schrödinger equation. The procedure is applied to theoretical prediction of conformational population of 1,2-difluorethane (1,2-DFE) and 1,2-dichloroethane (1,2-DCE) molecules. The predicted population for the anti form was 37% and 75%, for 1,2-DFE and 1,2-DCE respectively, in excellent agreement with experimental gas phase data available, 37 ± 5% and 78 ± 5%. These results provide great support to the use of the QPM model to account for the low vibrational frequency modes effect on the calculation of thermodynamic properties.

  3. Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone.

    Science.gov (United States)

    Dorofeeva, Olga V; Vogt, Natalja; Vogt, Jürgen; Popik, Mikhail V; Rykov, Anatolii N; Vilkov, Lev V

    2007-07-19

    The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.

  4. Conformal symmetry breaking and the energy-momentum tensor in four dimensions

    International Nuclear Information System (INIS)

    Kraus, E.; Sibold, K.

    1993-01-01

    We derive the conformal transformation properties of the energy-momentum tensor for the massless φ 4 -theory in four dimensions. For this purpose the consistency conditions arising from Weyl-transformations are essential. The breaking of Weyl-invariance can be completely absorbed by making the coupling of the elementary theory local and by introducing an external field which couples to the composite operators φ 2 . Only then can one stay in a completely local framework. (orig.)

  5. Radiation from a moving mirror in two dimensional space-time: conformal anomaly

    International Nuclear Information System (INIS)

    Fulling, S.A.; Davies, P.C.W.

    1976-01-01

    The energy-momentum tensor is calculated in the two dimensional quantum theory of a massless scalar field influenced by the motion of a perfectly reflecting boundary (mirror). The simple model system evidently can provide insight into more sophisticated processes, such as particle production in cosmological models and exploding black holes. In spite of the conformally static nature of the problem, the vacuum expectation value of the tensor for an arbitrary mirror trajectory exhibits a non-vanishing radiation flux (which may be readily computed). The expectation value of the instantaneous energy flux is negative when the proper acceleration of the mirror is increasing, but the total energy radiated during a bounded mirror motion is positive. A uniformly accelerating mirror does not radiate; however, the quantization does not coincide with the treatment of that system as a 'static universe'. The calculation of the expectation value requires a regularization procedure of covariant separation of points (in products of field operators) along time-like geodesics; more naive methods do not yield the same answers. A striking example involving two mirrors clarifies the significance of the conformal anomaly. (author)

  6. A pH-induced conformational switch in a tyrosine kinase inhibitor identified by electronic spectroscopy and quantum chemical calculations.

    Science.gov (United States)

    Khattab, Muhammad; Wang, Feng; Clayton, Andrew H A

    2017-11-24

    Tyrosine kinase inhibitors (TKIs) are a major class of drug utilised in the clinic. During transit to their cognate kinases, TKIs will encounter different pH environments that could have a major influence on TKI structure. To address this, we report UV-Vis spectroscopic and computational studies of the TKI, AG1478, as a function of pH. The electronic absorption spectrum of AG1478 shifted by 10 nm (from 342 nm to 332 nm) from acid to neutral pH and split into two peaks (at 334 nm and 345 nm) in highly alkaline conditions. From these transitions, the pKa value was calculated as 5.58 ± 0.01. To compute structures and spectra, time-dependent density functional theory (TD-DFT) calculations were performed along with conductor-like polarizable continuum model (CPCM) to account for implicit solvent effect. On the basis of the theoretical spectra, we could assign the AG1478 experimental spectrum at acidic pH to a mixture of two twisted conformers (71% AG1478 protonated at quinazolyl nitrogen N(1) and 29% AG1478 protonated at quinazolyl nitrogen N(3)) and at neutral pH to the neutral planar conformer. The AG1478 absorption spectrum (pH 13.3) was fitted to a mixture of neutral (70%) and NH-deprotonated species (30%). These studies reveal a pH-induced conformational transition in a TKI.

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

    Science.gov (United States)

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

    2017-11-01

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

  8. Fitting of Hadron Mass Spectra and Contributions to Perturbation Theory of Conformal Quantum Field Theory

    Science.gov (United States)

    Luna Acosta, German Aurelio

    The masses of observed hadrons are fitted according to the kinematic predictions of Conformal Relativity. The hypothesis gives a remarkably good fit. The isospin SU(2) gauge invariant Lagrangian L(,(pi)NN)(x,(lamda)) is used in the calculation of d(sigma)/d(OMEGA) to 2nd-order Feynman graphs for simplified models of (pi)N(--->)(pi)N. The resulting infinite mass sums over the nucleon (Conformal) families are done via the Generalized-Sommerfeld-Watson Transform Theorem. Even though the models are too simple to be realistic, they indicate that if (DELTA)-internal lines were to be included, 2nd-order Feynman graphs may reproduce the experimental data qualitatively. The energy -dependence of the propagator and couplings in Conformal QFT is different from that of ordinary QFT. Suggestions for further work are made in the areas of ultra-violet divergences and OPEC calculations.

  9. Atropisomerism about aryl-Csp(3) bonds: the electronic and steric influence of ortho-substituents on conformational exchange in cannabidiol and linderatin derivatives.

    Science.gov (United States)

    Berber, Hatice; Lameiras, Pedro; Denhez, Clément; Antheaume, Cyril; Clayden, Jonathan

    2014-07-03

    Terpenylation reactions of substituted phenols were used to prepare cannabidiol and linderatin derivatives, and their structure and conformational behavior in solution were investigated by NMR and, for some representative examples, by DFT. VT-NMR spectra and DFT calculations were used to determine the activation energies of the conformational change arising from restricted rotation about the aryl-Csp(3) bond that lead to two unequally populated rotameric epimers. The NBO calculation was applied to explain the electronic stabilization of one conformer over another by donor-acceptor charge transfer interactions. Conformational control arises from a combination of stereoelectronic and steric effects between substituents in close contact with each other on the two rings of the endocyclic epoxide atropisomers. This study represents the first exploration of the stereoelectronic origins of atropisomerism around C(sp(2))-C(sp(3)) single bonds through theoretical calculations.

  10. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

    Science.gov (United States)

    Iida, Shinji; Nakamura, Haruki; Higo, Junichi

    2016-06-15

    We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

  11. Conformational responses to changes in the state of ionization of titrable groups in proteins

    Science.gov (United States)

    Richman, Daniel Eric

    Electrostatic energy links the structural properties of proteins with some of their important biological functions, including catalysis, energy transduction, and binding and recognition. Accurate calculation of electrostatic energy is essential for predicting and for analyzing function from structure. All proteins have many ionizable residues at the protein-water interface. These groups tend to have ionization equilibria (pK a values) shifted slightly relative to their values in water. In contrast, groups buried in the hydrophobic interior usually have highly anomalous p Ka values. These shifts are what structure-based calculations have to reproduce to allow examination of contributions from electrostatics to stability, solubility and interactions of proteins. Electrostatic energies are challenging to calculate accurately because proteins are heterogeneous dielectric materials. Any individual ionizable group can experience very different local environments with different dielectric properties. The studies in this thesis examine the hypothesis that proteins reorganize concomitant with changes in their state of ionization. It appears that the pKa value measured experimentally reflects the average of pKa values experienced in the different electrostatic environments corresponding to different conformational microstates. Current computational models fail to sample conformational reorganization of the backbone correctly. Staphyloccocal nuclease (SNase) was used as a model protein in nuclear magnetic resonance (NMR) spectroscopy studies to characterize the conformational rearrangements of the protein coupled to changes in the ionization state of titrable groups. One set of experiments tests the hypothesis that proton binding to surface Asp and Glu side chains drives local unfolding by stabilizing less-native, more water-solvated conformations in which the side chains have normalized pKa values. Increased backbone flexibility in the ps-ns timescale, hydrogen bond (H

  12. Calculating Free Energies Using Average Force

    Science.gov (United States)

    Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.

  13. Binary cluster collision dynamics and minimum energy conformations

    Energy Technology Data Exchange (ETDEWEB)

    Muñoz, Francisco [Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle (Germany); Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Rogan, José; Valdivia, J.A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Varas, A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Nano-Bio Spectroscopy Group, ETSF Scientific Development Centre, Departamento de Física de Materiales, Universidad del País Vasco UPV/EHU, Av. Tolosa 72, E-20018 San Sebastián (Spain); Kiwi, Miguel, E-mail: m.kiwi.t@gmail.com [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile)

    2013-10-15

    The collision dynamics of one Ag or Cu atom impinging on a Au{sub 12} cluster is investigated by means of DFT molecular dynamics. Our results show that the experimentally confirmed 2D to 3D transition of Au{sub 12}→Au{sub 13} is mostly preserved by the resulting planar Au{sub 12}Ag and Au{sub 12}Cu minimum energy clusters, which is quite remarkable in view of the excess energy, well larger than the 2D–3D potential barrier height. The process is accompanied by a large s−d hybridization and charge transfer from Au to Ag or Cu. The dynamics of the collision process mainly yields fusion of projectile and target, however scattering and cluster fragmentation also occur for large energies and large impact parameters. While Ag projectiles favor fragmentation, Cu favors scattering due to its smaller mass. The projectile size does not play a major role in favoring the fragmentation or scattering channels. By comparing our collision results with those obtained by an unbiased minimum energy search of 4483 Au{sub 12}Ag and 4483 Au{sub 12}Cu configurations obtained phenomenologically, we find that there is an extra bonus: without increase of computer time collisions yield the planar lower energy structures that are not feasible to obtain using semi-classical potentials. In fact, we conclude that phenomenological potentials do not even provide adequate seeds for the search of global energy minima for planar structures. Since the fabrication of nanoclusters is mainly achieved by synthesis or laser ablation, the set of local minima configurations we provide here, and their distribution as a function of energy, are more relevant than the global minimum to analyze experimental results obtained at finite temperatures, and is consistent with the dynamical coexistence of 2D and 3D liquid Au clusters conformations obtained previously.

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

    Science.gov (United States)

    2010-01-01

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

  15. Probing the Conformational Landscape of a Polyether Building Block by Raman Jet Spectroscopy

    Science.gov (United States)

    Bocklitz, Sebastian; Suhm, Martin A.

    2015-06-01

    Polyethylene oxides (Polyethylene glycoles) represent a prominent class of water-soluble polymers. Surprisingly, already 1,2-dimethoxyethane as the simplest representative of this polymer family has an undetermined conformational preference in the gas phase. Here, we address this problem by spontaneous Raman scattering in a supersonic jet. Variation of carrier gas, stagnation pressure, nozzle distance and temperature provides information on the three lowest conformations and their mutual interconversion during collisions in the expansion. The results are compared to quantum chemical calculations of the potential energy landscape and of normal modes.

  16. Employing conformational analysis in the molecular modeling of agrochemicals: insights on QSAR parameters of 2,4-D

    Directory of Open Access Journals (Sweden)

    Matheus Puggina de Freitas

    2013-12-01

    Full Text Available A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D, a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

  17. Diagnosing Chaos Using Four-Point Functions in Two-Dimensional Conformal Field Theory.

    Science.gov (United States)

    Roberts, Daniel A; Stanford, Douglas

    2015-09-25

    We study chaotic dynamics in two-dimensional conformal field theory through out-of-time-order thermal correlators of the form ⟨W(t)VW(t)V⟩. We reproduce holographic calculations similar to those of Shenker and Stanford, by studying the large c Virasoro identity conformal block. The contribution of this block to the above correlation function begins to decrease exponentially after a delay of ~t_{*}-(β/2π)logβ^{2}E_{w}E_{v}, where t_{*} is the fast scrambling time (β/2π)logc and E_{w},E_{v} are the energy scales of the W,V operators.

  18. 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.

  19. Conformal symmetry and string theories

    International Nuclear Information System (INIS)

    Kumar, A.

    1987-01-01

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

  20. On functional representations of the conformal algebra

    Energy Technology Data Exchange (ETDEWEB)

    Rosten, Oliver J.

    2017-07-15

    Starting with conformally covariant correlation functions, a sequence of functional representations of the conformal algebra is constructed. A key step is the introduction of representations which involve an auxiliary functional. It is observed that these functionals are not arbitrary but rather must satisfy a pair of consistency equations corresponding to dilatation and special conformal invariance. In a particular representation, the former corresponds to the canonical form of the exact renormalization group equation specialized to a fixed point whereas the latter is new. This provides a concrete understanding of how conformal invariance is realized as a property of the Wilsonian effective action and the relationship to action-free formulations of conformal field theory. Subsequently, it is argued that the conformal Ward Identities serve to define a particular representation of the energy-momentum tensor. Consistency of this construction implies Polchinski's conditions for improving the energy-momentum tensor of a conformal field theory such that it is traceless. In the Wilsonian approach, the exactly marginal, redundant field which generates lines of physically equivalent fixed points is identified as the trace of the energy-momentum tensor. (orig.)

  1. Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction.

    Science.gov (United States)

    Hao, Xiaohu; Zhang, Guijun; Zhou, Xiaogen

    2018-04-01

    Computing conformations which are essential to associate structural and functional information with gene sequences, is challenging due to the high dimensionality and rugged energy surface of the protein conformational space. Consequently, the dimension of the protein conformational space should be reduced to a proper level, and an effective exploring algorithm should be proposed. In this paper, a plug-in method for guiding exploration in conformational feature space with Lipschitz underestimation (LUE) for ab-initio protein structure prediction is proposed. The conformational space is converted into ultrafast shape recognition (USR) feature space firstly. Based on the USR feature space, the conformational space can be further converted into Underestimation space according to Lipschitz estimation theory for guiding exploration. As a consequence of the use of underestimation model, the tight lower bound estimate information can be used for exploration guidance, the invalid sampling areas can be eliminated in advance, and the number of energy function evaluations can be reduced. The proposed method provides a novel technique to solve the exploring problem of protein conformational space. LUE is applied to differential evolution (DE) algorithm, and metropolis Monte Carlo(MMC) algorithm which is available in the Rosetta; When LUE is applied to DE and MMC, it will be screened by the underestimation method prior to energy calculation and selection. Further, LUE is compared with DE and MMC by testing on 15 small-to-medium structurally diverse proteins. Test results show that near-native protein structures with higher accuracy can be obtained more rapidly and efficiently with the use of LUE. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

    Science.gov (United States)

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

    2006-08-01

    Dimethyl sulfite has three conformers of low energy, GG, GT and GG', which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG' conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ mol -1, respectively, while the barriers associated with the GG'→GT and GT→GG isomerizations are 1.90 and 9.64 kJ mol -1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonstrated that the GG'→GT energy barrier is low enough to allow an extensive conversion of the GG' form into the GT conformer during deposition of the matrices, the extent of the conversion increasing along the series Arconformers could be trapped in both argon and krypton matrices, but, at a given temperature, the amount of GG' form trapped in krypton is considerably smaller than in argon, while the amount of GT form increases in relation to the most stable GG form. In addition, when xenon is used, no bands due to GG' are observed in the as-deposited spectra ( Tsubstrate≥10 K, the minimum substrate temperature accessible to our experimental set up), indicating that when the best relaxant gas is used the GG'→GT conversion during deposition of the matrix is complete even at 10 K. Annealing of the argon and krypton matrices shows that the increase of the temperature of the matrix first promotes the GG'→GT isomerization, and only at higher temperatures the GT→GG conversion starts to occur, in consonance with the relative energy barriers associated with these two processes. The results also indicate that dimethyl sulfite exhibits conformation selective aggregation, with the most stable form, which has the highest dipole moment, aggregating more easily than the remaining experimentally relevant conformers (GT and GG').

  3. Energy mesh optimization for multi-level calculation schemes

    International Nuclear Information System (INIS)

    Mosca, P.; Taofiki, A.; Bellier, P.; Prevost, A.

    2011-01-01

    The industrial calculations of third generation nuclear reactors are based on sophisticated strategies of homogenization and collapsing at different spatial and energetic levels. An important issue to ensure the quality of these calculation models is the choice of the collapsing energy mesh. In this work, we show a new approach to generate optimized energy meshes starting from the SHEM 281-group library. The optimization model is applied on 1D cylindrical cells and consists of finding an energy mesh which minimizes the errors between two successive collision probability calculations. The former is realized over the fine SHEM mesh with Livolant-Jeanpierre self-shielded cross sections and the latter is performed with collapsed cross sections over the energy mesh being optimized. The optimization is done by the particle swarm algorithm implemented in the code AEMC and multigroup flux solutions are obtained from standard APOLLO2 solvers. By this new approach, a set of new optimized meshes which encompass from 10 to 50 groups has been defined for PWR and BWR calculations. This set will allow users to adapt the energy detail of the solution to the complexity of the calculation (assembly, multi-assembly, two-dimensional whole core). Some preliminary verifications, in which the accuracy of the new meshes is measured compared to a direct 281-group calculation, show that the 30-group optimized mesh offers a good compromise between simulation time and accuracy for a standard 17 x 17 UO 2 assembly with and without control rods. (author)

  4. Conformation of the azo bond and its influence on the molecular and crystal structures, IR and Raman spectra, and electron properties of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine - Quantum chemical DFT calculations

    Science.gov (United States)

    Michalski, J.; Bryndal, I.; Lorenc, J.; Hermanowicz, K.; Janczak, J.; Hanuza, J.

    2018-02-01

    The crystal and molecular structures of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine have been determined by X-ray diffraction and quantum chemical DFT calculations. The crystal is monoclinic, space group Cc (No. 9) with Z = 4 with the unit cell parameters: a = 12.083(7), b = 12.881(6), c = 8.134(3) Å and β = 97.09(5)°. The azo-bridge appears in the trans conformation in which C2-N2-N2‧-C1‧ torsion angle takes a value - 178.6(3)°, whereas the dihedral angle between the planes of the phenyl and pyridine rings is 3.5(2)°. The IR and Raman spectra measured in the temperature range 80-350 K and quantum chemical calculations with the use of B3LYP/6-311G(2d,2p) approach confirmed the trans configuration of the azo-bridge as the most stable energetically and allowed determination of the energy other virtual structures. The observed effects were used in the discussion of vibrational dynamics of the studied compound. The energy gap between cis and trans conformers equals to 1.054 eV (0.03873 Hartree). The electron absorption and emission spectra have been measured and analyzed on the basis of DFT calculations. The life time of the excited state is 12 μs and the Stokes shift is close to 5470 cm- 1.

  5. Independent dose calculation of the Tps Iplan in radiotherapy conformed with MLC; Calculo independiente de dosis del TPS Iplan en radioterapia conformada con MLC

    Energy Technology Data Exchange (ETDEWEB)

    Adrada, A.; Tello, Z.; Medina, L.; Garrigo, E.; Venencia, D., E-mail: jorge.alberto.adrada@gmail.com [Instituto Privado de Radioterapia, Obispo Oro 423, X5000BFI Cordoba (Argentina)

    2014-08-15

    The systems utilization of independent dose calculation in three dimensional-Conformal Radiation Therapy (3D-Crt) treatments allows a direct verification of the treatments times. The utilization of these systems allows diminishing the probability of errors occurrence generated by the treatment planning system (Tps), allowing a detailed analysis of the dose to delivering and review of the normalization point (Np) or prescription. The independent dose calculation is realized across the knowledge of dosimetric parameters of the treatment machine and particular characteristics of every individual field. The aim of this work is develops a calculation system of punctual doses for isocentric fields conformed with multi-leaf collimation systems (MLC), where the dose calculation is in conformity with the suggested ones by ICRU Report No. 42, 1987. Calculation software was realized in C ++ under a free platform of programming (Code::Blocks). The system uses files in format Rtp, exported from the Tps to systems of record and verification (Lantis). This file contains detailed information of the dose, Um, position of the MLC sheets and collimators for every field of treatment. The size of equivalent field is obtained from the positions of every sheet; the effective depth of calculation can be introduced from the dosimetric report of the Tps or automatically from the DFS of the field. The 3D coordinates of the isocenter and the Np for the treatment plan must be introduced manually. From this information the system looks the dosimetric parameters and calculates the Um. The calculations were realized in two accelerators a NOVALIS Tx (Varian) with 120 sheets of high definition (hd-MLC) and a PRIMUS Optifocus (Siemens) with 82 sheets. 705 patients were analyzed for a total of 1082, in plans made for both equipment s, the average uncertainty with regard to the calculation of the Tps is-0.43% ± 2.42% in a range between [-7.90 %, 7.50 %]. The major uncertainty was in Np near of the

  6. The effect of tensile stress on the conformational free energy landscape of disulfide bonds.

    Directory of Open Access Journals (Sweden)

    Padmesh Anjukandi

    Full Text Available Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, χ2 and χ'2. Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The χ2 and χ'2 angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two a-carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox S(N2 reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides.

  7. Classification of methods for annual energy harvesting calculations of photovoltaic generators

    International Nuclear Information System (INIS)

    Rus-Casas, C.; Aguilar, J.D.; Rodrigo, P.; Almonacid, F.; Pérez-Higueras, P.J.

    2014-01-01

    Highlights: • The paper presents a novel classification of methods for annual energy harvesting calculation of grid-connected PV systems. • The methods are classified in direct and indirect methods. • Direct methods directly calculate the energy. Indirect methods calculate the energy from the power. • The classification can help the PV professionals in order to choose the most suitable method for each application. - Abstract: Estimating the energy provided by the generators of grid-connected photovoltaic systems is important in order to analyze their economic viability and supervise their operation. The energy harvesting calculation of a photovoltaic generator is not trivial; there are a lot of methods for this calculation. The aim of this paper is to develop a novel classification of methods for annual energy harvesting calculation of a generator of a grid-connected photovoltaic system. The methods are classified in two groups: (1) those that indirectly calculate the energy, i.e. they first calculate the power and from this, they calculate the energy, and (2) those that directly calculate the energy. Furthermore, the indirect methods are grouped in two categories: those that first calculate the I–V curve of the generator and from this, they calculate the power, and those that directly calculate the power. The study has shown that the existing methods differ in simplicity and accuracy, so that the proposed classification is useful in order to choose the most suitable method for each specific application

  8. Noether symmetries, energy-momentum tensors, and conformal invariance in classical field theory

    International Nuclear Information System (INIS)

    Pons, Josep M.

    2011-01-01

    In the framework of classical field theory, we first review the Noether theory of symmetries, with simple rederivations of its essential results, with special emphasis given to the Noether identities for gauge theories. With this baggage on board, we next discuss in detail, for Poincare invariant theories in flat spacetime, the differences between the Belinfante energy-momentum tensor and a family of Hilbert energy-momentum tensors. All these tensors coincide on shell but they split their duties in the following sense: Belinfante's tensor is the one to use in order to obtain the generators of Poincare symmetries and it is a basic ingredient of the generators of other eventual spacetime symmetries which may happen to exist. Instead, Hilbert tensors are the means to test whether a theory contains other spacetime symmetries beyond Poincare. We discuss at length the case of scale and conformal symmetry, of which we give some examples. We show, for Poincare invariant Lagrangians, that the realization of scale invariance selects a unique Hilbert tensor which allows for an easy test as to whether conformal invariance is also realized. Finally we make some basic remarks on metric generally covariant theories and classical field theory in a fixed curved background.

  9. “Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations

    Science.gov (United States)

    Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

    2015-01-01

    Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide-rich protein. In addition, sensitive 15N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. PMID:25676351

  10. Thermodynamic calculation of a district energy cycle

    International Nuclear Information System (INIS)

    Hoehlein, B.; Bauer, A.; Kraut, G.; Scherberich, F.D.

    1975-08-01

    This paper presents a calculation model for a nuclear district energy circuit. Such a circuit means the combination of a steam reforming plant with heat supply from a high-temperature nuclear reactor and a methanation plant with heat production for district heating or electricity production. The model comprises thermodynamic calculations for the endothermic methane reforming reaction as well as the exothermic CO-hydrogenation in adiabatic reactors and allows the optimization of the district energy circuit under consideration. (orig.) [de

  11. Conformation radiotherapy with eccentric multi-leaves, (1)

    International Nuclear Information System (INIS)

    Obata, Yasunori; Sakuma, Sadayuki.

    1986-01-01

    In order to extend the application of the conformation radiotherapy, the eccentric multi-leaves are equipped with the linear accelerator. The information of the position of the collimators and the dose distribution of the eccentric conformation radiotherapy are calculated by the improved algorism of the treatment planning system. In simple cases, the dose distributions for the distant region from the rotational center are measured and compared with the calculated values. Both distributions are well coincided with the error of about 5 % in the high dose region and 10 % in the low dose region. In eccentric conformation radiotherapy, it is difficult to deliver the planned dose to the lesion. The dose increases with the distance of the target area from the rotational center. And the measured value and the calculated value are well coincided with 1 % error. So after getting the dose ratio of the rotational center to the target area, the calculated dose can be delivered to the rotational center. The advantages of the eccentric conformation radiotherapy are a good coincidence of target area and treated area, a partial shielding and a hollow out technique without absorber. The limitation of the movement of the collimator from center is 5 cm at 1 m SCD. (author)

  12. Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

    International Nuclear Information System (INIS)

    Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K; Hajgato, B; Morini, F; Deleuze, M S

    2008-01-01

    The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn-Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn-Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase

  13. 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.

  14. Conformational Entropy as Collective Variable for Proteins.

    Science.gov (United States)

    Palazzesi, Ferruccio; Valsson, Omar; Parrinello, Michele

    2017-10-05

    Many enhanced sampling methods rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate descriptors has proven challenging. Here we suggest that the NMR S 2 order parameter can be used to this effect. We trace the validity of this statement to the suggested relation between S 2 and conformational entropy. Using the S 2 order parameter and a surrogate for the protein enthalpy in conjunction with metadynamics or variationally enhanced sampling, we are able to reversibly fold and unfold a small protein and draw its free energy at a fraction of the time that is needed in unbiased simulations. We also use S 2 in combination with the free energy flooding method to compute the unfolding rate of this peptide. We repeat this calculation at different temperatures to obtain the unfolding activation energy.

  15. Crystal structures and conformers of CyMe4-BTBP

    Directory of Open Access Journals (Sweden)

    Lyczko Krzysztof

    2015-12-01

    Full Text Available The crystal structure of new conformation of the CyMe4-BTBP ligand (ttc has been presented. The ttt conformer of this compound in a form of THF solvate has been also crystallized. The geometries of six possible conformations (ttt, ttc, tct, tcc, ctc and ccc of the CyMe4-BTBP ligand have been modeled in the gas phase and in solutions (MeOH and H2O by DFT calculations using B3LYP/6-31G(d,p method. According to the calculations, in the three different media the conformers with trans orientation of the N atoms in the bipyridyl moiety are the most stable.

  16. Calculation of pole profiles for the design of particle accelerators magnets. Equivalent current and conformal representation methods; Calcul de profils polaires destines a des aimants d'accelerateurs de particules. Methode des courants et methode des transformations conformes

    Energy Technology Data Exchange (ETDEWEB)

    Jaidane, S [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1968-04-01

    These two methods allow the determination of the shape of the poles in magnets, for a given field distribution in the air-gap. First method: The principle of the method consists to create the desired law of field by means of current sheets in which one can adjust the density given in a polynomial form. For the right distribution of these currents, the equipotential corresponding to the magnetic potential of the excitation coils is calculated. The pole profile of the H or C magnet identified with this equipotential line will finally take the place of the distribution of the current sheets used in the calculation. Steel permeability is assumed to be infinite and Foucault current effects are neglected in the case of variable fields. Second method: It consists to find a conformal representation that maps the pole profile plane upon the upper half of another plane where the equipotentials are two half straight lines, and where the field problems are easier to solve. Steel permeability is also considered to be infinite and the coils far from the pole faces. This known method has been applied to be compared with the first one. (author) [French] Ces deux methodes consistent a determiner la forme des pieces polaires d'aimants pour une distribution de champ determinee a l'avance dans l'entrefer. Premiere methode: Le principe de la methode consiste a creer la loi de champ desiree par l'intermediaire de nappes de courant dont on peut ajuster la densite exprimee sous une forme polynominale. Pour une distribution convenable de ces courants, on calcule l'equipotentielle correspondant au potentiel magnetique des bobines d'excitation. Le profil polaire d'un aimant en H ou C identifie a l'equipotentielle se substitue finalement a la repartition des nappes de courant utilisee dans la methode de calcul. La permeabilite de l'acier est supposee infinie et les courants de Foucault sont negliges dans le cas des champs variables. Seconde methode: Elle consiste a trouver une transformation

  17. Conformational analysis of some 4‧-substituted 2-(phenylselanyl)- 2-(methoxy)- acetophenones

    Science.gov (United States)

    Traesel, Henrique J.; Olivato, Paulo R.; Valença, J.; Rodrigues, Daniel N. S.; Zukerman-Schpector, Julio; Colle, Maurizio Dal

    2018-04-01

    A conformational study of some 4‧-substituited 2-(phenylselanyl)-2-(methoxy)-acetophenones (OMe 1, H 2, and Cl 3) was performed using IR carbonyl stretching band analysis supported by NBO and PCM calculations at the B3LYP/6-31 + G (d,p) level for 1-3 and using X-ray diffraction for 1 and 2. The computational results indicated the existence of three stable conformers for the series (c2, c3, and c1 in order of decreasing stability), whose relative abundance changes with solvent permittivity. The experimental trend observed for the components of the triplet carbonyl band in all solvents matches well with computational results and thus allows for their assignment to distinct conformers. The relative population of the c1 conformer increases in more polar solvents, becoming the most stable conformer in the highest permittivity solvent, acetonitrile, as indicated by IR spectra and PCM calculations. These findings are related to the quasi parallel geometry assumed by the Cδ+ = Oδ- and Cδ+-Oδ- dipoles, which favour stronger solvation. NBO analysis shows that the sum of the energies (ΣE) of the relevant orbital interactions stabilizes the c3 conformer of 1-3 slightly, likely due to the minor contribution of the LPO5→σ*C3sbnd Se10 interaction. However, only the c1 conformer is significantly destabilized by the Oδ-(1)CO … Oδ-(5)OMe short contact electrostatic repulsion, which is also responsible for its highest νCO frequency. In addition, the LPO5→ σ*C2sbnd C3 orbital interaction accounts for the lowest νCO frequency of c3 conformer. X-ray single crystal analysis of compounds 1 and 2 indicates that in the solid state they assume the least stable c1 conformation found in the gas phase. Molecules of these compounds are stabilized in the crystal through a series of Csbnd H⋯O and Csbnd H … π intermolecular interactions.

  18. Intramolecular Hydrogen Bonding and Conformational Preferences of Arzanol—An Antioxidant Acylphloroglucinol

    Directory of Open Access Journals (Sweden)

    Liliana Mammino

    2017-08-01

    Full Text Available Arzanol is a naturally-occurring prenylated acylphloroglucinol isolated from Helichrysum italicum and exhibiting anti-oxidant, antibiotic and antiviral activities. The molecule contains an α-pyrone moiety attached to the phloroglucinol moiety through a methylene bridge. The presence of several hydrogen bond donor or acceptor sites makes intramolecular hydrogen bonding patterns the dominant stabilising factor. Conformers with all the possible different hydrogen bonding patterns were calculated at the HF/6-31G(d,p and DFT/B3LYP/6-31+G(d,p levels with fully relaxed geometry in vacuo and in three solvents—chloroform, acetonitrile and water (these levels being chosen to enable comparisons with previous studies on acylphloroglucinols. Calculations in solution were performed with the Polarisable Continuum Model. The results show that the lowest energy conformers have the highest number of stronger intramolecular hydrogen bonds. The influence of intramolecular hydrogen bonding patterns on the other molecular properties is also analysed.

  19. NEXAFS spectroscopy of ionic liquids: experiments versus calculations.

    Science.gov (United States)

    Fogarty, Richard M; Matthews, Richard P; Clough, Matthew T; Ashworth, Claire R; Brandt-Talbot, Agnieszka; Corbett, Paul J; Palgrave, Robert G; Bourne, Richard A; Chamberlain, Thomas W; Vander Hoogerstraete, Tom; Thompson, Paul B J; Hunt, Patricia A; Besley, Nicholas A; Lovelock, Kevin R J

    2017-11-29

    Experimental near edge X-ray absorption fine structure (NEXAFS) spectra are reported for 12 ionic liquids (ILs) encompassing a range of chemical structures for both the sulfur 1s and nitrogen 1s edges and compared with time-dependent density functional theory (TD-DFT) calculations. The energy scales for the experimental data were carefully calibrated against literature data. Gas phase calculations were performed on lone ions, ion pairs and ion pair dimers, with a wide range of ion pair conformers considered. For the first time, it is demonstrated that TD-DFT is a suitable method for simulating NEXAFS spectra of ILs, although the number of ions included in the calculations and their conformations are important considerations. For most of the ILs studied, calculations on lone ions in the gas phase were sufficient to successfully reproduce the experimental NEXAFS spectra. However, for certain ILs - for example, those containing a protic ammonium cation - calculations on ion pairs were required to obtain a good agreement with experimental spectra. Furthermore, significant conformational dependence was observed for the protic ammonium ILs, providing insight into the predominant liquid phase cation-anion interactions. Among the 12 investigated ILs, we find that four have an excited state that is delocalised across both the cation and the anion, which has implications for any process that depends on the excited state, for example, radiolysis. Considering the collective experimental and theoretical data, we recommend that ion pairs should be the minimum number of ions used for the calculation of NEXAFS spectra of ILs.

  20. 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

  1. Calculation of absolute protein-ligand binding free energy using distributed replica sampling.

    Science.gov (United States)

    Rodinger, Tomas; Howell, P Lynne; Pomès, Régis

    2008-10-21

    Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

  2. 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.

  3. 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

  4. Cohesion energy calculations for ternary ionic novel crystals

    International Nuclear Information System (INIS)

    Vazquez P, G.; Cabrera, E.; Mijangos, R.R.; Valdez, E.; Duarte, C.

    2001-01-01

    The present work calculates the value of the link energy of a crystalline ternary structure newly formed by alkali halides. The ternary structure prepared with different concentrations of KCl x KBrRbCl 2 maintains a very good miscibility and stability. The calculation is based on the use of a generalization of the Vegard law (which generally is valid for binary compounds) for calculating the values of the lattice constant and the repulsive m exponent. The value of the lattice parameter given by X-ray diffractometry agrees with the close approximation of the calculated value of the method used. It also compares the value of energy cohesion obtained by the Born expression with more complex approximations. (Author)

  5. THz time domain spectroscopy of biomolecular conformational modes

    International Nuclear Information System (INIS)

    Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

    2002-01-01

    We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

  6. Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

    Science.gov (United States)

    Denning, Elizabeth J; Mackerell, Alexander D

    2011-04-20

    Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into DNA (As-DNA) in bacteria may be possible. To help evaluate this possibility, ab initio quantum mechanical calculations are used to show that arsenodiester and phosphodiester linkages have similar geometric and conformational properties. Based on these results, it is suggested that the As-DNA will have similar conformational properties to phosphorus-based DNA, including the maintenance of base stacking.

  7. 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

  8. Ab initio calculations of the structure and conformations of 2,6-lutidine

    International Nuclear Information System (INIS)

    Porcinai, S.; Foggi, P.

    1997-01-01

    Ab initio molecular orbital calculations at the SCF level have been utilized to determine the structure and the electronic and vibrational properties of 2,6-lutidine (2,6-dimethyl-pyridine) in the ground electronic state. Comparative calculations have been performed on the parent molecule pyridine. Structure predictions of both molecules are in good agreement with experimental data. The most stable rotamer of 2,6-lutidine has C 2v symmetry with one of the C-H bonds of both the methyl groups lying in the plane of the aromatic ring and pointing in the opposite direction with respect to the nitrogen atom. This is the result of the minimization of competing forces deriving from steric hindrance and electronic stabilization. Vibrational frequencies and oscillator strengths of C-H stretching in the fundamental region have been calculated for both pyridine and the most stable rotamer of 2,6-lutidine and compared to IR data obtained in pure liquids. The potential energy profile of the C-H bond in and out of plane has been investigated up to five times the equilibrium distance. The trend of the potential curves confirms that the C-H bond lying in the plane has a higher dissociation energy than that of the in-plane bonds as observed in experiments on vibrational overtones

  9. Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

    International Nuclear Information System (INIS)

    Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima; Guimaraes, Luciana; Vieira Filho, Sidney A.

    2012-01-01

    Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

  10. Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Guimaraes, Luciana [Universidade Federal de Sao Joao Del-Rei (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Vieira Filho, Sidney A., E-mail: bibo@ef.ufop.br [Universidade Federal de Ouro Preto (UFOP), MG (Brazil). Dept. de Farmacia

    2012-07-01

    Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

  11. Assessment of conformity and suitability for use of the energy subsystem of interoperable high-speed lines; Konformitaetsbewertung und EG-Pruefverfahren fuer das Teilsystem Energie

    Energy Technology Data Exchange (ETDEWEB)

    Behrends, D. [Steglitzer Damm, Deutschen Bahn, Berlin (Germany); Brodkorb, A.; Matthes, R. [Siemens AG, Erlangen (Germany)

    2003-05-01

    The directive 96/48/EG governs the conformity assessment of conformity of interoperability constituents and of suitability for use of subsystems of the trans-European high-speed rail system. The assessment of the overhead contact line type SICAT H 1.0 and the energy subsystem of the new high-speed line Belgian boundary-Rotterdam-Hoofddop (HSL Zuid) in the Netherlands establish examples for the application of the technical specification for the energy subsystem. (orig.) [German] Die Richtlinie 96/48/EG regelt die Bewertung der Konformitaet von Komponenten und das EG-Pruefverfahren von Teilsystemen des interoperablen transeuropaeischen Hochgeschwindigkeitsbahnsystems. Beispiele fuer diese beiden Vorgaenge sind die Bewertung der Oberleitungsbauart SICAT H 1.0 und die Pruefung der Energieversorgung der Hochgeschwindigkeitsstrecke belgische Grenze-Rotterdam-Hoofddop (HSL Zuid) in den Niederlanden. (orig.)

  12. Full charge-density calculation of the surface energy of metals

    DEFF Research Database (Denmark)

    Vitos, Levente; Kollár, J..; Skriver, Hans Lomholt

    1994-01-01

    of a spherically symmetrized charge density, while the Coulomb and exchange-correlation contributions are calculated by means of the complete, nonspherically symmetric charge density within nonoverlapping, space-filling Wigner-Seitz cells. The functional is used to assess the convergence and the accuracy......We have calculated the surface energy and the work function of the 4d metals by means of an energy functional based on a self-consistent, spherically symmetric atomic-sphere potential. In this approach the kinetic energy is calculated completely within the atomic-sphere approximation (ASA) by means...... of the linear-muffin-tin-orbitals (LMTO) method and the ASA in surface calculations. We find that the full charge-density functional improves the agreement with recent full-potential LMTO calculations to a level where the average deviation in surface energy over the 4d series is down to 10%....

  13. Spatial and null infinity via advanced and retarded conformal factors

    International Nuclear Information System (INIS)

    Hayward, Sean A.

    2003-01-01

    A new approach to space-time asymptotics is presented, refining Penrose's idea of conformal transformations with infinity represented by the conformal boundary of space-time. It is proposed that the Penrose conformal factor be a product of advanced and retarded conformal factors, which asymptotically relate physical and conformal null coordinates and vanish at future and past null infinity respectively. A refined definition of asymptotic flatness at both spatial and null infinity is given, including that the conformal boundary is locally a light cone, with spatial infinity as the vertex. It is shown how to choose the conformal factors so that this asymptotic light cone is locally a metric light cone. The theory is implemented in the spin-coefficient (or null-tetrad) formalism by a joint transformation of the spin-metric and spin-basis (or metric and tetrad). Asymptotic regularity conditions are proposed, based on the conformal boundary locally being a smoothly embedded metric light cone. These conditions ensure that the Bondi-Sachs energy-flux integrals of ingoing and outgoing gravitational radiation decay at spatial infinity such that the total radiated energy is finite, and that the Bondi-Sachs energy-momentum has a unique limit at spatial infinity, coinciding with the uniquely rendered ADM energy-momentum

  14. FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular conformational analysis of 2,5-di-tert-butyl-hydroquinone

    Science.gov (United States)

    Subramanian, N.; Sundaraganesan, N.; Dereli, Ö.; Türkkan, E.

    2011-12-01

    The purpose of finding conformer among six different possible conformers of 2,5-di-tert-butyl-hydroquinone (DTBHQ), its equilibrium geometry and harmonic wavenumbers were calculated by the B3LYP/6-31G(d,p) method. The infrared and Raman spectra of DTBHQ were recorded in the region 400-4000 cm -1 and 50-3500 cm -1, respectively. In addition, the IR spectra in CCl 4 at various concentrations of DTBHQ are also recorded. The computed vibrational wavenumbers were compared with the IR and Raman experimental data. Computational calculations at B3LYP level with two different basis sets 6-31G(d,p) and 6-311++G(d,p) are also employed in the study of the possible conformer of DTBHQ. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA 4 program. The general agreement between the observed and calculated frequencies was established.

  15. Multicavity SCRF calculation of ion hydration energies

    International Nuclear Information System (INIS)

    Diercksen, B.H.F.; Karelson, M.; Tamm, T.

    1994-01-01

    The hydration energies of the proton, hydroxyl ion, and several inorganic ions were calculated using the multicavity self-consistent reaction field (MCa SCRF) method developed for the quantum-mechanical modeling of rotationally or flexible systems in dielectric media. The ionic complexes H 3 O + (H2O) 4 , OH - (H2O) 4 , NH + 4 (H2O) 4 , and Hal - (H2O) 4 , where Hal = F, Cl, or Br, have been studied. Each complex was divided between five spheres, corresponding to the central ion and four water molecules in their first coordination sphere, respectively. Each cavity was surrounded by a polarizable medium with the dielectric permittivity of water at room temperature (80). The ionic hydration energies of ions were divided into specific and nonspecific parts. After accounting for the cavity-formation energy using scaled particle theory, good agreement between the total calculated and experimental hydration energies was obtained for all ions studied

  16. Virial-statistic method for calculation of atom and molecule energies

    International Nuclear Information System (INIS)

    Borisov, Yu.A.

    1977-01-01

    A virial-statistical method has been applied to the calculation of the atomization energies of the following molecules: Mo(CO) 6 , Cr(CO) 6 , Fe(CO) 5 , MnH(CO) 5 , CoH(CO) 4 , Ni(CO) 4 . The principles of this method are briefly presented. Calculation results are given for the individual contributions to the atomization energies together with the calculated and experimental atomization energies (D). For the Mo(CO) 6 complex Dsub(calc) = 1759 and Dsub(exp) = 1763 kcal/mole. Calculated and experimental combination heat values for carbonyl complexes are presented. These values are shown to be adequately consistent [ru

  17. Calculation of the band gap energy of ionic crystals

    International Nuclear Information System (INIS)

    Aguado, A.; Lopez, J.M.; Alonso, J.A.; Ayuela, A.; Rivas S, J.F.; Berrondo, M.

    1998-01-01

    The band gap of alkali halides, alkaline-earth oxides, Al 2 O 3 and SiO 2 crystals has been calculated using the perturbed-ion model supplemented with some assumptions for the treatment of excited states. The gap is calculated in several ways: as a difference between one-electron energy eigenvalues and as a difference between the total energies of appropriate electronic states of the crystal, both at the HF level and with inclusion of Coulomb correlation effects. The results compare well with experimental band gap energies and with other theoretical calculations, suggesting that the picture of bonding and excitation given by the model can be useful in ionic materials. (Author)

  18. Comments on conformal masses, asymptotic backgrounds and conservation laws

    International Nuclear Information System (INIS)

    Deruelle, Nathalie; Katz, Joseph

    2006-01-01

    The 'conformal mass prescriptions' were used recently to calculate the mass of spacetimes in higher dimensional and higher curvature theories of gravity. These definitions are closely related to Komar integrals for spacetimes that are conformally flat at great distances from the sources. We derive these relations without using the conformal infinity formalism

  19. Determinants of conformal wave operators in four dimensions

    International Nuclear Information System (INIS)

    Blau, S.K.; Visser, M.; Wipf, A.

    1988-01-01

    We consider conformally coupled wave operators in four dimensions. Such operators are associated with conformally coupled massless scalars, massless spin 1/2 particles, and abelian gauge bosons. We explicitly calculate the change in the determinant of these wave operators as a function of conformal deformations of the background metric. This variation is given in terms of a geometrical object, the second Seeley-de Witt coefficient. (orig.)

  20. "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations.

    Science.gov (United States)

    Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

    2015-03-23

    Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20-40 % at 298 K in a disulfide-rich protein. In addition, sensitive (15) N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR "dark matter". Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  1. Low-energy levels calculation for 193Ir

    International Nuclear Information System (INIS)

    Zahn, Guilherme Soares; Zamboni, Cibele Bugno; Genezini, Frederico Antonio; Mesa-Hormaza, Joel; Cruz, Manoel Tiago Freitas da

    2006-01-01

    In this work, a model based on single particle plus pairing residual interaction was used to study the low-lying excited states of the 193 Ir nucleus. In this model, the deformation parameters in equilibrium were obtained by minimizing the total energy calculated by the Strutinsky prescription; the macroscopic contribution to the potential was taken from the Liquid Droplet Model, with the shell and paring corrections used as as microscopic contributions. The nuclear shape was described using the Cassinian ovoids as base figures; the single particle energy spectra and wave functions for protons and neutrons were calculated in a deformed Woods-Saxon potential, where the parameters for neutrons were obtained from the literature and the parameters for protons were adjusted in order to describe the main sequence of angular momentum and parity of the band heads, as well as the proton binding energy of 193 Ir. The residual pairing interaction was calculated using the BCS prescription with Lipkin-Nogami approximation. The results obtained for the first three band heads (the 3/2 + ground state, the 1/2 + excited state at E ∼ 73 keV and the the 11/2 - isomeric state at E ∼ 80 keV) showed a very good agreement, but the model so far greatly overestimated the energy of the next band head, a 7/2 - at E ∼ 299 keV. (author)

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

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  3. Total energy calculations for structural phase transformations

    International Nuclear Information System (INIS)

    Ye, Y.Y.; Chan, C.T.; Ho, K.M.; Harmon, B.N.

    1990-01-01

    The structural integrity and physical properties of crystalline solids are frequently limited or enhanced by the occurrence of phase transformations. Martensitic transformations involve the collective displacement of atoms from one ordered state to another. Modern methods to determine the microscopic electronic changes as the atoms move are now accurate enough to evaluate the very small energy differences involved. Extensive first principles calculations for the prototypical martensitic transformation from body-centered cubic (bcc) to closepacked 9R structure in sodium metal are described. The minimum energy coordinate or configuration path between the bcc and 9R structures is determined as well as paths to other competing close-packed structures. The energy barriers and important anharmonic interactions are identified and general conclusions drawn. The calculational methods used to solve the Schrodinger equation include pseudopotentials, fast Fourier transforms, efficient matrix diagnonalization, and supercells with many atoms

  4. Calculation Tool for Determining the Net Energy Gain

    DEFF Research Database (Denmark)

    Laustsen, Jacob Birck; Svendsen, Svend

    2002-01-01

    is dependent on both the U-values and the g-values. Beyond this it is dependent on the orientation of the windows and the climate and the actual period. This makes it difficult to choose the glazings and windows that are optimal with regard to energy performance in a given case. These facts have aroused a need...... for simple and accurate methods to determine and compare the energy performance of different window products. When choosing windows for new buildings or retrofitting a calculation tool that in a simple way determines the net energy gain from the specific windows in the actual building will ease the selection...... of the best window solution. Such a tool combined with a database with window products can make calculations of the heat loss or energy demand corresponding to the requirements in the new building code easier and more correct. In the paper, methods to determine energy performance data and the net energy gain...

  5. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

    Science.gov (United States)

    Deng, Nanjie; Flynn, William F; Xia, Junchao; Vijayan, R S K; Zhang, Baofeng; He, Peng; Mentes, Ahmet; Gallicchio, Emilio; Levy, Ronald M

    2016-09-01

    We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate

  6. Calculating Casimir energies in renormalizable quantum field theory

    International Nuclear Information System (INIS)

    Milton, Kimball A.

    2003-01-01

    Quantum vacuum energy has been known to have observable consequences since 1948 when Casimir calculated the force of attraction between parallel uncharged plates, a phenomenon confirmed experimentally with ever increasing precision. Casimir himself suggested that a similar attractive self-stress existed for a conducting spherical shell, but Boyer obtained a repulsive stress. Other geometries and higher dimensions have been considered over the years. Local effects, and divergences associated with surfaces and edges were studied by several authors. Quite recently, Graham et al. have reexamined such calculations, using conventional techniques of perturbative quantum field theory to remove divergences, and have suggested that previous self-stress results may be suspect. Here we show that the examples considered in their work are misleading; in particular, it is well known that in two space dimensions a circular boundary has a divergence in the Casimir energy for massless fields, while for general spatial dimension D not equal to an even integer the corresponding Casimir energy arising from massless fields interior and exterior to a hyperspherical shell is finite. It has also long been recognized that the Casimir energy for massive fields is divergent for curved boundaries. These conclusions are reinforced by a calculation of the relevant leading Feynman diagram in D and in three dimensions. There is therefore no doubt of the validity of the conventional finite Casimir calculations

  7. Calculated stacking-fault energies of elemental metals

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1993-01-01

    -sphere approximations. The results are in excellent agreement with recent layer Korringa-Kohn-Rostoker Green's-function calculations where stacking-fault energies for Ni, Cu, Rh, Pd, Ag, Ir, and Au were found by means of the the so-called force theorem. We find that the self-consistent fault energies for all the metals...

  8. Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols.

    Science.gov (United States)

    Lando, David; Stevens, Tim J; Basu, Srinjan; Laue, Ernest D

    2018-01-01

    Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range cis- and trans-chromosomal contacts.

  9. Conformational effects in photoelectron circular dichroism

    Science.gov (United States)

    Turchini, S.

    2017-12-01

    Photoelectron circular dichroism (PECD) is a novel type of spectroscopy, which presents surprising sensitivity to conformational effects in chiral systems. While classical photoelectron spectroscopy mainly responds to conformational effects in terms of energy level shifts, PECD provides a rich and detailed response to tiny changes in electronic and structural properties by means of the intensity dispersion of the circular dichroism as a function of photoelectron kinetic energy. In this work, the basics of PECD will be outlined, emphasizing the role of interference from the l,l+/- 1 outgoing partial wave of the photoelectron in the PECD transition matrix element, which is responsible for the extreme sensitivity to conformational effects. Examples using molecular systems and interfaces will shed light on the powerful application of PECD to classical conformational effects such as group substitution, isomerism, conformer population and clustering. Moreover, the PECD results will be reported in challenging new fields where conformations play a key role, such as vibrational effects, transient chirality and time- resolved experiments. To date, PECD has mostly been based on synchrotron radiation facilities, but it also has a future as a table-top lab experiment by means of multiphoton ionization. An important application of PECD as an analytical tool will be reported. The aim of this review is to illustrate that in PECD, the presence of conformational effects is essential for understanding a wide range of effects from a new perspective, making it different from classical spectroscopy.

  10. 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.

  11. 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)

  12. Poster - 21: Verification of Monitor Unit Calculations for Breast Field-In-Field Three-Dimensional Conformal Radiotherapy Plans

    International Nuclear Information System (INIS)

    Kosztyla, Robert; Pierce, Greg; Ploquin, Nicolas; Roumeliotis, Michael; Schinkel, Colleen

    2016-01-01

    Purpose: To determine the source of systematic monitor unit (MU) calculation discrepancies between RadCalc and Eclipse treatment planning software for three-dimensional conformal radiotherapy field-in-field breast treatments. Methods: Data were reviewed for 28 patients treated with a field-in-field breast technique with MU calculations from RadCalc that were larger than MU calculations from Eclipse for at least one field. The distance of the calculation point from the jaws was measured in each field’s beam’s-eye-view and compared with the percentage difference in MU (%ΔMU) between RadCalc and Eclipse. 10×10, 17×13 and 20×20 cm 2 beam profiles were measured using the Profiler 2 diode array for 6-MV photon beams and compared with profiles calculated with Eclipse and RadCalc using a gamma analysis (3%, 3 mm). Results: The mean %ΔMU was 1.3%±0.3%. There was a statistically-significant correlation between %ΔMU and the distance of the calculation point from the Y jaw (r=−0.43, p<0.001). RadCalc profiles differed from measured profiles, especially near the jaws. The gamma pass rate for 6-MV fields of 17×13 cm 2 field size was 95%±1% for Eclipse-generated profiles and 53%±20% for RadCalc-generated profiles (p=0.01). Conclusions: Calculations using RadCalc for field-in-field breast plans resulted in MUs that were larger than expected from previous clinical experience with wedged plans with calculation points far from the jaws due to the position of the calculation point near the jaws in the beam’s-eye-view of each field.

  13. Poster - 21: Verification of Monitor Unit Calculations for Breast Field-In-Field Three-Dimensional Conformal Radiotherapy Plans

    Energy Technology Data Exchange (ETDEWEB)

    Kosztyla, Robert; Pierce, Greg; Ploquin, Nicolas; Roumeliotis, Michael; Schinkel, Colleen [Tom Baker Cancer Centre, Calgary, AB, Tom Baker Cancer Centre, Tom Baker Cancer Centre, Tom Baker Cancer Centre, Calgary, AB, Tom Baker Cancer Centre, Calgary, AB (Canada)

    2016-08-15

    Purpose: To determine the source of systematic monitor unit (MU) calculation discrepancies between RadCalc and Eclipse treatment planning software for three-dimensional conformal radiotherapy field-in-field breast treatments. Methods: Data were reviewed for 28 patients treated with a field-in-field breast technique with MU calculations from RadCalc that were larger than MU calculations from Eclipse for at least one field. The distance of the calculation point from the jaws was measured in each field’s beam’s-eye-view and compared with the percentage difference in MU (%ΔMU) between RadCalc and Eclipse. 10×10, 17×13 and 20×20 cm{sup 2} beam profiles were measured using the Profiler 2 diode array for 6-MV photon beams and compared with profiles calculated with Eclipse and RadCalc using a gamma analysis (3%, 3 mm). Results: The mean %ΔMU was 1.3%±0.3%. There was a statistically-significant correlation between %ΔMU and the distance of the calculation point from the Y jaw (r=−0.43, p<0.001). RadCalc profiles differed from measured profiles, especially near the jaws. The gamma pass rate for 6-MV fields of 17×13 cm{sup 2} field size was 95%±1% for Eclipse-generated profiles and 53%±20% for RadCalc-generated profiles (p=0.01). Conclusions: Calculations using RadCalc for field-in-field breast plans resulted in MUs that were larger than expected from previous clinical experience with wedged plans with calculation points far from the jaws due to the position of the calculation point near the jaws in the beam’s-eye-view of each field.

  14. Conformal symmetry in two dimensions: An explicit recurrence formula for the conformal partial wave amplitude

    International Nuclear Information System (INIS)

    Zamolodchikov, A.B.

    1984-01-01

    An explicit recurrence relation for the conformal block functions is presented. This relation permits one to evaluate the X-expansion of these functions order-by-order and appropriate for numerical calculations. (orig.)

  15. Monte carlo calculation of energy deposition and ionization yield for high energy protons

    International Nuclear Information System (INIS)

    Wilson, W.E.; McDonald, J.C.; Coyne, J.J.; Paretzke, H.G.

    1985-01-01

    Recent calculations of event size spectra for neutrons use a continuous slowing down approximation model for the energy losses experienced by secondary charged particles (protons and alphas) and thus do not allow for straggling effects. Discrepancies between the calculations and experimental measurements are thought to be, in part, due to the neglect of straggling. A tractable way of including stochastics in radiation transport calculations is via the Monte Carlo method and a number of efforts directed toward simulating positive ion track structure have been initiated employing this technique. Recent results obtained with our updated and extended MOCA code for charged particle track structure are presented here. Major emphasis has been on calculating energy deposition and ionization yield spectra for recoil proton crossers since they are the most prevalent event type at high energies (>99% at 14 MeV) for small volumes. Neutron event-size spectra can be obtained from them by numerical summing and folding techniques. Data for ionization yield spectra are presented for simulated recoil protons up to 20 MeV in sites of diameters 2-1000 nm

  16. Accuracy of pencil-beam redefinition algorithm dose calculations in patient-like cylindrical phantoms for bolus electron conformal therapy.

    Science.gov (United States)

    Carver, Robert L; Hogstrom, Kenneth R; Chu, Connel; Fields, Robert S; Sprunger, Conrad P

    2013-07-01

    The purpose of this study was to document the improved accuracy of the pencil beam redefinition algorithm (PBRA) compared to the pencil beam algorithm (PBA) for bolus electron conformal therapy using cylindrical patient phantoms based on patient computed tomography (CT) scans of retromolar trigone and nose cancer. PBRA and PBA electron dose calculations were compared with measured dose in retromolar trigone and nose phantoms both with and without bolus. For the bolus treatment plans, a radiation oncologist outlined a planning target volume (PTV) on the central axis slice of the CT scan for each phantom. A bolus was designed using the planning.decimal(®) (p.d) software (.decimal, Inc., Sanford, FL) to conform the 90% dose line to the distal surface of the PTV. Dose measurements were taken with thermoluminescent dosimeters placed into predrilled holes. The Pinnacle(3) (Philips Healthcare, Andover, MD) treatment planning system was used to calculate PBA dose distributions. The PBRA dose distributions were calculated with an in-house C++ program. In order to accurately account for the phantom materials a table correlating CT number to relative electron stopping and scattering powers was compiled and used for both PBA and PBRA dose calculations. Accuracy was determined by comparing differences in measured and calculated dose, as well as distance to agreement for each measurement point. The measured doses had an average precision of 0.9%. For the retromolar trigone phantom, the PBRA dose calculations had an average ± 1σ dose difference (calculated - measured) of -0.65% ± 1.62% without the bolus and -0.20% ± 1.54% with the bolus. The PBA dose calculation had an average dose difference of 0.19% ± 3.27% without the bolus and -0.05% ± 3.14% with the bolus. For the nose phantom, the PBRA dose calculations had an average dose difference of 0.50% ± 3.06% without bolus and -0.18% ± 1.22% with the bolus. The PBA dose calculations had an average dose difference of 0.65%

  17. Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

    Science.gov (United States)

    2015-01-01

    Molecular docking is a powerful tool used in drug discovery and structural biology for predicting the structures of ligand–receptor complexes. However, the accuracy of docking calculations can be limited by factors such as the neglect of protein reorganization in the scoring function; as a result, ligand screening can produce a high rate of false positive hits. Although absolute binding free energy methods still have difficulty in accurately rank-ordering binders, we believe that they can be fruitfully employed to distinguish binders from nonbinders and reduce the false positive rate. Here we study a set of ligands that dock favorably to a newly discovered, potentially allosteric site on the flap of HIV-1 protease. Fragment binding to this site stabilizes a closed form of protease, which could be exploited for the design of allosteric inhibitors. Twenty-three top-ranked protein–ligand complexes from AutoDock were subject to the free energy screening using two methods, the recently developed binding energy analysis method (BEDAM) and the standard double decoupling method (DDM). Free energy calculations correctly identified most of the false positives (≥83%) and recovered all the confirmed binders. The results show a gap averaging ≥3.7 kcal/mol, separating the binders and the false positives. We present a formula that decomposes the binding free energy into contributions from the receptor conformational macrostates, which provides insights into the roles of different binding modes. Our binding free energy component analysis further suggests that improving the treatment for the desolvation penalty associated with the unfulfilled polar groups could reduce the rate of false positive hits in docking. The current study demonstrates that the combination of docking with free energy methods can be very useful for more accurate ligand screening against valuable drug targets. PMID:25189630

  18. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A.

    Science.gov (United States)

    Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris

    2016-04-15

    The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.

  19. A novel lattice energy calculation technique for simple inorganic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kaya, Cemal [Department of Chemistry, Faculty of Science, Cumhuriyet University, 58140 Sivas (Turkey); Kaya, Savaş, E-mail: savaskaya@cumhuriyet.edu.tr [Department of Chemistry, Faculty of Science, Cumhuriyet University, 58140 Sivas (Turkey); Banerjee, Priyabrata [Surface Engineering and Tribology Group, CSIR-Central Mechanical Engineering Research Institute, Mahatma Gandhi Avenue, Durgapur 713209 (India)

    2017-01-01

    In this pure theoretical study, a hitherto unexplored equation based on Shannon radii of the ions forming that crystal and chemical hardness of any crystal to calculate the lattice energies of simple inorganic ionic crystals has been presented. To prove the credibility of this equation, the results of the equation have been compared with experimental outcome obtained from Born-Fajans-Haber- cycle which is fundamentally enthalpy-based thermochemical cycle and prevalent theoretical approaches proposed for the calculation of lattice energies of ionic compounds. The results obtained and the comparisons made have demonstrated that the new equation is more useful compared to other theoretical approaches and allows to exceptionally accurate calculation of lattice energies of inorganic ionic crystals without doing any complex calculations.

  20. New method of ionization energy calculation for two-electron ions

    International Nuclear Information System (INIS)

    Ershov, D.K.

    1997-01-01

    A new method for calculation of the ionization energy of two-electron ions is proposed. The method is based on the calculation of the energy of second electron interaction with the field of an one-electron ion the potential of which is well known

  1. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    Science.gov (United States)

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  2. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

    Science.gov (United States)

    Krystek, S; Stouch, T; Novotny, J

    1993-12-05

    An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated

  3. Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

    Science.gov (United States)

    Gunde, R.; Ha, T.-K.; Günthard, H. H.

    1990-08-01

    In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix

  4. Theoretical searches and spectral computations of preferred conformations of various absolute configurations for a cyclodipeptide, cordycedipeptide A from the culture liquid of Cordyceps sinensis

    Science.gov (United States)

    Mang, Chao-Yong; Liu, Cai-Ping; Liu, Guang-Ming; Jiang, Bei; Lan, Hai; Wu, Ke-Chen; Yan, Ya; Li, Hai-Fei; Yang, Ming-Hui; Zhao, Yu

    2015-02-01

    A cyclic dipeptide often has the multiple configurations and the abundant conformations. The density functional theory (DFT) method is used to search the preferred conformation of the most probable configuration for cordycedipeptide A isolated from the culture liquid of Cordyceps sinensis. The time-dependent DFT approach is exploited to describe the profile of electronic circular dichroism (CD). The calculated results show that the most probable configuration is 3S6R7S, whose preferred conformation has a negative optical rotation and a positive lowest energy electronic CD band.

  5. 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

  6. A Python tool to set up relative free energy calculations in GROMACS.

    Science.gov (United States)

    Klimovich, Pavel V; Mobley, David L

    2015-11-01

    Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations.

  7. Calculations of nuclear energies using the energy density formalism

    International Nuclear Information System (INIS)

    Pu, W.W.T.

    1975-01-01

    The energy density formalism (EDF) is used to investigate two problems. In this formalism the energy of the nucleus is expressed as a functional of its density. The nucleus energy is obtained by minimizing the functional with respect to the density. The first problem has to do with the stability of nuclei having shapes of different degrees of central depression (bubble shapes). It is shown that the bubble shapes are energetically favorable only for unrealistically large nuclei. Particularly, the super heavy nucleus that has been suggested (Z = 114, N = 184) prefers a shape with constant central density. These results are in good agreement with earlier calculations using the liquid drop model. The second problem concerns an anomaly detected experimentally in the isotope shift of mercury. The isotope shifts among a long chain of mercury isotopes show a sudden change as the neutron number is reduced. In particular, the experimental result suggests that the effective size of the charge distributions of 183 Hg and 185 Hg are as large as that of 196 Hg. Such sudden changes in other nuclei have been attributed to a sudden onset of permanent quadruple deformation. In the case of mercury there is no experimental evidence for deformed shapes. It was, therefore, suggested that the proton distribution might develop a central depression in the lighter isotopes. The EDF is used to investigate the mercury isotope shift anomaly following the aforementioned suggestion. Specifically, nucleon densities with different degrees of central depression are generated. Energies corresponding to these densities are obtained. To allow for shell effects, nucleon densities are obtained from single-particle wave functions. Calculations are made for a few mercury isotopes, especially for 184 Hg. The results are that in all cases the energy is lower for densities corresponding to a solid spherical shape

  8. Conformal solids and holography

    Science.gov (United States)

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

    2017-12-01

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

  9. Numerical calculation of the tensor of diffusion in the nuclear reactor cells by Monte-Carlo method

    International Nuclear Information System (INIS)

    Gorodkov, S.S.; Kalugin, M.A.

    2009-01-01

    New algorithm based on the sequential application of the RMS path method has been proposed for the diffusion constants calculation. The offered algorithm conforms to the diffusion constants calculation in arbitrary segments of nuclear reactors without detail description of geometry, dependence of cross-sections from energy or neutron scattering anisotropy by kernel medium. The proposed algorithm is used for the diffusion constants calculation in uranium-graphite reactor sells

  10. Conformally symmetric traversable wormholes

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  11. EPP Energy Efficiency Calculation and Influencing Factor Analysis: Cases in China

    Directory of Open Access Journals (Sweden)

    Jingmin Wang

    2015-01-01

    Full Text Available Efficiency power plant (EPP promotes the use of energy efficiency power plant technology and energy efficient equipment, coupled with its low-input, zero pollution, zero emissions, and other advantages, having an important role in the control of energy consumption and energy saving. In order to carry out scientific EPP investment decisions, the level of energy efficiency is an important basis for investment decisions. This paper introduces total factor energy efficiency (TFEE in energy efficiency calculation of EPP, constructs energy efficiency calculation model considering environmental benefits, and takes the micro and macro cases in China for analysis; the results show that the TFEE of both single energy efficiency project and EPP are at a relatively high level (above 0.7, and there is a huge gap between calculation results considering and without considering the environmental benefit. In order to discuss energy efficiency influencing factors, the paper analyzes generalized technological advances variation feature of China typical provinces implementing EPP based on generalized technological advances decomposition model by Malmquist index, finding that the steady growth of M index in these provinces is derived from the management level of implementation of EPP and the large-scale production capacity of formation and management. We hope the models and conclusions could provide some references on EPP energy efficiency calculation and decision.

  12. CNDO/2-SCF and PCILO (MO) calculations on the 1-butene/NA/and (charge-transfer) complex

    Energy Technology Data Exchange (ETDEWEB)

    Lochmann, R; Meiler, W

    1977-01-01

    CNDO/2-SCF and PCILO (MO) calculations on the 1-Butene/Na/sup +/ (charge-transfer) complex involving the olefinic m electrons were made in connection with butene adsorption in zeolites, including the effect of the cation on the conformation of the butene in the zeolite cavity. Calculations were made of rotational energy barriers, preferred cation arrangements with respect to the butene molecule, and charge distributions by both methods. Taking into account systematic errors with the two methods, it is concluded that the PCILO method, which predicts a stabilization of the skew over the cis conformation by the cation, gives closer agreement with experiment. Graph, tables, diagrams, and 19 references.

  13. Wilson loop invariants from WN conformal blocks

    Directory of Open Access Journals (Sweden)

    Oleg Alekseev

    2015-12-01

    Full Text Available Knot and link polynomials are topological invariants calculated from the expectation value of loop operators in topological field theories. In 3D Chern–Simons theory, these invariants can be found from crossing and braiding matrices of four-point conformal blocks of the boundary 2D CFT. We calculate crossing and braiding matrices for WN conformal blocks with one component in the fundamental representation and another component in a rectangular representation of SU(N, which can be used to obtain HOMFLY knot and link invariants for these cases. We also discuss how our approach can be generalized to invariants in higher-representations of WN algebra.

  14. Conformity of LINAC-Based Stereotactic Radiosurgery Using Dynamic Conformal Arcs and Micro-Multileaf Collimator

    International Nuclear Information System (INIS)

    Hazard, Lisa J.; Wang, Brian; Skidmore, Thomas B.; Chern, Shyh-Shi; Salter, Bill J.; Jensen, Randy L.; Shrieve, Dennis C.

    2009-01-01

    Purpose: To assess the conformity of dynamic conformal arc linear accelerator-based stereotactic radiosurgery and to describe a standardized method of isodose surface (IDS) selection. Methods and Materials: In 174 targets, the conformity index (CI) at the prescription IDS used for treatment was calculated as CI = (PIV/PVTV)/(PVTV/TV), where TV is the target volume, PIV (prescription isodose volume) is the total volume encompassed by the prescription IDS, and PVTV is the TV encompassed by the IDS. In addition, a 'standardized' prescription IDS (sIDS) was chosen according to the following criteria: 95% of the TV was encompassed by the PIV and 99% of TV was covered by 95% of the prescription dose. The CIs at the sIDS were also calculated. Results: The median CI at the prescription IDS and sIDS was 1.63 and 1.47, respectively (p < 0.001). In 132 of 174 cases, the volume of normal tissue in the PIV was reduced by the prescription to the sIDS compared with the prescription IDS, in 20 cases it remained unchanged, and in 22 cases it was increased. Conclusion: The CIs obtained with linear accelerator-based stereotactic radiosurgery are comparable to those previously reported for gamma knife stereotactic radiosurgery. Using a uniform method to select the sIDS, adequate target coverage was usually achievable with prescription to an IDS greater than that chosen by the treating physician (prescription IDS), providing sparing of normal tissue. Thus, the sIDS might aid physicians in identifying a prescription IDS that balances coverage and conformity

  15. Calculations of proton-binding thermodynamics in proteins.

    Science.gov (United States)

    Beroza, P; Case, D A

    1998-01-01

    Computational models of proton binding can range from the chemically complex and statistically simple (as in the quantum calculations) to the chemically simple and statistically complex. Much progress has been made in the multiple-site titration problem. Calculations have improved with the inclusion of more flexibility in regard to both the geometry of the proton binding and the larger scale protein motions associated with titration. This article concentrated on the principles of current calculations, but did not attempt to survey their quantitative performance. This is (1) because such comparisons are given in the cited papers and (2) because continued developments in understanding conformational flexibility and interaction energies will be needed to develop robust methods with strong predictive power. Nevertheless, the advances achieved over the past few years should not be underestimated: serious calculations of protonation behavior and its coupling to conformational change can now be confidently pursued against a backdrop of increasing understanding of the strengths and limitations of such models. It is hoped that such theoretical advances will also spur renewed experimental interest in measuring both overall titration curves and individual pKa values or pKa shifts. Exploration of the shapes of individual titration curves (as measured by Hill coefficients and other parameters) would also be useful in assessing the accuracy of computations and in drawing connections to functional behavior.

  16. Experimental verification of stored energy calculations

    International Nuclear Information System (INIS)

    Hann, C.R.; Christensen, J.A.; Lanning, D.D.; Marshall, R.K.; Williford, R.E.

    1975-01-01

    A description is provided of irradiation tests designed to provide data needed to verify existing steady state fuel performance codes. The tests are being conducted in the Halden Reactor, and are designed to provide data pertinent to stored energy calculations over a range of linear heat ratings utilized in contemporary power reactors

  17. 94: Treatment plan optimization for conformal therapy

    International Nuclear Information System (INIS)

    Rosen, I.I.; Lane, R.G.

    1987-01-01

    Computer-controlled conformal radiation therapy techniques can deliver complex treatments utilizing large numbers of beams, gantry angles and beam shapes. Linear programming is well-suited for planning conformal treatments. Given a list of available treatment beams, linear programming calculates the relative weights of the beams such that the objective function is optimized and doses to constraint points are within the prescribed limits. 5 refs.; 3 figs

  18. Transport calculation of medium-energy protons and neutrons by Monte Carlo method

    International Nuclear Information System (INIS)

    Ban, Syuuichi; Hirayama, Hideo; Katoh, Kazuaki.

    1978-09-01

    A Monte Carlo transport code, ARIES, has been developed for protons and neutrons at medium energy (25 -- 500 MeV). Nuclear data provided by R.G. Alsmiller, Jr. were used for the calculation. To simulate the cascade development in the medium, each generation was represented by a single weighted particle and an average number of emitted particles was used as the weight. Neutron fluxes were stored by the collisions density method. The cutoff energy was set to 25 MeV. Neutrons below the cutoff were stored to be used as the source for the low energy neutron transport calculation upon the discrete ordinates method. Then transport calculations were performed for both low energy neutrons (thermal -- 25 MeV) and secondary gamma-rays. Energy spectra of emitted neutrons were calculated and compared with those of published experimental and calculated results. The agreement was good for the incident particles of energy between 100 and 500 MeV. (author)

  19. Numerical calculations near spatial infinity

    International Nuclear Information System (INIS)

    Zenginoglu, Anil

    2007-01-01

    After describing in short some problems and methods regarding the smoothness of null infinity for isolated systems, I present numerical calculations in which both spatial and null infinity can be studied. The reduced conformal field equations based on the conformal Gauss gauge allow us in spherical symmetry to calculate numerically the entire Schwarzschild-Kruskal spacetime in a smooth way including spacelike, null and timelike infinity and the domain close to the singularity

  20. Calculations of energy consumption in ventilation systems

    Energy Technology Data Exchange (ETDEWEB)

    Kreslins, Andris; Ramata, Anna [Riga Technical University (Latvia)], e-mail: kreslins@rbf.rtu.lv, email: Anna.Ramata@rtu.lv

    2011-07-01

    Energy cost is an important economic factor in the food industry production process. With the rising price of energy, a reduction in energy consumption would greatly impact production and the end product. The aim of this study was to develop a methodology for optimizing energy consumption. A comparison between a traditional ventilation system and a mechanical system was carried out; the necessary enthalpy for heating the air supply and thermal energy consumption were calculated and compared for both systems during the heating season, from October to April, using climatological data for Latvia. Results showed that energy savings of 46% to 87% can be achieved by applying the methodology in the design of industrial buildings; in addition, a well-designed ventilation system increases the workers' productivity. This study presented a methodology which can optimize energy consumption in the food industry sector.

  1. Conformational changes in hemoglobin triggered by changing the iron charge

    International Nuclear Information System (INIS)

    Croci, S.; Achterhold, K.; Ortalli, I.; Parak, F. G.

    2008-01-01

    In this work the hemoglobin conformational changes induced by changing the iron charge have been studied and compared with Myoglobin. Moessbauer spectroscopy was used to follow the change of the iron conformation. In order to compare the conformational relaxation of hemoglobin and myoglobin, and to study a possible influence of the quaternary structure, an intermediate metastable state of hemoglobin has been created by low temperature X-ray irradiation of methemoglobin. The irradiation reduces the Fe(III) of the heme groups to Fe(II) Low Spin, where the water is still bound on the sixth coordination. Heating cycles performed at temperatures from 140 K to 200 K allow the molecules to overcome an activation energy barrier and to relax into a stable conformation such as deoxy-hemoglobin or carboxy-hemoglobin, if CO is present. Slightly different structures (conformational substates) reveal themselves as a distribution of energy barriers (ΔG). The distribution of the activation energy, for the decay of the Fe(II) Low Spin intermediate, has been fitted with a Gaussian. For comparison, published myoglobin data were re-analysed in the same way. The average energy value at characteristic temperature is very similar in case of myoglobin and hemoglobin. The larger Gaussian energy distribution for myoglobin with respect to hemoglobin shows that more conformational substates are available. This may be caused by a larger area exposed to water. In hemoglobin, part of the surface of the chains is not water accessible due to the quaternary structure.

  2. Conformation sensitive charge transport in conjugated polymers

    International Nuclear Information System (INIS)

    Mattias Andersson, L.; Hedström, Svante; Persson, Petter

    2013-01-01

    Temperature dependent charge carrier mobility measurements using field effect transistors and density functional theory calculations are combined to show how the conformation dependent frontier orbital delocalization influences the hole- and electron mobilities in a donor-acceptor based polymer. A conformationally sensitive lowest unoccupied molecular orbital results in an electron mobility that decreases with increasing temperature above room temperature, while a conformationally stable highest occupied molecular orbital is consistent with a conventional hole mobility behavior and also proposed to be one of the reasons for why the material works well as a hole transporter in amorphous bulk heterojunction solar cells

  3. Synthesis and conformational analysis of new arylated-diphenylurea derivatives related to sorafenib drug via Suzuki-Miyaura cross-coupling reaction

    Science.gov (United States)

    Al-Masoudi, Najim A.; Essa, Ali Hashem; Alwaaly, Ahmed A. S.; Saeed, Bahjat A.; Langer, Peter

    2017-10-01

    Sorafenib, is a relatively new cytostatic drug approved for the treatment of renal cell and hepatocellular carcinoma. The development of new sorafenib analogues offers the possibility of generating structures of increased potency. To this end, a series of arylated-diphenylurea analogues 17-31 were synthesized via Suzuki-Miyaura coupling reaction, related to sorafenib by treatment of three diarylureas 2-4 having 3-bromo, 4-chloro and 2-iodo groups with various arylboronic acids. Conformational analysis of the new arylated urea analogues has been investigated using MOPAC 2016 of semi empirical PM7 Hamiltonian computational method. Our results showed that all compounds preferred the trans-trans conformations. Compound 17 has been selected to calculate the torsional energy profiles for rotation around the urea bonds and found to be existed predominantly in the trans-trans conformation with only very minimal fluctuation in conformation.

  4. 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.

  5. 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.

  6. 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.

  7. 18 CFR 153.21 - Conformity with requirements.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Conformity with requirements. 153.21 Section 153.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Requirements § 153.21 Conformity with requirements. (a) General Rule. Applications under subparts B and C of...

  8. On C{sub J} and C{sub T} in conformal QED

    Energy Technology Data Exchange (ETDEWEB)

    Giombi, Simone; Tarnopolsky, Grigory [Princeton University, Department of Physics,Jadwin Hall, Washington Road, Princeton NJ 08544 (United States); Klebanov, Igor R. [Princeton University, Department of Physics,Jadwin Hall, Washington Road, Princeton NJ 08544 (United States); Princeton Center for Theoretical Science, Princeton University,Jadwin Hall, Washington Road, Princeton NJ 08544 (United States)

    2016-08-26

    QED with a large number N of massless fermionic degrees of freedom has a conformal phase in a range of space-time dimensions. We use a large N diagrammatic approach to calculate the leading corrections to C{sub T}, the coefficient of the two-point function of the stress-energy tensor, and C{sub J}, the coefficient of the two-point function of the global symmetry current. We present explicit formulae as a function of d and check them versus the expectations in 2 and 4−ϵ dimensions. Using our results in higher even dimensions we find a concise formula for C{sub T} of the conformal Maxwell theory with higher derivative action F{sub μν}(−∇{sup 2}){sup (d/2)−2}F{sup μν}. In d=3, QED has a topological symmetry current, and we calculate the correction to its two-point function coefficient, C{sub J}{sup top}. We also show that some RG flows involving QED in d=3 obey C{sub T}{sup UV}>C{sub T}{sup IR} and discuss possible implications of this inequality for the symmetry breaking at small values of N.

  9. A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space.

    Science.gov (United States)

    Hao, Xiao-Hu; Zhang, Gui-Jun; Zhou, Xiao-Gen; Yu, Xu-Feng

    2016-01-01

    To address the searching problem of protein conformational space in ab-initio protein structure prediction, a novel method using abstract convex underestimation (ACUE) based on the framework of evolutionary algorithm was proposed. Computing such conformations, essential to associate structural and functional information with gene sequences, is challenging due to the high-dimensionality and rugged energy surface of the protein conformational space. As a consequence, the dimension of protein conformational space should be reduced to a proper level. In this paper, the high-dimensionality original conformational space was converted into feature space whose dimension is considerably reduced by feature extraction technique. And, the underestimate space could be constructed according to abstract convex theory. Thus, the entropy effect caused by searching in the high-dimensionality conformational space could be avoided through such conversion. The tight lower bound estimate information was obtained to guide the searching direction, and the invalid searching area in which the global optimal solution is not located could be eliminated in advance. Moreover, instead of expensively calculating the energy of conformations in the original conformational space, the estimate value is employed to judge if the conformation is worth exploring to reduce the evaluation time, thereby making computational cost lower and the searching process more efficient. Additionally, fragment assembly and the Monte Carlo method are combined to generate a series of metastable conformations by sampling in the conformational space. The proposed method provides a novel technique to solve the searching problem of protein conformational space. Twenty small-to-medium structurally diverse proteins were tested, and the proposed ACUE method was compared with It Fix, HEA, Rosetta and the developed method LEDE without underestimate information. Test results show that the ACUE method can more rapidly and more

  10. All unitary ray representations of the conformal group SU(2,2) with positive energy

    International Nuclear Information System (INIS)

    Mack, G.

    1975-12-01

    We find all those unitary irreducible representations of the infinitely - sheeted covering group G tilde of the conformal group SU(2,2)/Z 4 which have positive energy P 0 >= O. They are all finite component field representations and are labelled by dimension d and a finite dimensional irreducible representation (j 1 , j 2 ) of the Lorentz group SL(2C). They all decompose into a finite number of unitary irreducible representations of the Poincare subgroup with dilations. (orig.) [de

  11. Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

    Science.gov (United States)

    Nagata, Yuki

    2010-02-01

    A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

  12. Conformationally averaged vertical detachment energy of finite size NO3(-)·nH2O clusters: a route connecting few to many.

    Science.gov (United States)

    Pathak, Arup Kumar; Samanta, Alok Kumar; Maity, Dilip Kumar

    2011-04-07

    We report conformationally averaged VDEs (VDE(w)(n)) for different sizes of NO(3)(-)·nH(2)O clusters calculated by using uncorrelated HF, correlated hybrid density functional (B3LYP, BHHLYP) and correlated ab intio (MP2 and CCSD(T)) theory. It is observed that the VDE(w)(n) at the B3LYP/6-311++G(d,p), B3LYP/Aug-cc-Pvtz and CCSD(T)/6-311++G(d,p) levels is very close to the experimentally measured VDE. It is shown that the use of calculated results of the conformationally averaged VDE for small-sized solvated negatively-charged clusters and a microscopic theory-based general expression for the same provides a route to obtain the VDE for a wide range of cluster sizes, including bulk.

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

    International Nuclear Information System (INIS)

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

    1986-01-01

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

  14. Theoretical conformational analysis of the bovine adrenal medulla 12 residue peptide molecule

    Science.gov (United States)

    Akhmedov, N. A.; Tagiyev, Z. H.; Hasanov, E. M.; Akverdieva, G. A.

    2003-02-01

    The spatial structure and conformational properties of the bovine adrenal medulla 12 residue peptide Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Arg7-Val8-Gly9-Arg10-Pro11-Glu12 (BAM-12P) molecule were studied by theoretical conformational analysis. It is revealed that this molecule can exist in several stable states. The energy and geometrical parameters for the low-energy conformations are obtained. The conformationally rigid and labile segments of this molecule were revealed.

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

    International Nuclear Information System (INIS)

    Sochen, N.

    1992-05-01

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

  16. Conformal three dimensional radiotherapy treatment planning in Lund

    International Nuclear Information System (INIS)

    Knoos, T.; Nilsson, P.; Anders, A.

    1995-01-01

    The use of conformal therapy is based on 3-dimensional treatment planning as well as on methods and routines for 3-dimensional patient mapping, 3-dimensional virtual simulation and others. The management of patients at the Radiotherapy Department at the University Hospital in Lund (Sweden) is discussed. About 2100 new patients are annually treated with external radiotherapy using seven linear accelerators. Three of the accelerators have dual photon energies and electron treatment facilities. A multi-leaf collimator as well as an electronic portal imaging device are available on one machine. Two simulators and an in-house CT-scanner are used for treatment planning. From 1988 to 1992 Scandiplan (Umplan) was used. Since 1992, the treatment planning system is TMS (HELAX AB, Sweden), which is based on the pencil beam algorithm of Ahnesjo. The calculations use patient modulated accelerator specific energy fluence spectra which are compiled with pencil beams from Monte Carlo generated energy absorption kernels. Heterogeneity corrections are performed with results close to conventional algorithms. Irregular fields, either from standard or individual blocks and from multi-leaf collimators are handled by the treatment planning system. The field shape is determined conveniently using the beam's eye view. The final field shape is exported electronically to either the block cutting machine or the multileaf collimator control computer. All patient fields are checked against the beam's eye view during simulation using manual methods. Treatment verification is performed by portal films and in vivo dosimetry with silicon diodes or TL-dosimetry. Up to now, approximately 4400 patients have received a highly individualized 3-dimensional conformal treatment

  17. Topics in conformal field theory

    International Nuclear Information System (INIS)

    Kiritsis, E.B.

    1988-01-01

    In this work two major topics in Conformal Field Theory are discussed. First a detailed investigation of N = 2 Superconformal theories is presented. The structure of the representations of the N = 2 superconformal algebras is investigated and the character formulae are calculated. The general structure of N = 2 superconformal theories is elucidated and the operator algebra of the minimal models is derived. The first minimal system is discussed in more detail. Second, applications of the conformal techniques are studied in the Ashkin-Teller model. The c = 1 as well as the c = 1/2 critical lines are discussed in detail

  18. Conformational Study of Taurine in the Gas Phase

    Science.gov (United States)

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

    2009-08-01

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

  19. Analysis of daylight calculated using the EnergyPlus programme

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Greici; Ghisi, Enedir [Universidade Federal de Santa Catarina, Departamento de Engenharia Civil, Laboratorio de Eficiencia Energetica em Edificacoes, Caixa Postal 476, Florianopolis - SC 88040-900 (Brazil)

    2010-09-15

    In order to properly evaluate the thermal energy performance of buildings it is also necessary to analyse the use of daylight, since this influences the thermal load of a building. In this context, the aim of this study was to evaluate the calculation of internal illuminances carried out using the EnergyPlus simulation programme. The analysis was carried out through a comparison of the Useful Daylight Illuminances (UDI) and the daylight factor (DF) estimated using the EnergyPlus programme with the results from another two programmes: Daysim/Radiance and TropLux. Also, the external horizontal illuminance estimated using EnergyPlus was compared with that measured in Florianopolis, Santa Catarina State, Brazil, between 2003 and 2005. The simulations were carried out for three different rooms: one square (5 m x 5 m x 3 m), one shallow rectangular (10 m x 5 m x 3 m) and one deep rectangular (5 m x 10 m x 3 m). From this analysis it was verified that the EnergyPlus programme has a problem related to both the DF and the external illuminance values. A comparison between the DF values calculated using the three programmes shows that there is a problem in EnergyPlus related to solving the internal reflection, such that the greater the importance of the portion of light reflected, the greater the difference found between the programmes. A comparison between the calculated and measured external horizontal illuminances shows differences greater than 100% both for the diffuse and direct illuminances indicating that the EnergyPlus programme overestimates these values. (author)

  20. Advancing Drug Discovery through Enhanced Free Energy Calculations.

    Science.gov (United States)

    Abel, Robert; Wang, Lingle; Harder, Edward D; Berne, B J; Friesner, Richard A

    2017-07-18

    A principal goal of drug discovery project is to design molecules that can tightly and selectively bind to the target protein receptor. Accurate prediction of protein-ligand binding free energies is therefore of central importance in computational chemistry and computer aided drug design. Multiple recent improvements in computing power, classical force field accuracy, enhanced sampling methods, and simulation setup have enabled accurate and reliable calculations of protein-ligands binding free energies, and position free energy calculations to play a guiding role in small molecule drug discovery. In this Account, we outline the relevant methodological advances, including the REST2 (Replica Exchange with Solute Temperting) enhanced sampling, the incorporation of REST2 sampling with convential FEP (Free Energy Perturbation) through FEP/REST, the OPLS3 force field, and the advanced simulation setup that constitute our FEP+ approach, followed by the presentation of extensive comparisons with experiment, demonstrating sufficient accuracy in potency prediction (better than 1 kcal/mol) to substantially impact lead optimization campaigns. The limitations of the current FEP+ implementation and best practices in drug discovery applications are also discussed followed by the future methodology development plans to address those limitations. We then report results from a recent drug discovery project, in which several thousand FEP+ calculations were successfully deployed to simultaneously optimize potency, selectivity, and solubility, illustrating the power of the approach to solve challenging drug design problems. The capabilities of free energy calculations to accurately predict potency and selectivity have led to the advance of ongoing drug discovery projects, in challenging situations where alternative approaches would have great difficulties. The ability to effectively carry out projects evaluating tens of thousands, or hundreds of thousands, of proposed drug candidates

  1. To the calculation of energy resolution of ionization calorimeter

    International Nuclear Information System (INIS)

    Uchajkin, V.V.; Lagutin, A.A.

    1976-01-01

    The question of energy resolution of the ionization calorimeter is considered analytically. A method is discussed for calculating the probability characteristics (mean value and dispersion) of energy losses of an electron-photon shower by ionization in the calorimeter volume

  2. Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

    DEFF Research Database (Denmark)

    Christensen, I T; Jørgensen, Flemming Steen

    1997-01-01

    . A series of methyl-substituted 1,3-dioxanes were investigated at 1000 K, and the number of chair-chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy......-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method...

  3. 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.

  4. Energy response and compensation filters for pips detector

    International Nuclear Information System (INIS)

    Wang Lin; Ye Zhiyao; Dong Binjiang

    2007-01-01

    This paper introduces the analysis of energy response and the choice of proper compensation filters for PIPS detector. With PRESTA-CG program, filters conformed to the national standard of PRC were picked out by calculation. Then the chosen filters were tested through experiments. Good agreement was obtained between measured results and calculated values by Monte Carlo method. (authors)

  5. Additional conformer observed in the microwave spectrum of methyl vinyl ketone

    Science.gov (United States)

    Wilcox, David S.; Shirar, Amanda J.; Williams, Owen L.; Dian, Brian C.

    2011-05-01

    A chirped-pulse Fourier transform microwave spectrometer was used to record the rotational spectrum of methyl vinyl ketone (MVK, 3-butene-2-one). Two stable conformations were identified: the previously documented antiperiplanar (ap) conformer and synperiplanar (sp), which is reported for the first time in this microwave study. Methyl torsional analysis resulted in V3 barrier heights of 433.8(1) and 376.6(2) cm-1 for ap- and sp-MVK, respectively. Heavy atom isotopic species of both conformers were detected in natural abundance allowing bond lengths and angles of the molecular frames to be calculated through Kraitchman analysis. A comparison with ab initio calculations is included.

  6. Finite element calculation of the interaction energy of shape memory alloy

    International Nuclear Information System (INIS)

    Yang, Seung Yong

    2004-01-01

    Strain energy due to the mechanical interaction between self-accommodation groups of martensitic phase transformation is called interaction energy. Evaluation of the interaction energy should be accurate since the energy appears in constitutive models for predicting the mechanical behavior of shape memory alloy. In this paper, the interaction energy is evaluated in terms of theoretical formulation and explicit finite element calculation. A simple example with two habit plane variants was considered. It was shown that the theoretical formulation assuming elastic interaction between the self-accommodation group and matrix gives larger interaction energy than explicit finite element calculation in which transformation softening is accounted for

  7. Conformational analysis of cellobiose by electronic structure theories.

    Science.gov (United States)

    French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

    2012-03-01

    Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

  8. Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: Comparison with distance geometry calculations

    International Nuclear Information System (INIS)

    Beckers, Mischa L.M.; Buydens, Lutgarde M.C.; Pikkemaat, Jeroen A.; Altona, Cornelis

    1997-01-01

    The three-dimensional spatial structure of a methylene-acetal-linked thymine dimer present in a 10 base-pair (bp) sense-antisense DNA duplex was studied with a genetic algorithm designed to interpret NOE distance restraints. Trial solutions were represented by torsion angles. This means that bond angles for the dimer trial structures are kept fixed during the genetic algorithm optimization. Bond angle values were extracted from a 10 bp sense-antisense duplex model that was subjected to energy minimization by means of a modified AMBER force field. A set of 63 proton-proton distance restraints defining the methylene-acetal-linked thymine dimer was available. The genetic algorithm minimizes the difference between distances in the trial structures and distance restraints. A large conformational search space could be covered in the genetic algorithm optimization by allowing a wide range of torsion angles. The genetic algorithm optimization in all cases led to one family of structures. This family of the methylene-acetal-linked thymine dimer in the duplex differs from the family that was suggested from distance geometry calculations. It is demonstrated that the bond angle geometry around the methylene-acetal linkage plays an important role in the optimization

  9. Calculation of transformers leakage reactance using electromagnetic energy technique

    International Nuclear Information System (INIS)

    Feiz, J.; Mohseni, H.; Sabet Marzooghi, S.; Naderian Jahromi, A.

    2004-01-01

    Determination of transformer leakage reactance using magnetic cores has long been an area of interest to engineers involved in the design of power and distribution transformers. This is required for predicting the performance of transformers before actual assembly of the transformers. In this paper a closed form solution technique applicable to the leakage reactance calculations for transformers is presented. An emphasis is on the development of a simple method to calculate the leakage reactance of the distribution transformers and smaller transformers. Energy technique procedure for computing the leakage reactances in distribution transformers is presented. This method is very efficient compared with the use of flux element and image technique and is also remarkably accurate. Examples of calculated leakage inductances and the short circuit impedance are given for illustration. For validation, the results are compared with the results obtained using test. This paper presents a novel technique for calculation of the leakage inductance in different parts of the transformer using the electromagnetic stored energy

  10. Neutron energy spectra calculations in the low power research reactor

    International Nuclear Information System (INIS)

    Omar, H.; Khattab, K.; Ghazi, N.

    2011-01-01

    The neutron energy spectra have been calculated in the fuel region, inner and outer irradiation sites of the zero power research reactor using the MCNP-4C code and the combination of the WIMS-D/4 transport code for generation of group constants and the three-dimensional CITATION diffusion code for core analysis calculations. The neutron energy spectrum has been divided into three regions and compared with the proposed empirical correlations. The calculated thermal and fast neutron fluxes in the low power research reactor MNSR inner and outer irradiation sites have been compared with the measured results. Better agreements have been noticed between the calculated and measured results using the MCNP code than those obtained by the CITATION code. (author)

  11. Applications of neural network prediction of conformational states for small peptides from spectra and of fold classes

    DEFF Research Database (Denmark)

    Bohr, Henrik; Røgen, Peter; Jalkanen, Karl J.

    2001-01-01

    but already at this stage they could be compared with reasonable agreements to experiments. The neural networks are shown to be good in distinguishing the different conformers of the small alanine peptides. especially when in the gas phase. Also the task of predicting protein fold-classes, defined from line...... to construct vibrational spectra for each of the conformational states with low energy. From the spectra, neural networks could be trained to distinguish between the various states and thus be able to generate a larger set of relevant structures and their relation to secondary structures of the peptides....... The calculations were done both with solvent atoms (up to ten water molecules) and without, and hence the neural networks could be used to monitor the influence of the solvent on hydrogen bond formation. The calculations at this stage only involved very short peptide fragments of a few alanine amino acids...

  12. Precise calculation of the energies of heavy hydrogenlike ions

    International Nuclear Information System (INIS)

    Driker, M.N.; Ivanova, E.P.; Ivanov, L.N.

    1983-01-01

    Energies of the 1s, 2s, and 2p states are calculated for hydrogenlike ions with z = 30--170. The calculation is based on Dirac's equation taking into account radiation effects and the finiteness of the nucleus. The hyperfine splitting constants are calculated taking the finiteness of the nucleus into account, and derivatives are taken with respect to the volume of the nucleus for all S-state characteristics

  13. Equivalence of Stress and Energy Calculations of Mean Stress

    DEFF Research Database (Denmark)

    Pedersen, Ole Bøcker; Brown, L. M.

    1977-01-01

    Calculations of the mean stress in a plastically deformed matrix containing randomly distributed elastic inclusions are considered. The mean stress for an elastically homogeneous material is calculated on the basis of an energy consideration which completely accounts for elastic interactions....... The result is shown to be identical to that obtained from a stress calculation. The possibility of including elastic interactions in the case of elastic inhomogeneity is discussed....

  14. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i......We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged...... in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We...

  15. Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet.

    Science.gov (United States)

    Jaiyong, Panichakorn; Bryce, Richard A

    2017-06-14

    Noncovalent functionalization of graphene by carbohydrates such as β-cyclodextrin (βCD) has the potential to improve graphene dispersibility and its use in biomedical applications. Here we explore the ability of approximate quantum chemical methods to accurately model βCD conformation and its interaction with graphene. We find that DFTB3, SCC-DFTB and PM3CARB-1 methods provide the best agreement with density functional theory (DFT) in calculation of relative energetics of gas-phase βCD conformers; however, the remaining NDDO-based approaches we considered underestimate the stability of the trans,gauche vicinal diol conformation. This diol orientation, corresponding to a clockwise hydrogen bonding arrangement in the glucosyl residue of βCD, is present in the lowest energy βCD conformer. Consequently, for adsorption on graphene of clockwise or counterclockwise hydrogen bonded forms of βCD, calculated with respect to this unbound conformer, the DFTB3 method provides closer agreement with DFT values than PM7 and PM6-DH2 approaches. These findings suggest approximate quantum chemical methods as potentially useful tools to guide the design of carbohydrate-graphene interactions, but also highlights the specific challenge to NDDO-based methods in capturing the relative energetics of carbohydrate hydrogen bond networks.

  16. Conformal scalar field on the hyperelliptic curve and critical Ashkin-Teller multipoint correlation functions

    International Nuclear Information System (INIS)

    Zamolodchikov, A.B.

    1987-01-01

    A multipoint conformal block of Ramond states of the two-dimensional free scalar field is calculated. This function is related to the free energy of the scalar field on the hyperelliptic Riemann surface under a particular choice of boundary conditions. Being compactified on the circle this field leads to the crossing symmetric correlation functions with a discrete spectrum of scale dimensions. These functions are supposed to describe multipoint spin correlations of the critical Ashkin-Teller model. (orig.)

  17. An investigation of fission models for high-energy radiation transport calculations

    International Nuclear Information System (INIS)

    Armstrong, T.W.; Cloth, P.; Filges, D.; Neef, R.D.

    1983-07-01

    An investigation of high-energy fission models for use in the HETC code has been made. The validation work has been directed checking the accuracy of the high-energy radiation transport computer code HETC to investigate the appropriate model for routine calculations, particularly for spallation neutron source applications. Model calculations are given in terms of neutron production, fission fragment energy release, and residual nuclei production for high-energy protons incident on thin uranium targets. The effect of the fission models on neutron production from thick uranium targets is also shown. (orig.)

  18. Conformal field theory in conformal space

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  19. Sophisticated Calculation of the 1oo4-architecture for Safety-related Systems Conforming to IEC61508

    International Nuclear Information System (INIS)

    Hayek, A; Al Bokhaiti, M; Schwarz, M H; Boercsoek, J

    2012-01-01

    With the publication and enforcement of the standard IEC 61508 of safety related systems, recent system architectures have been presented and evaluated. Among a number of techniques and measures to the evaluation of safety integrity level (SIL) for safety-related systems, several measures such as reliability block diagrams and Markov models are used to analyze the probability of failure on demand (PFD) and mean time to failure (MTTF) which conform to IEC 61508. The current paper deals with the quantitative analysis of the novel 1oo4-architecture (one out of four) presented in recent work. Therefore sophisticated calculations for the required parameters are introduced. The provided 1oo4-architecture represents an advanced safety architecture based on on-chip redundancy, which is 3-failure safe. This means that at least one of the four channels have to work correctly in order to trigger the safety function.

  20. Calculated intensity of high-energy neutron beams

    International Nuclear Information System (INIS)

    Mustapha, B.; Nolen, J.A.; Back, B.B.

    2004-01-01

    The flux, energy and angular distributions of high-energy neutrons produced by in-flight spallation and fission of a 400 MeV/A 238 U beam and by the break-up of a 400 MeV/A deuteron beam are calculated. In both cases very intense secondary neutron beams are produced, peaking at zero degrees, with a relatively narrow energy spread. Such secondary neutron beams can be produced with the primary beams from the proposed rare isotope accelerator driver linac. The break-up of a 400 kW deuteron beam on a liquid-lithium target can produce a neutron flux of >10 10 neutrons/cm 2 /s at a distance of 10 m from the target

  1. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  2. Calculations for very low energy scattering of positrons by molecular hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, J.N. [School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD (United Kingdom)], E-mail: james.cooper@maths.nottingham.ac.uk; Armour, E.A.G. [School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD (United Kingdom)

    2008-02-15

    We give a progress report on ongoing calculations of phase shifts for very low energy elastic scattering of positrons by molecular hydrogen, using the generalised Kohn variational method. Further, provisional calculations of Z{sub eff} for molecular hydrogen at low energies are presented and discussed. The preliminary nature of the work is emphasised throughout.

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

    Science.gov (United States)

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

    2017-05-03

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

  4. Calculation of the yearly energy performance of heating systems based on the European Building Energy Directive and related CEN Standards

    DEFF Research Database (Denmark)

    Olesen, Bjarne W.; de Carli, Michele

    2011-01-01

    According to the Energy Performance of Buildings Directive (EPBD) all new European buildings (residential, commercial, industrial, etc.) must since 2006 have an energy declaration based on the calculated energy performance of the building, including heating, ventilating, cooling and lighting syst......–20% of the building energy demand. The additional loss depends on the type of heat emitter, type of control, pump and boiler. Keywords: Heating systems; CEN standards; Energy performance; Calculation methods......According to the Energy Performance of Buildings Directive (EPBD) all new European buildings (residential, commercial, industrial, etc.) must since 2006 have an energy declaration based on the calculated energy performance of the building, including heating, ventilating, cooling and lighting...... systems. This energy declaration must refer to the primary energy or CO2 emissions. The European Organization for Standardization (CEN) has prepared a series of standards for energy performance calculations for buildings and systems. This paper presents related standards for heating systems. The relevant...

  5. A new approach to the electron self energy calculation

    International Nuclear Information System (INIS)

    Persson, H.; Lindgren, I.; Salomonson, S.

    1993-01-01

    We present a new practical way to calculate the first order self energy in any model potential (local or non-local). The main idea is to introduce a new straightforward way of renormalization to avoid the usual potential expansion implying a large number of diagrams in higher order QED effects. The renormalization procedure is based on defining the divergent mass term in coordinate space and decomposing it into a divergent sum over finite partial wave contributions. The unrenormalized bound self energy is equally decomposed into a partial wave (l) sum. For each partial wave the difference is taken and the sum becomes convergent. The comparably rapid asymptotic behaviour of the method is l -3 . The method is applied to lithium-like uranium, and the self energy in a Coulomb field, the finite nucleus effect and the screened self energy is calculated to an accuracy of at least one tenth of an eV. (orig.)

  6. On the Conformable Fractional Quantum Mechanics

    Science.gov (United States)

    Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

    2018-05-01

    In this paper, a conformable fractional quantum mechanic has been introduced using three postulates. Then in such a formalism, Schr¨odinger equation, probability density, probability flux and continuity equation have been derived. As an application of considered formalism, a fractional-radial harmonic oscillator has been considered. After obtaining its wave function and energy spectrum, effects of the conformable fractional parameter on some quantities have been investigated and plotted for different excited states.

  7. Dose calculation methods in photon beam therapy using energy deposition kernels

    International Nuclear Information System (INIS)

    Ahnesjoe, A.

    1991-01-01

    The problem of calculating accurate dose distributions in treatment planning of megavoltage photon radiation therapy has been studied. New dose calculation algorithms using energy deposition kernels have been developed. The kernels describe the transfer of energy by secondary particles from a primary photon interaction site to its surroundings. Monte Carlo simulations of particle transport have been used for derivation of kernels for primary photon energies form 0.1 MeV to 50 MeV. The trade off between accuracy and calculational speed has been addressed by the development of two algorithms; one point oriented with low computional overhead for interactive use and one for fast and accurate calculation of dose distributions in a 3-dimensional lattice. The latter algorithm models secondary particle transport in heterogeneous tissue by scaling energy deposition kernels with the electron density of the tissue. The accuracy of the methods has been tested using full Monte Carlo simulations for different geometries, and found to be superior to conventional algorithms based on scaling of broad beam dose distributions. Methods have also been developed for characterization of clinical photon beams in entities appropriate for kernel based calculation models. By approximating the spectrum as laterally invariant, an effective spectrum and dose distribution for contaminating charge particles are derived form depth dose distributions measured in water, using analytical constraints. The spectrum is used to calculate kernels by superposition of monoenergetic kernels. The lateral energy fluence distribution is determined by deconvolving measured lateral dose distributions by a corresponding pencil beam kernel. Dose distributions for contaminating photons are described using two different methods, one for estimation of the dose outside of the collimated beam, and the other for calibration of output factors derived from kernel based dose calculations. (au)

  8. 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

  9. Total energy calculations and bonding at interfaces

    International Nuclear Information System (INIS)

    Louie, S.G.

    1984-08-01

    Some of the concepts and theoretical techniques employed in recent ab initio studies of the electronic and structural properties of surfaces and interfaces are discussed. Results of total energy calculations for the 2 x 1 reconstructed diamond (111) surface and for stacking faults in Si are reviewed. 30 refs., 8 figs

  10. Calculated microdose spectra for intermediate energy neutrons (1 to 100 keV)

    International Nuclear Information System (INIS)

    Al-Affan, I.A.M.; Watt, D.E.

    1983-01-01

    Basic formulae for calculation of energy deposition events due to insiders, starters, stoppers and crossers, using the continuous slowing down approximation have been modified to allow for the enhanced energy deposition in spherical volumes due to elastic scattering interactions which reduce the penetration depth of the charged particle recoils. Energy deposition spectra have been obtained for energies of 1, 10, 50, 100 keV in 0.2 μm and 1 μm tissue-equivalent spheres. From these, frequency and dose distributions in lineal energy and in specific energy density have been calculated. Also calculated for different neutron energies are values of zeta, the energy average of event size, as a function of the diameter of the sensitive site. The structure of the energy event distributions can be interpreted in terms of the basic physics. The effect of the modifications to the basic formulae is to increase the number of energy deposition events due to insiders and to decrease the number of starters, stoppers and crossers. The degree of the effect increases with decreasing neutron energy, increasing sphere size, and the change is most significant for low energy deposition events. (author)

  11. Calculated microdose spectra for intermediate energy neutrons (1 to 100 keV)

    Energy Technology Data Exchange (ETDEWEB)

    Al-Affan, I.A.M.; Watt, D.E. (Dundee Univ. (UK). Dept. of Medical Biophysics); Colautti, P.; Talpo, G. (Laboratori Nazionali dell' Infn, 35020, Legnaro (Padova) (Italy))

    1983-01-01

    Basic formulae for calculation of energy deposition events due to insiders, starters, stoppers and crossers, using the continuous slowing down approximation have been modified to allow for the enhanced energy deposition in spherical volumes due to elastic scattering interactions which reduce the penetration depth of the charged particle recoils. Energy deposition spectra have been obtained for energies of 1, 10, 50, 100 keV in 0.2 ..mu..m and 1 ..mu..m tissue-equivalent spheres. From these, frequency and dose distributions in lineal energy and in specific energy density have been calculated. Also calculated for different neutron energies are values of zeta, the energy average of event size, as a function of the diameter of the sensitive site. The structure of the energy event distributions can be interpreted in terms of the basic physics. The effect of the modifications to the basic formulae is to increase the number of energy deposition events due to insiders and to decrease the number of starters, stoppers and crossers. The degree of the effect increases with decreasing neutron energy, increasing sphere size, and the change is most significant for low energy deposition events.

  12. Zero-point energy constraint in quasi-classical trajectory calculations.

    Science.gov (United States)

    Xie, Zhen; Bowman, Joel M

    2006-04-27

    A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.

  13. Analytic aspects of rational conformal field theories

    International Nuclear Information System (INIS)

    Kiritsis, E.B.; Lawrence Berkeley Lab., CA

    1990-01-01

    The problem of deriving linear differential equations for correlation functions of Rational Conformal Field Theories is considered. Techniques from the theory of fuchsian differential equations are used to show that knowledge of the central charge, dimensions of primary fields and fusion rules are enough to fix the differential equations for one- and two-point functions on the tours. Any other correlation function can be calculated along similar lines. The results settle the issue of 'exact solution' of rational conformal field theories. (orig.)

  14. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    Science.gov (United States)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B

  15. Conformal three dimensional radiotherapy treatment planning in Lund

    Energy Technology Data Exchange (ETDEWEB)

    Knoos, T; Nilsson, P [Lund Univ. (Sweden). Dept. of Radiation Physics; Anders, A [Lund Univ. (Sweden). Dept. of Oncology

    1995-12-01

    The use of conformal therapy is based on 3-dimensional treatment planning as well as on methods and routines for 3-dimensional patient mapping, 3-dimensional virtual simulation and others. The management of patients at the Radiotherapy Department at the University Hospital in Lund (Sweden) is discussed. About 2100 new patients are annually treated with external radiotherapy using seven linear accelerators. Three of the accelerators have dual photon energies and electron treatment facilities. A multi-leaf collimator as well as an electronic portal imaging device are available on one machine. Two simulators and an in-house CT-scanner are used for treatment planning. From 1988 to 1992 Scandiplan (Umplan) was used. Since 1992, the treatment planning system is TMS (HELAX AB, Sweden), which is based on the pencil beam algorithm of Ahnesjo. The calculations use patient modulated accelerator specific energy fluence spectra which are compiled with pencil beams from Monte Carlo generated energy absorption kernels. Heterogeneity corrections are performed with results close to conventional algorithms. Irregular fields, either from standard or individual blocks and from multi-leaf collimators are handled by the treatment planning system. The field shape is determined conveniently using the beam`s eye view. The final field shape is exported electronically to either the block cutting machine or the multileaf collimator control computer. All patient fields are checked against the beam`s eye view during simulation using manual methods. Treatment verification is performed by portal films and in vivo dosimetry with silicon diodes or TL-dosimetry. Up to now, approximately 4400 patients have received a highly individualized 3-dimensional conformal treatment.

  16. Structural characteristics and harmonic vibrational analysis of the stable conformer of 2,3-epoxypropanol by quantum chemical methods.

    Science.gov (United States)

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

    2012-10-01

    The FT-IR and FT-Raman spectra of H bond inner conformer of 2,3-epoxypropanol have been recorded in the regions 3700-400 and 3700-100 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The normal coordinate analysis was carried out to confirm the precision of the assignments. The structure of the conformers H bond inner and H bond outer1 were optimised and the structural characteristics were determined by density functional theory (DFT) using B3LYP and MP2 methods with 6-31G** and 6-311++G** basis sets. The vibrational frequencies were calculated in all these methods and were compared with the experimental frequencies which yield good agreement between observed and calculated frequencies. The electronic properties HOMO and LUMO energies were measured by time-dependent TD-DFT approach. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Impact of dietary fiber energy on the calculation of food total energy value in the Brazilian Food Composition Database.

    Science.gov (United States)

    Menezes, Elizabete Wenzel de; Grande, Fernanda; Giuntini, Eliana Bistriche; Lopes, Tássia do Vale Cardoso; Dan, Milana Cara Tanasov; Prado, Samira Bernardino Ramos do; Franco, Bernadette Dora Gombossy de Melo; Charrondière, U Ruth; Lajolo, Franco Maria

    2016-02-15

    Dietary fiber (DF) contributes to the energy value of foods and including it in the calculation of total food energy has been recommended for food composition databases. The present study aimed to investigate the impact of including energy provided by the DF fermentation in the calculation of food energy. Total energy values of 1753 foods from the Brazilian Food Composition Database were calculated with or without the inclusion of DF energy. The energy values were compared, through the use of percentage difference (D%), in individual foods and in daily menus. Appreciable energy D% (⩾10) was observed in 321 foods, mainly in the group of vegetables, legumes and fruits. However, in the Brazilian typical menus containing foods from all groups, only D%foods, when individually considered. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Renyi entropy and conformal defects

    Energy Technology Data Exchange (ETDEWEB)

    Bianchi, Lorenzo [Humboldt-Univ. Berlin (Germany). Inst. fuer Physik; Hamburg Univ. (Germany). II. Inst. fuer Theoretische Physik; Meineri, Marco [Scuola Normale Superiore, Pisa (Italy); Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada); Istituto Nazionale di Fisica Nucleare, Pisa (Italy); Myers, Robert C. [Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada); Smolkin, Michael [California Univ., Berkely, CA (United States). Center for Theoretical Physics and Department of Physics

    2016-04-18

    We propose a field theoretic framework for calculating the dependence of Renyi entropies on the shape of the entangling surface in a conformal field theory. Our approach rests on regarding the corresponding twist operator as a conformal defect and in particular, we define the displacement operator which implements small local deformations of the entangling surface. We identify a simple constraint between the coefficient defining the two-point function of the displacement operator and the conformal weight of the twist operator, which consolidates a number of distinct conjectures on the shape dependence of the Renyi entropy. As an example, using this approach, we examine a conjecture regarding the universal coefficient associated with a conical singularity in the entangling surface for CFTs in any number of spacetime dimensions. We also provide a general formula for the second order variation of the Renyi entropy arising from small deformations of a spherical entangling surface, extending Mezei's results for the entanglement entropy.

  19. Renyi entropy and conformal defects

    International Nuclear Information System (INIS)

    Bianchi, Lorenzo; Myers, Robert C.; Smolkin, Michael

    2016-01-01

    We propose a field theoretic framework for calculating the dependence of Renyi entropies on the shape of the entangling surface in a conformal field theory. Our approach rests on regarding the corresponding twist operator as a conformal defect and in particular, we define the displacement operator which implements small local deformations of the entangling surface. We identify a simple constraint between the coefficient defining the two-point function of the displacement operator and the conformal weight of the twist operator, which consolidates a number of distinct conjectures on the shape dependence of the Renyi entropy. As an example, using this approach, we examine a conjecture regarding the universal coefficient associated with a conical singularity in the entangling surface for CFTs in any number of spacetime dimensions. We also provide a general formula for the second order variation of the Renyi entropy arising from small deformations of a spherical entangling surface, extending Mezei's results for the entanglement entropy.

  20. Calculation of the atomic states energies in the Thomas - Fermi approximation

    Directory of Open Access Journals (Sweden)

    S. N. Fedotkin

    2017-12-01

    Full Text Available A method for calculating the energies of levels for many-electron neutral atoms is proposed. In this case, in addition to the Coulomb field of the nucleus, an important contribution to the energy is connected with the interaction between the electrons. This interaction is taken into account approximately by perturbation theory in the framework of the Thomas - Fermi statistical model. Using the Taytz approximation for the mean potential the analytical expressions for the energies of s-states are obtained with principal quantum numbers n = 1, 2, 3, 4. The energies are calculated for the nuclear charges in the interval 1 < Z ≤ 100. A good agreement with the experimental values of the energies was obtained.

  1. FT-IR, FT-Raman, UV spectra and DFT calculations on monomeric and dimeric structure of 2-amino-5-bromobenzoic acid.

    Science.gov (United States)

    Karabacak, Mehmet; Cinar, Mehmet

    2012-02-01

    In this work, the molecular conformation, vibrational and electronic transition analysis of 2-amino-5-bromobenzoic acid (2A5BrBA) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000 cm(-1) and 50-4000 cm(-1), respectively. There are four conformers, C1, C2, C3 and C4 for this molecule. The geometrical parameters, energies and wavenumbers have been obtained for all four conformers. The computational results diagnose the most stable conformer of 2A5BrBA as the C1 form. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. The UV spectra of investigated compound were recorded in the region of 200-400 nm for ethanol and water solutions. The electronic properties were evaluated with help of time-dependent DFT (TD-DFT) theoretically and results were compared with experimental observations. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. The observed and the calculated geometric parameters, vibrational wavenumbers and electronic transitions were compared with observed data and found to be in good agreement. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Conformational dependence of a protein kinase phosphate transfer reaction

    Science.gov (United States)

    Labute, Montiago; Henkelman, Graeme; Tung, Chang-Shung; Fenimore, Paul; McMahon, Ben

    2007-03-01

    Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005).

  3. Hot-electron-mediated desorption rates calculated from excited-state potential energy surfaces

    DEFF Research Database (Denmark)

    Olsen, Thomas; Gavnholt, Jeppe; Schiøtz, Jakob

    2009-01-01

    We present a model for desorption induced by (multiple) electronic transitions [DIET (DIMET)] based on potential energy surfaces calculated with the delta self-consistent field extension of density-functional theory. We calculate potential energy surfaces of CO and NO molecules adsorbed on variou...

  4. Calculation of Collective Variable-based PMF by Combining WHAM with Umbrella Sampling

    International Nuclear Information System (INIS)

    Xu Wei-Xin; Li Yang; Zhang, John Z. H.

    2012-01-01

    Potential of mean force (PMF) with respect to localized reaction coordinates (RCs) such as distance is often applied to evaluate the free energy profile along the reaction pathway for complex molecular systems. However, calculation of PMF as a function of global RCs is still a challenging and important problem in computational biology. We examine the combined use of the weighted histogram analysis method and the umbrella sampling method for the calculation of PMF as a function of a global RC from the coarse-grained Langevin dynamics simulations for a model protein. The method yields the folding free energy profile projected onto a global RC, which is in accord with benchmark results. With this method rare global events would be sufficiently sampled because the biased potential can be used for restricting the global conformation to specific regions during free energy calculations. The strategy presented can also be utilized in calculating the global intra- and intermolecular PMF at more detailed levels. (cross-disciplinary physics and related areas of science and technology)

  5. Calculation of the surface free energy of fcc copper nanoparticles

    International Nuclear Information System (INIS)

    Jia Ming; Lai Yanqing; Tian Zhongliang; Liu Yexiang

    2009-01-01

    Using molecular dynamics simulations with the modified analytic embedded-atom method we calculate the Gibbs free energy and surface free energy for fcc Cu bulk, and further obtain the Gibbs free energy of nanoparticles. Based on the Gibbs free energy of nanoparticles, we have investigated the heat capacity of copper nanoparticles. Calculation results indicate that the Gibbs free energy and the heat capacity of nanoparticles can be divided into two parts: bulk quantity and surface quantity. The molar heat capacity of the bulk sample is lower compared with the molar heat capacity of nanoparticles, and this difference increases with the decrease in the particle size. It is also observed that the size effect on the thermodynamic properties of Cu nanoparticles is not really significant until the particle is less than about 20 nm. It is the surface atoms that decide the size effect on the thermodynamic properties of nanoparticles

  6. Annotated references on shielding experiment and calculation of high energy particles

    International Nuclear Information System (INIS)

    Hirayama, H.; Ban, S.; Nakamura, T.

    1990-12-01

    The literature on shielding experiment and calculation of high energy particles above 20 MeV has been surveyed. The survey covers thirteen journals, from 1965 up to 1989. For each paper, applicable information is listed on type and energy of the projectile, the accelerator used, composition and thickness of the target and shielding materials, shielding geometry, the experimental and calculational methods, and the quantities obtained. The references on shielding experiment and on shielding calculation are accessed through two indices which list the projectile-target and shielding material combination, shielding geometry and the projectile energy range. The literature on neutron, photon and hadron production from thick target bombarded by charged particles has been surveyed mainly from 1984 as a complement of the previous work. (author)

  7. Open conformal systems and perturbations of transfer operators

    CERN Document Server

    Pollicott, Mark

    2017-01-01

    The focus of this book is on open conformal dynamical systems corresponding to the escape of a point through an open Euclidean ball. The ultimate goal is to understand the asymptotic behavior of the escape rate as the radius of the ball tends to zero. In the case of hyperbolic conformal systems this has been addressed by various authors. The conformal maps considered in this book are far more general, and the analysis correspondingly more involved. The asymptotic existence of escape rates is proved and they are calculated in the context of (finite or infinite) countable alphabets, uniformly contracting conformal graph-directed Markov systems, and in particular, conformal countable alphabet iterated function systems. These results have direct applications to interval maps, meromorphic maps and rational functions. Towards this goal the authors develop, on a purely symbolic level, a theory of singular perturbations of Perron--Frobenius (transfer) operators associated with countable alphabet subshifts of finite t...

  8. Subsurface Shielding Source Term Specification Calculation

    International Nuclear Information System (INIS)

    S.Su

    2001-01-01

    The purpose of this calculation is to establish appropriate and defensible waste-package radiation source terms for use in repository subsurface shielding design. This calculation supports the shielding design for the waste emplacement and retrieval system, and subsurface facility system. The objective is to identify the limiting waste package and specify its associated source terms including source strengths and energy spectra. Consistent with the Technical Work Plan for Subsurface Design Section FY 01 Work Activities (CRWMS M and O 2001, p. 15), the scope of work includes the following: (1) Review source terms generated by the Waste Package Department (WPD) for various waste forms and waste package types, and compile them for shielding-specific applications. (2) Determine acceptable waste package specific source terms for use in subsurface shielding design, using a reasonable and defensible methodology that is not unduly conservative. This calculation is associated with the engineering and design activity for the waste emplacement and retrieval system, and subsurface facility system. The technical work plan for this calculation is provided in CRWMS M and O 2001. Development and performance of this calculation conforms to the procedure, AP-3.12Q, Calculations

  9. Difference between standard and quasi-conformal BFKL kernels

    International Nuclear Information System (INIS)

    Fadin, V.S.; Fiore, R.; Papa, A.

    2012-01-01

    As it was recently shown, the colour singlet BFKL kernel, taken in Möbius representation in the space of impact parameters, can be written in quasi-conformal shape, which is unbelievably simple compared with the conventional form of the BFKL kernel in momentum space. It was also proved that the total kernel is completely defined by its Möbius representation. In this paper we calculated the difference between standard and quasi-conformal BFKL kernels in momentum space and discovered that it is rather simple. Therefore we come to the conclusion that the simplicity of the quasi-conformal kernel is caused mainly by using the impact parameter space.

  10. Conformational and vibrational analysis of 5-hydroxy 2-nitrobenzaldehyde by AB initio hartree-fock, density functional theory calculations

    International Nuclear Information System (INIS)

    Cinakli, S.; Sert, Y.; Boeyuekata, M.; Ucun, F.

    2010-01-01

    The vibrational spectra of benzaldehyde and its derivatives have been studied earlier. The substitution of a functional group changes the spectra markedly. Recent spectroscopic studies of the benzaldehyde and their derivatives have been motivated because the vibrational spectra are very useful for understanding of specific biological process and in the analysis of relatively complex systems. The optimized molecular structure, vibrational frequencies and corresponding vibrational assignments, the total energy calculations, relative energies, the mean vibrational deviations of the two planar O-cis and O-trans roomers of 5-Hydroxy 2-nitrobenzaldehydes have been calculated using ab initio Hartree Fock (HF) and Density Functional Theory (B3LYP) with 6-311++G(d,p) basis set. All computations have been performed on personal computer using the Gaussian 03 program package. The calculations were adapted to Cs symmetries of all the molecules. The O-trans rotomers with lower energy of all the molecules have been found as preferential rotomers in the ground state.

  11. Effect of Atomic Charges on Octanol–Water Partition Coefficient Using Alchemical Free Energy Calculation

    Directory of Open Access Journals (Sweden)

    Koji Ogata

    2018-02-01

    Full Text Available The octanol–water partition coefficient (logPow is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values.

  12. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors

    Science.gov (United States)

    Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

    2018-02-01

    Optimization of fragment size d-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

  13. Calculation of the Energy Dependence of Dosimeter Response to Ionizing Photons

    DEFF Research Database (Denmark)

    Miller, Arne; McLaughlin, W. L.

    1982-01-01

    Using a program in BASIC applied to a desk-top calculator, simplified calculations provide approximate energy dependence correction factors of dosimeter readings of absorbed dose according to Bragg-Gray cavity theories. Burlin's general cavity theory is applied in the present calculations, and ce...

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

    Science.gov (United States)

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

    2016-02-01

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

  15. Conformal anomaly and elimination of infrared divergences in curved spacetime

    International Nuclear Information System (INIS)

    Grib, A.A.; Nesteruk, A.V.; Pritomanov, S.A.

    1984-01-01

    The relation between the problem of eliminating the infrared divergences and the conformal anomaly of the regularized energy-momentum tensor is studied in homogeneous isotropic and anisotropic spacetime. It is shown that elimination of the infrared divergence by means of a cutoff or the introduction of a conformally invariant mass of the field leads to the absence of the conformal anomaly

  16. Calculation of quantum-mechanical system energy spectra using path integrals

    International Nuclear Information System (INIS)

    Evseev, A.M.; Dmitriev, V.P.

    1977-01-01

    A solution of the Feynman quantum-mechanical integral connecting a wave function (psi (x, t)) at a moment t+tau (tau → 0) with the wave function at the moment t is provided by complex variable substitution and subsequent path integration. Time dependence of the wave function is calculated by the Monte Carlo method. The Fourier inverse transformation of the wave function by path integration calculated has been applied to determine the energy spectra. Energy spectra are presented of a hydrogen atom derived from wave function psi (x, t) at different x, as well as boson energy spectra of He, Li, and Be atoms obtained from psi (x, t) at X = O

  17. Improvements to robotics-inspired conformational sampling in rosetta.

    Directory of Open Access Journals (Sweden)

    Amelie Stein

    Full Text Available To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new "next-generation KIC" method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.

  18. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Nilanjan Sil

    2017-12-18

    Dec 18, 2017 ... Abstract. In the present paper, we have studied the binding energy of the shallow donor hydrogenic impurity, which is confined in an inhomogeneous cylindrical quantum dot (CQD) of GaAs-AlxGa1−xAs. Perturbation method is used to calculate the binding energy within the framework of effective mass ...

  19. A comment on the calculation of the total-factor energy efficiency (TFEE) index

    International Nuclear Information System (INIS)

    Chang, Ming-Chung

    2013-01-01

    This study provides a no-output growth model to conveniently calculate the total-factor energy efficiency (TFEE) index originally proposed by Hu and Wang (2006). The TFEE index serves as a very well-known and popular means of estimating overall energy efficiency. While many previous studies have used the indicator of energy inefficiency, including the indicator of energy intensity (i.e., Energy input/Gross Domestic Product (GDP)) to measure energy efficiency, Hu and Kao (2007) point out that the indicator of energy intensity is not only a partial-factor energy efficiency indicator, but that this partial-factor ratio is also quite inappropriate for analyzing the impact of changing energy use over time. The TFEE index overcomes the disadvantage of the indicator of energy intensity as mentioned above, but five steps are needed to calculate the TFEE score. In this study, we provide a no-output growth model to conveniently calculate the TFEE score. Furthermore, we extend this no-output growth model to an output growth model. This study concludes that the output growth model not only makes it easier to calculate the TFEE index than the model proposed by Hu and Wang (2006) and Hu and Kao (2007), but that it can also obtain better TFEE scores. - Highlights: ► The comment is on the total-factor energy efficiency (TFEE) index. ► Two extension models are no-output growth model and output growth model. ► The model in this study makes it easier to calculate the TFEE index.

  20. Conformational preferences of DNA following damage by aristolochic acids: Structural and energetic insights into the different mutagenic potential of the ALI and ALII-N(6)-dA adducts.

    Science.gov (United States)

    Kathuria, Preetleen; Sharma, Purshotam; Abendong, Minette N; Wetmore, Stacey D

    2015-04-21

    Aristolochic acids (AAI and AAII), produced by the Aristolochiaceae family of plants, are classified as group I (human) carcinogens by the International Agency for Research on Cancer. These acids are metabolized in cells to yield aristolactams (ALI and ALII, respectively), which further form bulky adducts with the purine nucleobases. Specifically, the adenine lesions are more persistent in cells and have been associated with chronic renal diseases and related carcinogenesis. To understand the structural basis of the nephrotoxicity induced by AAs, the ALI-N(6)-dA and ALII-N(6)-dA lesions are systematically studied using computational methods. Density functional theory calculations indicate that the aristolactam moiety intrinsically prefers a planar conformation with respect to adenine. Nucleoside and nucleotide models suggest that the anti and syn orientations about the glycosidic bond are isoenergetic for both adducts. Molecular dynamics simulations and free energy calculations reveal that the anti base-displaced intercalated conformation is the most stable conformer for both types of AL-N(6)-dA adducted DNA, which agrees with previous experimental work on the ALII-N(6)-dA adduct and thereby validates our approach. Interestingly, this conformer differs from the dominant conformations adopted by other N6-linked adenine lesions, including those derived from polycyclic aromatic hydrocarbons. Furthermore, the second most stable syn base-displaced intercalated conformation lies closer in energy to the anti base-displaced intercalated conformation for ALI-N(6)-dA compared to ALII-N(6)-dA. This indicates that a mixture of conformations may be detectable for ALI-N(6)-dA in DNA. If this enhanced conformational flexibility of double-stranded DNA persists when bound to a lesion-bypass polymerase, this provides a possible structural explanation for the previously observed greater nephrotoxic potential for the ALI versus ALII-N(6)-dA adduct. In addition, the structural

  1. Conformal Collineations of the Ricci and Energy-Momentum Tensors in Static Plane Symmetric Space-Times

    Science.gov (United States)

    Akhtar, S. S.; Hussain, T.; Bokhari, A. H.; Khan, F.

    2018-04-01

    We provide a complete classification of static plane symmetric space-times according to conformal Ricci collineations (CRCs) and conformal matter collineations (CMCs) in both the degenerate and nondegenerate cases. In the case of a nondegenerate Ricci tensor, we find a general form of the vector field generating CRCs in terms of unknown functions of t and x subject to some integrability conditions. We then solve the integrability conditions in different cases depending upon the nature of the Ricci tensor and conclude that the static plane symmetric space-times have a 7-, 10- or 15-dimensional Lie algebra of CRCs. Moreover, we find that these space-times admit an infinite number of CRCs if the Ricci tensor is degenerate. We use a similar procedure to study CMCs in the case of a degenerate or nondegenerate matter tensor. We obtain the exact form of some static plane symmetric space-time metrics that admit nontrivial CRCs and CMCs. Finally, we present some physical applications of our obtained results by considering a perfect fluid as a source of the energy-momentum tensor.

  2. Calculation of embodied energy in Sino-USA trade: 1997–2011

    International Nuclear Information System (INIS)

    Yang, Ranran; Long, Ruyin; Yue, Ting; Shi, Haihong

    2014-01-01

    In order to find efficient trade measures to reduce China's energy consumption and to provide theoretical support for the climate talks between China and America, we investigate the impact of Sino-USA trade on energy consumption from the perspective of embodied energy. An Environmental Input–Output Life Cycle Assessment (EIO-LCA) model was established to calculate the total energy consumption coefficient, the direct consumption coefficient and the complete consumption coefficient of the sectors of the national economies of China and America. After taking into consideration the data of every sector of the national economy in Sino-USA trade, energy embodied in the import and export trade between China and America was calculated to verify the real energy flows in Sino-USA trade. The research results suggest the following: China is the net exporter of embodied energy in Sino-USA trade, and coal, crude oil and natural gas are the major components. In 1997–2011, the net exports of China's embodied energy totaled 1523,082,200 t of standard coal, the amount of China's energy consumption increased by 895,527,900 t of standard coal, and America's energy consumption decreased by 11,871,200 t of standard coal as a result of Sino-USA trade. On this basis, corresponding policies and recommendations are proposed. - Highlights: • An EIO-LCA model is established to examine China's embodied energy in Sino-USA trade. • Embodied energy is calculated from the perspective of energy sources. • China is found to be the net exporter of embodied energy in Sino-USA trade. • Coal, crude oil and natural gas are the major components of China's net embodied energy exports. • China's energy consumption has increased and America's has shifted to China in Sino-USA trade

  3. 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.

  4. Shielding calculation for treatment rooms of high energy linear accelerator

    International Nuclear Information System (INIS)

    Elleithy, M.A.

    2006-01-01

    A review of German Institute of Standardization (DIN) scheme of the shielding calculation and the essential data required has been done for X-rays and electron beam in the energy range from 1 MeV to 50 MeV. Shielding calculation was done for primary and secondary radiations generated during X-ray operation of Linac. In addition, shielding was done against X-rays generated (Bremsstrahlung) by useful electron beams. The calculations also covered the neutrons generated from the interactions of useful X-rays (at energies above 8 MeV) with the surrounding. The present application involved the computation of shielding against the double scattered components of X-rays and neutrons in the maze area and the thickness of the paraffin wax of the room door. A new developed computer program was designed to assist shielding thickness calculations for a new Linac installation or in replacing an existing machine. The program used a combination of published tables and figures in computing the shielding thickness at different locations for all possible radiation situations. The DIN published data of 40 MeV accelerator room was compared with the program calculations. It was found that there is good agreement between both calculations. The developed program improved the accuracy and speed of calculation

  5. Theoretical high energy physics: Progress report, May 1, 1988--April 30, 1989

    International Nuclear Information System (INIS)

    Lee, T.D.

    1989-05-01

    This paper discusses theoretical research done in high energy physics at Columbia University. Some of the topics discussed are: conformal field theory; QCD calculations; study of long-range forces; superconductivity; and cosmology

  6. Application of Indenting Method for Calculation of Activation Energy

    International Nuclear Information System (INIS)

    Kim, Jong-Seog; Kim, Tae-Ryong

    2006-01-01

    For the calculation of activation energy of cable materials, we used to apply the break-elongation test in accordance with ASTM D412(Stand Test Methods for Rubber Properties in Tension). For the cable jacket and insulation which have regular thickness, break-elongation test had been preferred since it showed linear character in the activation energy curve. But, for the cable which has irregular thickness or rugged surface of cable inside, break-elongation test show scattered data which can not be used for the calculation of activation energy. It is not easy to prepare break-elongation specimen for the cable smaller than 13mm diameter in accordance with ASTM D412. In the cases of above, we sometime use TGA method which heat the specimen from 50 .deg. C to 700 .deg. C at heating rates of 10, 15, 20 .deg. C/min. But, TGA is suspected for the representative of natural aging in the plant since it measure the weight decreasing rate during burning which may have different aging mechanism with that of natural aging. To solve above problems, we investigated alternatives such as indenter test. Indenter test is very convenient since it does not ask for a special test specimen as the break-elongation test does. Regular surface of cable outside is the only requirement of indenter test. Experience of activation energy calculation by using the indenter test is described herein

  7. Control of the conformations of ion Coulomb crystals in a Penning trap

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, R. C.; Mavadia, S.; Goodwin, J. F.; Stutter, G.; Bharadia, S.; Crick, D. R.; Segal, D. M. [Blackett Laboratory, Imperial College London, London SW7 2AZ (United Kingdom)

    2015-06-29

    Ion Coulomb crystals containing small numbers of ions have been created and manipulated in a wide range of configurations in a Penning trap, from a linear string, through various three-dimensional conformations, to a planar crystal. We show that the dynamics of the system simplifies enormously in a frame which rotates at half the cyclotron frequency and we discuss the effect of the radial cooling laser beam in this frame. Simulations show that the crystal conformations can be reproduced by finding the minimum energy configuration in a frame whose radial potential is modified by the rotation of the ion crystal. The rotation frequency of the crystal deduced from the simulations is consistent with the known laser parameters. We also show that even though the number of ions in our system is small (typically less than 20), the system still behaves like a plasma and its static properties can be calculated using the standard model for a single-component plasma in a trap.

  8. Control of the conformations of ion Coulomb crystals in a Penning trap

    International Nuclear Information System (INIS)

    Thompson, R. C.; Mavadia, S.; Goodwin, J. F.; Stutter, G.; Bharadia, S.; Crick, D. R.; Segal, D. M.

    2015-01-01

    Ion Coulomb crystals containing small numbers of ions have been created and manipulated in a wide range of configurations in a Penning trap, from a linear string, through various three-dimensional conformations, to a planar crystal. We show that the dynamics of the system simplifies enormously in a frame which rotates at half the cyclotron frequency and we discuss the effect of the radial cooling laser beam in this frame. Simulations show that the crystal conformations can be reproduced by finding the minimum energy configuration in a frame whose radial potential is modified by the rotation of the ion crystal. The rotation frequency of the crystal deduced from the simulations is consistent with the known laser parameters. We also show that even though the number of ions in our system is small (typically less than 20), the system still behaves like a plasma and its static properties can be calculated using the standard model for a single-component plasma in a trap

  9. Efficiency of free-energy calculations of spin lattices by spectral quantum algorithms

    International Nuclear Information System (INIS)

    Master, Cyrus P.; Yamaguchi, Fumiko; Yamamoto, Yoshihisa

    2003-01-01

    Ensemble quantum algorithms are well suited to calculate estimates of the energy spectra for spin-lattice systems. Based on the phase estimation algorithm, these algorithms efficiently estimate discrete Fourier coefficients of the density of states. Their efficiency in calculating the free energy per spin of general spin lattices to bounded error is examined. We find that the number of Fourier components required to bound the error in the free energy due to the broadening of the density of states scales polynomially with the number of spins in the lattice. However, the precision with which the Fourier components must be calculated is found to be an exponential function of the system size

  10. Calculation and Measurement of Low-Energy Radiative Moller Scattering

    Science.gov (United States)

    Epstein, Charles; DarkLight Collaboration

    2017-09-01

    A number of current nuclear physics experiments have come to rely on precise knowledge of electron-electron (Moller) and positron-electron (Bhabha) scattering. Some of these experiments, having lepton beams on targets containing atomic electrons, use these purely-QED processes as normalization. In other scenarios, with electron beams at low energy and very high intensity, Moller scattering and radiative Moller scattering have such enormous cross-sections that the backgrounds they produce must be understood. In this low-energy regime, the electron mass is also not negligible in the calculation of the cross section. This is important, for example, in the DarkLight experiment (100 MeV). As a result, we have developed a new event generator for the radiative Moller and Bhabha processes, with new calculations that keep all terms of the electron mass. The MIT High Voltage Research Laboratory provides us a unique opportunity to study this process experimentally and compare it with our work, at a low beam energy of 2.5 MeV where the effects of the electron mass are significant. We are preparing a dedicated apparatus consisting of a magnetic spectrometer in order to directly measure this process. An overview of the calculation and the status of the experiment will be presented.

  11. Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (phi-psi) space

    NARCIS (Netherlands)

    Liu, Z.; Ensing, B.; Moore, P.B.

    2011-01-01

    The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (phi-psi) conformational space. The FES is obtained from metadynamics simulations with five commonly used

  12. Stored energy calculation: the state of the art

    International Nuclear Information System (INIS)

    Cunningham, M.E.; Lanning, D.D.; Olsen, A.R.; Williford, R.E.; Hann, C.R.

    1978-05-01

    The report is the result of an investigation to determine the current state of the art of fuel temperature, gap conductance, and stored energy calculations. Major emphasis was placed on the propagation of input and model uncertainties. To support this study a comparison was made to the observed variability of experimental data for fuel centerline temperature and gap conductance values. The uncertainty analysis was performed by identifying major thermal models and collecting them into an abstract of a thermal performance code. Uncertainties in the calculations were determined using the method of propagation of uncertainties with a first order Taylor series approximation to the nonlinear functions. Output uncertainty results are presented for the beginning of fuel life, the end of life, and throughout a typical power history. Also presented is an influence and importance analysis for the input parameters. It is concluded that the relative uncertainty in stored energy is approximately +-20 percent at beginning of fuel life, and increases to +-25 to 40 percent contact. The foregoing are 3 sigma (99.9 percent) confidence intervals. The most important contributors to stored energy uncertainty are linear heat rating and fuel thermal conductivity

  13. 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.

  14. Extraction of conformal data in critical quantum spin chains using the Koo-Saleur formula

    Science.gov (United States)

    Milsted, Ashley; Vidal, Guifre

    2017-12-01

    We study the emergence of two-dimensional conformal symmetry in critical quantum spin chains on the finite circle. Our goal is to characterize the conformal field theory (CFT) describing the universality class of the corresponding quantum phase transition. As a means to this end, we propose and demonstrate automated procedures which, using only the lattice Hamiltonian H =∑jhj as an input, systematically identify the low-energy eigenstates corresponding to Virasoro primary and quasiprimary operators, and assign the remaining low-energy eigenstates to conformal towers. The energies and momenta of the primary operator states are needed to determine the primary operator scaling dimensions and conformal spins, an essential part of the conformal data that specifies the CFT. Our techniques use the action, on the low-energy eigenstates of H , of the Fourier modes Hn of the Hamiltonian density hj. The Hn were introduced as lattice representations of the Virasoro generators by Koo and Saleur [Nucl. Phys. B 426, 459 (1994), 10.1016/0550-3213(94)90018-3]. In this paper, we demonstrate that these operators can be used to extract conformal data in a nonintegrable quantum spin chain.

  15. Verification of the DUCT-III for calculation of high energy neutron streaming

    Energy Technology Data Exchange (ETDEWEB)

    Masukawa, Fumihiro; Nakano, Hideo; Nakashima, Hiroshi; Sasamoto, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Tayama, Ryu-ichi; Handa, Hiroyuki; Hayashi, Katsumi [Hitachi Engineering Co., Ltd., Hitachi, Ibaraki (Japan); Hirayama, Hideo [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Shin, Kazuo [Kyoto Univ., Kyoto (Japan)

    2003-03-01

    A large number of radiation streaming calculations under a variety of conditions are required as a part of shielding design for a high energy proton accelerator facility. Since sophisticated methods are very time consuming, simplified methods are employed in many cases. For accuracy evaluation of a simplified code DUCT-III for high energy neutron streaming calculations, two kinds of benchmark problems based on the experiments were analyzed. Through comparison of the DUCT-III calculations with both the measurements and the sophisticated Monte Carlo calculations, DUCT-III was seen reliable enough for applying to the shielding design for the Intense Proton Accelerator Facility. (author)

  16. Verification of the DUCT-III for calculation of high energy neutron streaming

    CERN Document Server

    Masukawa, F; Hayashi, K; Hirayama, H; Nakano, H; Nakashima, H; Sasamoto, N; Shin, K; Tayama, R I

    2003-01-01

    A large number of radiation streaming calculations under a variety of conditions are required as a part of shielding design for a high energy proton accelerator facility. Since sophisticated methods are very time consuming, simplified methods are employed in many cases. For accuracy evaluation of a simplified code DUCT-III for high energy neutron streaming calculations, two kinds of benchmark problems based on the experiments were analyzed. Through comparison of the DUCT-III calculations with both the measurements and the sophisticated Monte Carlo calculations, DUCT-III was seen reliable enough for applying to the shielding design for the Intense Proton Accelerator Facility.

  17. Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer

    Science.gov (United States)

    Hameed, Rabia; Khan, Afsar; van Mourik, Tanja

    2018-05-01

    B3LYP and MP2 calculations with the commonly-used 6-31+G(d) basis set predict qualitatively different structures for the Tyr-Gly conformer book1, which is the most stable conformer identified in a previous study. The structures differ mainly in the ψtyr Ramachandran angle (138° in the B3LYP structure and 120° in the MP2 structure). The causes for the discrepant structures are attributed to missing dispersion in the B3LYP calculations and large intramolecular BSSE in the MP2 calculations. The correct ψtyr value is estimated to be 130°. The MP2/6-31+G(d) profile identified an additional conformer, not present on the B3LYP surface, with a ψtyr value of 96° and a more folded structure. This minimum is, however, likely an artefact of large intramolecular BSSE values. We recommend the use of basis sets of at least quadruple-zeta quality in density functional theory (DFT), DFTaugmented with an empirical dispersion term (DFT-D) and second-order Møller-Plesset perturbation theory (MP2 ) calculations in cases where intramolecular BSSE is expected to be large.

  18. Exploring the relationship between the conformation and pKa

    DEFF Research Database (Denmark)

    Olsen, Jacob Ingemar; Sauer, Stephan P. A.; Pedersen, Christian Marcus

    2015-01-01

    Four substituted cis and trans-4,5-dihydroxyhexahydropyridazines that were expected to undergo pH induced conformational switching were synthesized and carefully investigated by NMR analyses and calculations. For two of the compounds a large difference in pKa existed between the two possible chair...... conformers and for one compound this resulted in conformational switching as a result of pH change. For the first time it is shown that the pKa directly reflects the conformational equilibrium of conformers....

  19. Understanding modern magnets through conformal mapping

    International Nuclear Information System (INIS)

    Halbach, K.

    1989-10-01

    I want to show with the help of a number of examples that conformal mapping is a unique and enormously powerful tool for thinking about, and solving, problems. Usually one has to write down only a few equations, and sometimes none at all exclamation point When I started getting involved in work for which conformal mapping seemed to be a powerful tool, I did not think that I would ever be able to use that technique successfully because it seemed to require a nearly encyclopedic memory, an impression that was strengthened when I saw K. Kober's Dictionary of Conformal Representations. This attitude changed when I started to realize that beyond the basics of the theory of a function of a complex variable, I needed to know only about a handful of conformal maps and procedures. Consequently, my second goal for this talk is to show that in most cases conformal mapping functions can be obtained by formulating the underlying physics appropriately. This means particularly that encyclopedic knowledge of conformal maps is not necessary for successful use of conformal mapping techniques. To demonstrate these facts I have chosen examples from an area of physics/engineering in which I am active, namely accelerator physics. In order to do that successfully I start with a brief introduction into high energy charged particle storage ring technology, even though not all examples used in this paper to elucidate my points come directly from this particular field of accelerator technology

  20. Nuclear magnetic resonance study of alkane conformational statistics

    Science.gov (United States)

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

    2011-12-01

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

  1. Improved initial guess for minimum energy path calculations

    International Nuclear Information System (INIS)

    Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt; Jónsson, Hannes

    2014-01-01

    A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used

  2. Comparison between calculation and measurement of energy deposited by 800 MeV protons

    International Nuclear Information System (INIS)

    Loewe, W.E.

    1980-01-01

    The High Energy Transport Code, HETC, was obtained from the Radiation Shielding Information Center (RSIC) at Oak Ridge National Laboratory and altered as necessary to run on a CDC 7600 using the LTSS software in use at LLNL. HETC was then used to obtain calculated estimates of energy deposited, for comparison with a series of benchmark experiments done by LLNL. These experiments used proton beams of various energies incident on well-defined composite targets in good geometry. In this report, two aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam are discussed. Both aspects involve the fact that workers at SAI had previously used their version of HETC to calculate this experiment and reported their comparison with the measured data. The first aspect addressed is that their calculated data and LLNL calculations do not agree, suggesting an error in the conversion process from the RSIC code. The second aspect is not independent of the first, but is of sufficient importance to merit separate emphasis. It is that the SAI calculations agree well with experiments at the detector plate located some distance from the shower plate, whereas the LLNL calculations show a clearcut discrepancy there in comparison with the experiment. A contract was let in January 1980 by LLNL with SAI in order to obtain full details on the two cited aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam. The ensuing discussion is based on the final report of that contracted work

  3. Monte Carlo calculations for intermediate-energy standard neutron field

    International Nuclear Information System (INIS)

    Joneja, O.P.; Subbukutty, K.; Iyengar, S.B.D.; Navalkar, M.P.

    Intermediate-Energy Standard Neutron Field (ISNF) which produces a well characterised spectrum in the energy range of interest for fast reactors including breeders, has been set up at NBS using thin enriched 235 U fission sources. A proposal has been made for setting up a similar facility at BARC using however, easily available natural U instead of enriched U sources, to start with. In order to simulate the neutronics of such a facility Monte Carlo method of calculations has been adopted and developed. The results of these calculations have been compared with those of NBS and it is found that there may be a maximum difference of 10% in spectrum characteristics for the two cases of using thick and thin fission sources. (K.B.)

  4. Conformational impact of structural modifications in 2-fluorocyclohexanone

    Directory of Open Access Journals (Sweden)

    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.

  5. 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.

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

    Science.gov (United States)

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

    2017-10-01

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

  7. Calculation of the Coulomb nuclear energy for the 1fsub(7/2) shell

    International Nuclear Information System (INIS)

    Kaminski, V.A.; Shpikovski, S.

    1980-01-01

    Calculated was the Coulomb energy for nuclei with half-filled 1fsub(7/2) shell i.e. for configurations, where quasiparticle basis can serve as a total basis for precise calculations. Presented are calculation results of vector and tensor components of the Coulomb energy for Ca-Se-Ti-V isobaric pairs, as well as experimental and theoretical values for the Coulomb displacements. To estimate the Coulomb energies used were wave functions of a Hamiltonian taking account of pair and quadrupole interactions. There is good agreement with experimental data. Quasiparticle consideration is useful for calculating matrix elements of half-filled shells and for the cases of such an isospin value, where the technique of genealogical coefficients becomes extremely cumbersome

  8. Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

    Science.gov (United States)

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

    2017-06-07

    We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

  9. Methodology to Calculate the Costs of a Floating Offshore Renewable Energy Farm

    Directory of Open Access Journals (Sweden)

    Laura Castro-Santos

    2016-04-01

    Full Text Available This paper establishes a general methodology to calculate the life-cycle cost of floating offshore renewable energy devices, applying it to wave energy and wind energy devices. It is accounts for the contributions of the six main phases of their life-cycle: concept definition, design and development, manufacturing, installation, exploitation and dismantling, the costs of which have been defined. Moreover, the energy produced is also taken into account to calculate the Levelized Cost of Energy of a floating offshore renewable energy farm. The methodology proposed has been applied to two renewable energy devices: a floating offshore wave energy device and a floating offshore wind energy device. Two locations have been considered: Aguçadoura and São Pedro de Moel, both in Portugal. Results indicate that the most important cost in terms of the life-cycle of a floating offshore renewable energy farm is the exploitation cost, followed by the manufacturing and the installation cost. In addition, the best area in terms of costs is the same independently of the type of floating offshore renewable energy considered: Aguçadoura. However, the results in terms of Levelized Cost of Energy are different: Aguçadoura is better when considering wave energy technology and the São Pedro de Moel region is the best option when considering floating wind energy technology. The method proposed aims to give a direct approach to calculate the main life-cycle cost of a floating offshore renewable energy farm. It helps to assess its feasibility and evaluating the relevant characteristics that influence it the most.

  10. High energy ion range and deposited energy calculation using the Boltzmann-Fokker-Planck splitting of the Boltzmann transport equation

    International Nuclear Information System (INIS)

    Mozolevski, I.E.

    2001-01-01

    We consider the splitting of the straight-ahead Boltzmann transport equation in the Boltzmann-Fokker-Planck equation, decomposing the differential cross-section into a singular part, corresponding to small energy transfer events, and in a regular one, which corresponds to large energy transfer. The convergence of implantation profile, nuclear and electronic energy depositions, calculated from the Boltzmann-Fokker-Planck equation, to the respective exact distributions, calculated from Monte-Carlo method, was exanimate in a large-energy interval for various values of splitting parameter and for different ion-target mass relations. It is shown that for the universal potential there exists an optimal value of splitting parameter, for which range and deposited energy distributions, calculated from the Boltzmann-Fokker-Planck equation, accurately approximate the exact distributions and which minimizes the computational expenses

  11. Ab initio calculation of electron excitation energies in solids

    International Nuclear Information System (INIS)

    Louie, S.G.

    1996-02-01

    Progress in the first-principles calculation of electron excitation energies in solids is discussed. Quasiparticle energies are computed by expanding the electron self energy to first order in the screened Coulomb interaction in the so-called GW approximation. The method was applied to explain and predict spectroscopic properties of a variety of systems. Several illustrative applications to semiconductors, materials under pressure, chemisorption, and point defects in solids are presented. A recent reformulation of the method employing mixed- space functions and imaginary time techniques is also discussed

  12. Conformal branching rules and modular invariants

    International Nuclear Information System (INIS)

    Walton, M.A.

    1989-01-01

    Using the outer automorphisms of the affine algebra SU(n), we show how the branching rules for the conformal subalgebra SU(pq) contains SU(p) x SU(q) may be simply calculated. We demonstrate that new modular invariant combinations of SU(n) characters are obtainable from the branching rules. (orig.)

  13. Yang–Mills equations on conformally connected torsion-free 4-manifolds with different signatures

    Directory of Open Access Journals (Sweden)

    Vyacheslav A. Luk'yanov

    2017-12-01

    Full Text Available In this paper we study spaces of conformal torsion-free connection of dimension 4 whose connection matrix satisfies the Yang–Mills equations. Here we generalize and strengthen the results obtained by us in previous articles, where the angular metric of these spaces had Minkowski signature. The generalization is that here we investigate the spaces of all possible metric signatures, and the enhancement is due to the fact that additional attention is paid to calculating the curvature matrix and establishing the properties of its components. It is shown that the Yang–Mills equations on 4-manifolds of conformal torsion-free connection for an arbitrary signature of the angular metric are reduced to Einstein's equations, Maxwell's equations and the equality of the Bach tensor of the angular metric and the energy-momentum tensor of the skew-symmetric charge tensor. It is proved that if the Weyl tensor is zero, the Yang–Mills equations have only self-dual or anti-self-dual solutions, i.e the curvature matrix of a conformal connection consists of self-dual or anti-self-dual external 2-forms. With the Minkowski signature (antiself-dual external 2-forms can only be zero. The components of the curvature matrix are calculated in the case when the angular metric of an arbitrary signature is Einstein, and the connection satisfies the Yang–Mills equations. In the Euclidean and pseudo-Euclidean 4-spaces we give some particular self-dual and anti-self-dual solutions of the Maxwell equations, to which all the Yang–Mills equations are reduced in this case.

  14. Relativistic deformed mean-field calculation of binding energy differences of mirror nuclei

    International Nuclear Information System (INIS)

    Koepf, W.; Barreiro, L.A.

    1996-01-01

    Binding energy differences of mirror nuclei for A=15, 17, 27, 29, 31, 33, 39 and 41 are calculated in the framework of relativistic deformed mean-field theory. The spatial components of the vector meson fields and the photon are fully taken into account in a self-consistent manner. The calculated binding energy differences are systematically smaller than the experimental values and lend support to the existence of the Okamoto-Nolen-Schiffer anomaly found decades ago in nonrelativistic calculations. For the majority of the nuclei studied, however, the results are such that the anomaly is significantly smaller than the one obtained within state-of-the-art nonrelativistic calculations. (author). 35 refs

  15. AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

    Science.gov (United States)

    Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

    2016-06-27

    Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection.

  16. Rapid roll inflation with conformal coupling

    International Nuclear Information System (INIS)

    Kofman, Lev; Mukohyama, Shinji

    2008-01-01

    Usual inflation is realized with a slow rolling scalar field minimally coupled to gravity. In contrast, we consider dynamics of a scalar with a flat effective potential, conformally coupled to gravity. Surprisingly, it contains an attractor inflationary solution with the rapidly rolling inflaton field. We discuss models with the conformal inflaton with a flat potential (including hybrid inflation). There is no generation of cosmological fluctuations from the conformally coupled inflaton. We consider realizations of modulated (inhomogeneous reheating) or curvaton cosmological fluctuations in these models. We also implement these unusual features for the popular string-theoretic warped inflationary scenario, based on the interacting D3-D3 branes. The original warped brane inflation suffers a large inflaton mass due to conformal coupling to 4-dimensional gravity. Instead of considering this as a problem and trying to cure it with extra engineering, we show that warped inflation with the conformally coupled, rapidly rolling inflaton is yet possible with N=37 efoldings, which requires low-energy scales 1-100 TeV of inflation. Coincidentally, the same warping numerology can be responsible for the hierarchy. It is shown that the scalars associated with angular isometries of the warped geometry of compact manifold (e.g. S 3 of Klebanov-Strassler (KS) geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities

  17. Rapid roll inflation with conformal coupling

    Science.gov (United States)

    Kofman, Lev; Mukohyama, Shinji

    2008-02-01

    Usual inflation is realized with a slow rolling scalar field minimally coupled to gravity. In contrast, we consider dynamics of a scalar with a flat effective potential, conformally coupled to gravity. Surprisingly, it contains an attractor inflationary solution with the rapidly rolling inflaton field. We discuss models with the conformal inflaton with a flat potential (including hybrid inflation). There is no generation of cosmological fluctuations from the conformally coupled inflaton. We consider realizations of modulated (inhomogeneous reheating) or curvaton cosmological fluctuations in these models. We also implement these unusual features for the popular string-theoretic warped inflationary scenario, based on the interacting D3-D¯3 branes. The original warped brane inflation suffers a large inflaton mass due to conformal coupling to 4-dimensional gravity. Instead of considering this as a problem and trying to cure it with extra engineering, we show that warped inflation with the conformally coupled, rapidly rolling inflaton is yet possible with N=37 efoldings, which requires low-energy scales 1 100 TeV of inflation. Coincidentally, the same warping numerology can be responsible for the hierarchy. It is shown that the scalars associated with angular isometries of the warped geometry of compact manifold (e.g. S3 of Klebanov-Strassler (KS) geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities.

  18. Nilpotent weights in conformal field theory

    Directory of Open Access Journals (Sweden)

    S. Rouhani

    2001-12-01

    Full Text Available   Logarithmic conformal field theory can be obtained using nilpotent weights. Using such scale transformations various properties of the theory were derived. The derivation of four point function needs a knowledge of singular vectors which is derived by including nilpotent variables into the Kac determinant. This leads to inhomogeneous hypergeometric functions. Finally we consider the theory near a boundary and also introduce the concept of superfields where a multiplet of conformal fields are dealt with together. This leads to the OPE of superfields and a logarithmic partner for the energy momentum tensor.

  19. Rényi entropy and conformal defects

    International Nuclear Information System (INIS)

    Bianchi, Lorenzo; Meineri, Marco; Myers, Robert C.; Smolkin, Michael

    2016-01-01

    We propose a field theoretic framework for calculating the dependence of Rényi entropies on the shape of the entangling surface in a conformal field theory. Our approach rests on regarding the corresponding twist operator as a conformal defect and in particular, we define the displacement operator which implements small local deformations of the entangling surface. We identify a simple constraint between the coefficient defining the two-point function of the displacement operator and the conformal weight of the twist operator, which consolidates a number of distinct conjectures on the shape dependence of the Rényi entropy. As an example, using this approach, we examine a conjecture regarding the universal coefficient associated with a conical singularity in the entangling surface for CFTs in any number of spacetime dimensions. We also provide a general formula for the second order variation of the Rényi entropy arising from small deformations of a spherical entangling surface, extending Mezei’s results for the entanglement entropy.

  20. Rényi entropy and conformal defects

    Energy Technology Data Exchange (ETDEWEB)

    Bianchi, Lorenzo [Institut für Physik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany); II. Institut für Theoretische Physik, Universität Hamburg,Luruper Chaussee 149, 22761 Hamburg (Germany); Meineri, Marco [Scuola Normale Superiore and Istituto Nazionale di Fisica Nucleare - Sezione di Pisa,Piazza dei Cavalieri 7, I-56126 Pisa (Italy); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo, ON N2L 2Y5 (Canada); Myers, Robert C. [Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo, ON N2L 2Y5 (Canada); Smolkin, Michael [Center for Theoretical Physics, Department of Physics, University of California,Berkeley, CA 94720 (United States)

    2016-07-14

    We propose a field theoretic framework for calculating the dependence of Rényi entropies on the shape of the entangling surface in a conformal field theory. Our approach rests on regarding the corresponding twist operator as a conformal defect and in particular, we define the displacement operator which implements small local deformations of the entangling surface. We identify a simple constraint between the coefficient defining the two-point function of the displacement operator and the conformal weight of the twist operator, which consolidates a number of distinct conjectures on the shape dependence of the Rényi entropy. As an example, using this approach, we examine a conjecture regarding the universal coefficient associated with a conical singularity in the entangling surface for CFTs in any number of spacetime dimensions. We also provide a general formula for the second order variation of the Rényi entropy arising from small deformations of a spherical entangling surface, extending Mezei’s results for the entanglement entropy.

  1. Workers’ Conformism

    Directory of Open Access Journals (Sweden)

    Nikolay Ivantchev

    2013-10-01

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

  2. Proton affinity of diastereoisomers of modified prolines using the kinetic method and density functional theory calculations: role of the cis/trans substituent on the endo/exo ring conformation.

    Science.gov (United States)

    Mezzache, S; Pepe, C; Karoyan, P; Fournier, F; Tabet, J-C

    2005-01-01

    The proton affinity (PA) of cis/trans-3-prolinoleucines and cis/trans-3-prolinoglutamic acids have been studied by the kinetic method and density functional theory (DFT) calculations. Several conformations of the neutral and the protonated modified prolines, in particular the endo and exo ring conformations, were analyzed with respect to their contribution to the PA values. When the substituent is an alkyl, both the diastereoisomers have the same PA value. However, the PA values for the diastereoisomers are different when the substituted chain contains functional groups (e.g. a carboxyl group). This variation in PA values could be attributed to the existence of intramolecular hydrogen bonds. Copyright (c) 2005 John Wiley & Sons, Ltd.

  3. Extrapolation procedures for calculating high-temperature gibbs free energies of aqueous electrolytes

    International Nuclear Information System (INIS)

    Tremaine, P.R.

    1979-01-01

    Methods for calculating high-temprature Gibbs free energies of mononuclear cations and anions from room-temperature data are reviewed. Emphasis is given to species required for oxide solubility calculations relevant to mass transport situations in the nuclear industry. Free energies predicted by each method are compared to selected values calculated from recently reported solubility studies and other literature data. Values for monatomic ions estimated using the assumption anti C 0 p(T) = anti C 0 p(298) agree best with experiment to 423 K. From 423 K to 523 K, free energies from an electrostatic model for ion hydration are more accurate. Extrapolations for hydrolyzed species are limited by a lack of room-temperature entropy data and expressions for estimating these entropies are discussed. (orig.) [de

  4. Calculation of CO2 emissions from the italian energy system

    International Nuclear Information System (INIS)

    Contaldi, M.; La Motta, S.

    2001-01-01

    The calculation of CO2 emissions from the Italian energy system is the object of this work. The inventory method used is the Reference Approach from the Intergovernmental Panel for Climate Change (IPCC, 1996 revised Guidelines for National Greenhouse Gas Inventories) and the energy consumption data are taken from the Italian Energy Balance edited by the Ministry of Industry. The years analysed are those from 1990 to 2000 [it

  5. Gas-phase Conformational Analysis of (R,R)-Tartaric Acid, its Diamide, N,N,N',N'- Tetramethyldiamide and Model Compounds

    Science.gov (United States)

    Hoffmann, Marcin; Szarecka, Agnieszka; Rychlewski, Jacek

    A review over most recent ab initio studies carried out at both RHF and MP2 levels on (R,R)-tartaric acid (TA), its diamide (DA), tetramethyldiamide (TMDA) and on three prototypic model systems (each of them constitutes a half of the respective parental molecule), i.e. 2-hydroxyacetic acid (HA), 2-hydroxyacetamide (HD) and 2-hydroxy-N,N-dimethylacetamide (HMD) is presented. (R,R)-tartaric acid and the derivatives have been completely optimized at RHF/6-31G* level and subsequently single-point energies of all conformers have been calculated with the use of second order perturbation theory according to the scheme: MP2/6-31G*//RHF/6-31G*. In the complete optimization of the model molecules at RHF level we have employed relatively large basis sets, augmented with polarisation and diffuse functions, namely 3-21G, 6-31G*, 6-31++G** and 6-311++G**. Electronic correlation has been included with the largest basis set used in this study, i.e. MP2/6-311++G**//RHF/6-311++G** single-point energy calculations have been performed. General confomational preferences of tartaric acid derivatives have been analysed as well as an attempt has been made to define main factors affecting the conformational behaviour of these molecules in the isolated state, in particular, the role and stability of intramolecular hydrogen bonding. In the case of the model compounds, our study principally concerned the conformational preferences and hydrogen bonding structure within the [alpha]-hydroxy-X moiety, where X=COOH, CONH2, CON(CH3)2.

  6. Conformation radiotherapy and conformal radiotherapy

    International Nuclear Information System (INIS)

    Morita, Kozo

    1999-01-01

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

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

    Science.gov (United States)

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

    2017-06-01

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

  8. Killing tensors and conformal Killing tensors from conformal Killing vectors

    International Nuclear Information System (INIS)

    Rani, Raffaele; Edgar, S Brian; Barnes, Alan

    2003-01-01

    Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors

  9. [Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

    Science.gov (United States)

    Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

    2016-01-01

    limits typical for the corresponding family. We observe that popular functionals in density functional theory calculations lead to the overestimated distances between base pairs, while MP2 computations and the newer complex functionals produce the structures that have too close atom-atom contacts. A detailed study of some complementary desoxydinucleoside monophosphate complexes with Na-ions highlights the existence of several energy minima corresponding to BI-conformations, in other words, the complexity of the relief pattern of the potential energy surface of complementary desoxydinucleoside monophosphate complexes. This accounts for variability of conformational parameters of duplex fragments with the same base sequence. Popular molecular mechanics force fields AMBER and CHARMM reproduce most of the conformational characteristics of desoxydinucleoside monophosphates and their complementary complexes with Na-ions but fail to reproduce some details of the dependence of the Watson-Crick duplex conformation on the nucleotide sequence.

  10. Gel dosimetry for conformal radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Gambarini, G [Department of Physics of the University and INFN, Milan (Italy)

    2005-07-01

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

  11. Conformal intensity-modulated radiotherapy (IMRT) delivered by robotic linac-conformality versus efficiency of dose delivery

    International Nuclear Information System (INIS)

    Webb, Steve

    2000-01-01

    Intensity-modulated radiotherapy (IMRT) may be delivered with a high-energy-photon linac mounted on a robotic gantry and executing a complex trajectory. In a previous paper an inverse-planning technique was developed for such an application. Here the work is extended to demonstrate the dependence of conformality on the size of the elemental pencil beam, on the complexity of the trajectory and on the sampling of azimuth and elevation of the collimated source. The improved conformality of complex trajectories is demonstrated and benchmarked relative to simpler trajectories, more representative of existing non-robotic IMRT techniques. Specifically, by choosing a very fine pencil beam, exquisitely conformal dose distributions have been obtained. Important sampling considerations have been determined. Expressions have been derived for the dosimetry and monitor-unit efficiency of robotic IMRT. Equivalent trajectories were computed for executing the complex robotic trajectories instead by using a conventional linac. The work benchmarks an ideal in IMRT against which more practical and more common techniques may be measured. (author)

  12. Higgs Critical Exponents and Conformal Bootstrap in Four Dimensions

    DEFF Research Database (Denmark)

    Antipin, Oleg; Mølgaard, Esben; Sannino, Francesco

    2015-01-01

    We investigate relevant properties of composite operators emerging in nonsupersymmetric, four-dimensional gauge-Yukawa theories with interacting conformal fixed points within a precise framework. The theories investigated in this work are structurally similar to the standard model of particle int...... bootstrap results are then compared to precise four dimensional conformal field theoretical results. To accomplish this, it was necessary to calculate explicitly the crossing symmetry relations for the global symmetry group SU($N$)$\\times$SU($N$)....

  13. Gamma-point lattice free energy estimates from O(1) force calculations

    DEFF Research Database (Denmark)

    Voss, Johannes; Vegge, Tejs

    2008-01-01

    We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum...

  14. N3 and O2 Protonated Conformers of the Cytosine Mononucleotides Coexist in the Gas Phase

    Science.gov (United States)

    Wu, R. R.; Hamlow, L. A.; He, C. C.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M. T.

    2017-08-01

    The gas-phase conformations of the protonated forms of the DNA and RNA cytosine mononucleotides, [pdCyd+H]+ and [pCyd+H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy over the IR fingerprint and hydrogen-stretching regions complemented by electronic structure calculations. The low-energy conformations of [pdCyd+H]+ and [pCyd+H]+ and their relative stabilities are computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers allow the conformers present in the experiments to be determined. Similar to that found in previous IRMPD action spectroscopy studies of the protonated forms of the cytosine nucleosides, [dCyd+H]+ and [Cyd+H]+, both N3 and O2 protonated cytosine mononucleotides exhibiting an anti orientation of cytosine are found to coexist in the experimental population. The 2'-hydroxyl substituent does not significantly influence the most stable conformations of [pCyd+H]+ versus those of [pdCyd+H]+, as the IRMPD spectral profiles of [pdCyd+H]+ and [pCyd+H]+ are similar. However, the presence of the 2'-hydroxyl substituent does influence the relative intensities of the measured IRMPD bands. Comparisons to IRMPD spectroscopy studies of the deprotonated forms of the cytosine mononucleotides, [pdCyd-H]- and [pCyd-H]-, provide insight into the effects of protonation versus deprotonation on the conformational features of the nucleobase and sugar moieties. Likewise, comparisons to results of IRMPD spectroscopy studies of the protonated cytosine nucleosides provide insight into the influence of the phosphate moiety on structure. Comparison with previous ion mobility results shows the superiority of IRMPD spectroscopy for distinguishing various protonation sites.

  15. 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

  16. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  17. Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems

    Science.gov (United States)

    Swinburne, Thomas D.; Marinica, Mihai-Cosmin

    2018-03-01

    The calculation of free energy differences for thermally activated mechanisms in the solid state are routinely hindered by the inability to define a set of collective variable functions that accurately describe the mechanism under study. Even when possible, the requirement of descriptors for each mechanism under study prevents implementation of free energy calculations in the growing range of automated material simulation schemes. We provide a solution, deriving a path-based, exact expression for free energy differences in the solid state which does not require a converged reaction pathway, collective variable functions, Gram matrix evaluations, or probability flux-based estimators. The generality and efficiency of our method is demonstrated on a complex transformation of C 15 interstitial defects in iron and double kink nucleation on a screw dislocation in tungsten, the latter system consisting of more than 120 000 atoms. Both cases exhibit significant anharmonicity under experimentally relevant temperatures.

  18. Application of wavelet scaling function expansion continuous-energy resonance calculation method to MOX fuel problem

    International Nuclear Information System (INIS)

    Yang, W.; Wu, H.; Cao, L.

    2012-01-01

    More and more MOX fuels are used in all over the world in the past several decades. Compared with UO 2 fuel, it contains some new features. For example, the neutron spectrum is harder and more resonance interference effects within the resonance energy range are introduced because of more resonant nuclides contained in the MOX fuel. In this paper, the wavelets scaling function expansion method is applied to study the resonance behavior of plutonium isotopes within MOX fuel. Wavelets scaling function expansion continuous-energy self-shielding method is developed recently. It has been validated and verified by comparison to Monte Carlo calculations. In this method, the continuous-energy cross-sections are utilized within resonance energy, which means that it's capable to solve problems with serious resonance interference effects without iteration calculations. Therefore, this method adapts to treat the MOX fuel resonance calculation problem natively. Furthermore, plutonium isotopes have fierce oscillations of total cross-section within thermal energy range, especially for 240 Pu and 242 Pu. To take thermal resonance effect of plutonium isotopes into consideration the wavelet scaling function expansion continuous-energy resonance calculation code WAVERESON is enhanced by applying the free gas scattering kernel to obtain the continuous-energy scattering source within thermal energy range (2.1 eV to 4.0 eV) contrasting against the resonance energy range in which the elastic scattering kernel is utilized. Finally, all of the calculation results of WAVERESON are compared with MCNP calculation. (authors)

  19. Conformal field theory between supersymmetry and indecomposable structures

    Energy Technology Data Exchange (ETDEWEB)

    Eberle, H.

    2006-07-15

    This thesis considers conformal field theory in its supersymmetric extension as well as in its relaxation to logarithmic conformal field theory. This thesis is concerned with the subspace of K3 compactifications which is not well known yet. In particular, we inspect the intersection point of the Z{sub 2} and Z{sub 4} orbifold subvarieties within the K3 moduli space, explicitly identify the two corresponding points on the subvarieties geometrically, and give an explicit isomorphism of the three conformal field theory models located at that point, a specific Z{sub 2} and Z{sub 4} orbifold model as well as the Gepner model (2){sup 4}. We also prove the orthogonality of the two subvarieties at the intersection point. This is the starting point for the programme to investigate generic points in K3 moduli space. We use the coordinate identification at the intersection point in order to relate the coordinates of both subvarieties and to explicitly calculate a geometric geodesic between the two subvarieties as well as its generator. A generic point in K3 moduli space can be reached by such a geodesic originating at a known model. We also present advances on the conformal field theoretic side of deformations along such a geodesic using conformal deformation theory. Moreover, we regard a relaxation of conformal field theory to logarithmic conformal field theory. In particular, we study general augmented c{sub p,q} minimal models which generalise the well-known (augmented) c{sub p,1} model series. We calculate logarithmic nullvectors in both types of models. But most importantly, we investigate the low lying Virasoro representation content and fusion algebra of two general augmented c{sub p,q} models, the augmented c{sub 2,3}=0 model as well as the augmented Yang-Lee model at c{sub 2,5}=-22/5. In particular, the true vacuum representation is rather given by a rank 1 indecomposable but not irreducible subrepresentation of a rank 2 representation. We generalise these generic

  20. Conformal field theory between supersymmetry and indecomposable structures

    International Nuclear Information System (INIS)

    Eberle, H.

    2006-07-01

    This thesis considers conformal field theory in its supersymmetric extension as well as in its relaxation to logarithmic conformal field theory. This thesis is concerned with the subspace of K3 compactifications which is not well known yet. In particular, we inspect the intersection point of the Z 2 and Z 4 orbifold subvarieties within the K3 moduli space, explicitly identify the two corresponding points on the subvarieties geometrically, and give an explicit isomorphism of the three conformal field theory models located at that point, a specific Z 2 and Z 4 orbifold model as well as the Gepner model (2) 4 . We also prove the orthogonality of the two subvarieties at the intersection point. This is the starting point for the programme to investigate generic points in K3 moduli space. We use the coordinate identification at the intersection point in order to relate the coordinates of both subvarieties and to explicitly calculate a geometric geodesic between the two subvarieties as well as its generator. A generic point in K3 moduli space can be reached by such a geodesic originating at a known model. We also present advances on the conformal field theoretic side of deformations along such a geodesic using conformal deformation theory. Moreover, we regard a relaxation of conformal field theory to logarithmic conformal field theory. In particular, we study general augmented c p,q minimal models which generalise the well-known (augmented) c p,1 model series. We calculate logarithmic nullvectors in both types of models. But most importantly, we investigate the low lying Virasoro representation content and fusion algebra of two general augmented c p,q models, the augmented c 2,3 =0 model as well as the augmented Yang-Lee model at c 2,5 =-22/5. In particular, the true vacuum representation is rather given by a rank 1 indecomposable but not irreducible subrepresentation of a rank 2 representation. We generalise these generic examples to give the representation content and

  1. Conformational change of spin labelled myoglobin

    International Nuclear Information System (INIS)

    Wajnberg, E.; Ribeiro, P.C.; Nascimento, O.R.; Bemski, G.

    1978-01-01

    A conformational change of spin labelled myoglobin have been followed by measuring the spin label's (isothiocyanate) correlation time for temperatures between 18 0 C and 44 0 C. The correlation time was calculated from Electrom Paramagnetic Ressonance Spectra using the components of the espectroscopic and hiperfine tensors obtained by fitting the powder spectra using Lefebvre and Maruani's program- [pt

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

    Science.gov (United States)

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

    2013-02-01

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

  3. Conventional method for the calculation of the global energy cost of buildings; Methode conventionnelle de calcul du cout global energetique des batiments

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-05-01

    A working group driven by Electricite de France (EdF), Chauffage Fioul and Gaz de France (GdF) companies has been built with the sustain of several building engineering companies in order to clarify the use of the method of calculation of the global energy cost of buildings. This global cost is an economical decision help criterion among others. This press kit presents, first, the content of the method (input data, calculation of annual expenses, calculation of the global energy cost, display of results and limitations of the method). Then it fully describes the method and its appendixes necessary for its implementation: economical and financial context, general data of the project in progress, environmental data, occupation and comfort level, variants, investment cost of energy systems, investment cost for the structure linked with the energy system, investment cost for other invariant elements of the structure, calculation of consumptions (space heating, hot water, ventilation), maintenance costs (energy systems, structure), operation and exploitation costs, tariffs and consumption costs and taxes, actualized global cost, annualized global cost, comparison between variants. The method is applied to a council building of 23 flats taken as an example. (J.S.)

  4. Toward understanding as photosynthetic biosignatures: light harvesting and energy transfer calculation

    Science.gov (United States)

    Komatsu, Y.; Umemura, M.; Shoji, M.; Shiraishi, K.; Kayanuma, M.; Yabana, K.

    2014-03-01

    Among several proposed biosignatures, red edge is a direct evidence of photosynthetic life if it is detected (Kiang et al 2007). Red edge is a sharp change in reflectance spectra of vegetation in NIR region (about 700-750 nm). The sign of red edge is observed by Earthshine or remote sensing (Wolstencroft & Raven 2002, Woolf et al 2002). But, why around 700-750 nm? The photosynthetic organisms on Earth have evolved to optimize the sunlight condition. However, if we consider about photosynthetic organism on extrasolar planets, they should have developed to utilize the spectra of its principal star. Thus, it is not strange even if it shows different vegetation spectra. In this study, we focused on the light absorption mechanism of photosynthetic organisms on Earth and investigated the fundamental properties of the light harvesting mechanisms, which is the first stage for the light absorption. Light harvesting complexes contain photosynthetic pigments like chlorophylls. Effective light absorption and the energy transfer are accomplished by the electronic excitations of collective photosynthetic pigments. In order to investigate this mechanism, we constructed an energy transfer model by using a dipole-dipole approximation for the interactions between electronic excitations. Transition moments and transition energies of each pigment are calculated at the time-dependent density functional theory (TDDFT) level (Marques & Gross 2004). Quantum dynamics simulation for the excitation energy transfer was calculated by the Liouvelle's equation. We adopted the model to purple bacteria, which has been studied experimentally and known to absorb lower energy. It is meaningful to focus on the mechanism of this bacteria, since in the future mission, M planets will become a important target. We calculated the oscillator strengths in one light harvesting complex and confirmed the validity by comparing to the experimental data. This complex is made of an inner and an outer ring. The

  5. Quantum complex rotation and uniform semiclassical calculations of complex energy eigenvalues

    International Nuclear Information System (INIS)

    Connor, J.N.L.; Smith, A.D.

    1983-01-01

    Quantum and semiclassical calculations of complex energy eigenvalues have been carried out for an exponential potential of the form V 0 r 2 exp(-r) and Lennard-Jones (12,6) potential. A straightforward method, based on the complex coordinate rotation technique, is described for the quantum calculation of complex eigenenergies. For singular potentials, the method involves an inward and outward integration of the radial Schroedinger equation, followed by matching of the logarithmic derivatives of the wave functions at an intermediate point. For regular potentials, the method is simpler, as only an inward integration is required. Attention is drawn to the World War II researches of Hartree and co-workers who anticipated later quantum mechanical work on the complex rotation method. Complex eigenenergies are also calculated from a uniform semiclassical three turning point quantization formula, which allows for the proximity of the outer pair of complex turning points. Limiting cases of this formula, which are valid for very narrow or very broad widths, are also used in the calculations. We obtain good agreement between the semiclassical and quantum results. For the Lennard-Jones (12,6) potential, we compare resonance energies and widths from the complex energy definition of a resonance with those obtained from the time delay definition

  6. Improvements to the nuclear model code GNASH for cross section calculations at higher energies

    International Nuclear Information System (INIS)

    Young, P.G.; Chadwick, M.B.

    1994-01-01

    The nuclear model code GNASH, which in the past has been used predominantly for incident particle energies below 20 MeV, has been modified extensively for calculations at higher energies. The model extensions and improvements are described in this paper, and their significance is illustrated by comparing calculations with experimental data for incident energies up to 160 MeV

  7. Notes on the Verlinde formula in nonrational conformal field theories

    International Nuclear Information System (INIS)

    Jego, Charles; Troost, Jan

    2006-01-01

    We review and extend evidence for the validity of a generalized Verlinde formula, in particular, nonrational conformal field theories. We identify a subset of representations of the chiral algebra in nonrational conformal field theories that give rise to an analogue of the relation between modular S-matrices and fusion coefficients in rational conformal field theories. To that end we review and extend the Cardy-type brane calculations in bosonic and supersymmetric Liouville theory (and its duals) as well as in H 3 + . We analyze the three-point functions of Liouville theory and of H 3 + in detail to directly identify the fusion coefficients from the operator product expansion. Moreover, we check the validity of a proposed generic formula for localized brane one-point functions in nonrational conformal field theories

  8. Impurities in semiconductors: total energy and infrared absorption calculations

    International Nuclear Information System (INIS)

    Yndurain, F.

    1987-01-01

    A new method to calculate the electronic structure of infinite nonperiodic system is discussed. The calculations are performed using atomic pseudopotentials and a basis of atomic Gaussiam wave functions. The Hartree-Fock self consistent equations are solved in the cluster-Bethe lattice system. Electron correlation is partially included in second order pertubation approximation. The formalism is applied to hydrogenated amorphous silicon. Total energy calculations of finite clusters of silicon atom in the presence of impurities, are also presented. The results show how atomic oxygen breaks the covalent silicon silicon bond forming a local configuration similar to that of SiO 2 . Calculations of the infrared absorption due to the presence of atomic oxygen in cristalline silicon are presented. The Born Hamiltonian to calculate the vibrational modes of the system and a simplied model to describe the infrared absorption mechanism are used. The interstitial and the the substitutional cases are considered and analysed. The position of the main infrared absorption peak, their intensities and their isotope shifts are calculated. The results are satisfactory agreement with the available data. (author) [pt

  9. Energy-depth relation of electrons in bulk targets by Monte-Carlo calculations

    International Nuclear Information System (INIS)

    Gaber, M.; Fitting, H.J.

    1984-01-01

    Monte-Carlo calculations are used to calculate the energy of penetrating electrons as a function of the depth in thick targets of Ti, Fe, Cu, As, In, and Au. It is shown that the mean energy ratio anti E(z)/E 0 decays exponentially with depth z and depends on the backscattering coefficient eta/sub B/ of the bulk material and the maximum range R(E 0 ) of the primary electrons with initial energy E 0 . Thereby a normalized plot anti E/E 0 as a function of the reduced depth z/R becomes possible. (author)

  10. Toward improved target conformity for two spot scanning proton therapy delivery systems using dynamic collimation

    Science.gov (United States)

    Moignier, Alexandra; Gelover, Edgar; Smith, Blake R.; Wang, Dongxu; Flynn, Ryan T.; Kirk, Maura L.; Lin, Liyong; Solberg, Timothy D.; Lin, Alexander; Hyer, Daniel E.

    2016-01-01

    Purpose: To quantify improvement in target conformity in brain and head and neck tumor treatments resulting from the use of a dynamic collimation system (DCS) with two spot scanning proton therapy delivery systems (universal nozzle, UN, and dedicated nozzle, DN) with median spot sizes of 5.2 and 3.2 mm over a range of energies from 100 to 230 MeV. Methods: Uncollimated and collimated plans were calculated with both UN and DN beam models implemented within our in-house treatment planning system for five brain and ten head and neck datasets in patients previously treated with spot scanning proton therapy. The prescription dose and beam angles from the clinical plans were used for both the UN and DN plans. The average reduction of the mean dose to the 10-mm ring surrounding the target between the uncollimated and collimated plans was calculated for the UN and the DN. Target conformity was analyzed using the mean dose to 1-mm thickness rings surrounding the target at increasing distances ranging from 1 to 10 mm. Results: The average reductions of the 10-mm ring mean dose for the UN and DN plans were 13.7% (95% CI: 11.6%–15.7%; p < 0.0001) and 11.5% (95% CI: 9.5%–13.5%; p < 0.0001) across all brain cases and 7.1% (95% CI: 4.4%–9.8%; p < 0.001) and 6.3% (95% CI: 3.7%–9.0%; p < 0.001), respectively, across all head and neck cases. The collimated UN plans were either more conformal (all brain cases and 60% of the head and neck cases) than or equivalent (40% of the head and neck cases) to the uncollimated DN plans. The collimated DN plans offered the highest conformity. Conclusions: The DCS added either to the UN or DN improved the target conformity. The DCS may be of particular interest for sites with UN systems looking for a more economical solution than upgrading the nozzle to improve the target conformity of their spot scanning proton therapy system. PMID:26936726

  11. Model calculation for energy loss in ion-surface collisions

    International Nuclear Information System (INIS)

    Miraglia, J.E.; Gravielle, M.S.

    2003-01-01

    The so-called local plasma approximation is generalized to deal with projectiles colliding with surfaces of amorphous solids and with a specific crystalline structure (plannar channeling). Energy loss of protons grazingly colliding with aluminum, SnTe alloy, and LiF surfaces is investigated. The calculations agree quite well with previous theoretical results and explain the experimental findings of energy loss for aluminum and SnTe alloy, but they fall short to explain the data for LiF surfaces

  12. Calculated energy response of lithium fluoride finger-tip dosimeters

    International Nuclear Information System (INIS)

    Johns, T.F.

    1965-07-01

    Calculations have been made of the energy response of the lithium fluoride thermoluminescent dosimeters being used at A.E.E. Winfrith for the measurement of radiation doses to the finger-tips of people handling radio-active materials. It is shown that the energy response is likely to be materially affected if the sachet in which the powder is held contains elements with atomic numbers much higher than 9 (e.g. if the sachet is made from polyvinyl chloride). (author)

  13. Effect of hydrophobic groups on the adsorption conformation of modified polycarboxylate superplasticizer investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Hongxia [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Wang, Yanwei, E-mail: wangyanwei@cnjsjk.cn [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Yang, Yong; Shu, Xin; Yan, Han [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Ran, Qianping, E-mail: qpran@cnjsjk.cn [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China)

    2017-06-15

    Highlights: • Adsorption conformation of comb-like PCE was studied by all-atom MD simulations. • A comparison is made between vacuum-based and solution-based simulations. • Effects of hydrophobic modifications on adsorption properties are elucidated. - Abstract: All-atom molecular dynamics (MD) simulations were used to study the adsorption conformations of hydrophobically-modified comb-shaped polycarboxylate ether-based (PCE) superplasticizer molecules on a model surface of dicalcium silicate (C{sub 2}S) in vacuum and in an explicit solution, respectively. Three different hydrophobic modifying groups, namely, the ethyl group, the n-butyl group and the phenyl group, decorated to the backbone, were examined. Comparing the hydrophobically-modified PCEs to the unmodified one, differences were found in the binding energy, the adsorption conformation and the water density at the interface. The interaction between PCE molecules and C{sub 2}S was weakened in a solution with explicit solvents than that obtained from vacuum-based simulations. The presence of hydrophobic groups lowered the polymer-surface binding energy, decreased the radius of gyration (Rg) of the adsorbed polymer, increased the peak position in the heavy-atom density profiles in the direction perpendicular to the surface, and also caused the adsorbed conformations to be more globular in shape. The parallel and perpendicular components (relative to the surface plane) of the geometric sizes of the adsorbed polymers were calculated, and the results showed that the presence of hydrophobically modifying groups decreased the in-plane radius while increased the adsorption layer thickness compared to the unmodified control. The presence of PCEs perturbed the dense water layer above the C{sub 2}S surface and lowered the water density. Perturbations to the interfacial water density were found to correlate nicely with the adsorbed conformations of PCEs.

  14. 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.

  15. Use of an expert system for energy cost calculations in the pulp and paper industry

    International Nuclear Information System (INIS)

    Viinikainen, S.; Malinen, H.

    1991-12-01

    In this paper, an application for the calculation of energy prices and product energy costs in the pulp and paper industry by using the Xi Plus expert system is presented. The use of expert systems in the energy field and also the Xi Plus expert system and its general features are also discussed. The application has been made after collecting data from several sources. It runs in an IBM AT compatible microcomputer therefore being easily used in mills. The name of the application is PRODUCT ENERGY COST. It has a three level structure: the mill level, the department level and the main equipment level. Currently, the mill level and, in the energy production area, the department level (power plant) and the equipment level (boilers, turbines) are used. The application consists of four knowledge base groups. Altogether there are 52 separate knowledge bases having 534 rules or demons. The knowledge base groups are: BASIC DATA, ENERGY USE, ENERGY PRODUCTION and ENERGY COSTS. The application can be used for various heat and electrical energy price calculations or for energy cost calculations for different pulp and paper products. In this study, the energy prices for kraft pulp, TMP, newsprint and fine paper in different operating conditions and the associated energy costs of the products are calculated. Also, in some cases a sensitivity analysis is done. The expert system is quite suitable for this type of calculation and the method could be further developed for specific industrial needs, e.g. to enhance the energy management systems

  16. Implications of conformal invariance for quantum field theories in d>2

    International Nuclear Information System (INIS)

    Osborn, H.

    1994-01-01

    Recently obtained results for two and three point functions for quasi-primary operators in conformally invariant theories in arbitrary dimensions d are described. As a consequence the three point function for the energy momentum tensor has three linearly independent forms for general d compatible with conformal invariance. The corresponding coefficients may be regarded as possible generalisations of the Virasoro central charge to d larger than 2. Ward identities which link two linear combinations of the coefficients to terms appearing in the energy momentum tensor trace anomaly on curved space are discussed. The requirement of positivity for expectation values of the energy density is also shown to lead to positivity conditions which are simple for a particular choice of the three coefficients. Renormalisation group like equations which express the constraints of broken conformal invariance for quantum field theories away from critical points are postulated and applied to two point functions. (orig.)

  17. Introduction to conformal field theory. With applications to string theory

    International Nuclear Information System (INIS)

    Blumenhagen, Ralph; Plauschinn, Erik

    2009-01-01

    Based on class-tested notes, this text offers an introduction to Conformal Field Theory with a special emphasis on computational techniques of relevance for String Theory. It introduces Conformal Field Theory at a basic level, Kac-Moody algebras, one-loop partition functions, Superconformal Field Theories, Gepner Models and Boundary Conformal Field Theory. Eventually, the concept of orientifold constructions is explained in detail for the example of the bosonic string. In providing many detailed CFT calculations, this book is ideal for students and scientists intending to become acquainted with CFT techniques relevant for string theory but also for students and non-specialists from related fields. (orig.)

  18. Supergravitational conformal Galileons

    Science.gov (United States)

    Deen, Rehan; Ovrut, Burt

    2017-08-01

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

  19. EELOSS: the program for calculation of electron energy loss data

    International Nuclear Information System (INIS)

    Tanaka, Shun-ichi

    1980-10-01

    A computer code EELOSS has been developed to obtain the electron energy loss data required for shielding and dosimetry of beta- and gamma-rays in nuclear plants. With this code, the following data are obtainable for any energy from 0.01 to 15 MeV in any medium (metal, insulator, gas, compound, or mixture) composed of any choice of 69 elements with atomic number 1 -- 94: a) Collision stopping power, b) Restricted collision stopping power, c) Radiative stopping power, and d) Bremsstrahlung production cross section. The availability of bremsstrahlung production cross section data obtained by the EELOSS code is demonstrated by the comparison of calculated gamma-ray spectrum with measured one in Pb layer, where electron-photon cascade is included implicitly. As a result, it is concluded that the uncertainty in the bremsstrahlung production cross sections is negligible in the practical shielding calculations of gamma rays of energy less than 15 MeV, since the bremsstrahlung production cross sections increase with the gamma-ray energy and the uncertainty for them decreases with increasing the gamma-ray energy. Furthermore, the accuracy of output data of the EELOSS code is evaluated in comparison with experimental data, and satisfactory agreements are observed concerning the stopping power. (J.P.N.)

  20. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

    2018-05-01

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  1. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

    Science.gov (United States)

    Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

    2018-05-01

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  2. MONTE CARLO CALCULATION OF THE ENERGY RESPONSE OF THE NARF HURST-TYPE FAST- NEUTRON DOSIMETER

    Energy Technology Data Exchange (ETDEWEB)

    De Vries, T. W.

    1963-06-15

    The response function for the fast-neutron dosimeter was calculated by the Monte Carlo technique (Code K-52) and compared with a calculation based on the Bragg-Gray principle. The energy deposition spectra so obtained show that the response spectra become softer with increased incident neutron energy ahove 3 Mev. The K-52 calculated total res nu onse is more nearly constant with energy than the BraggGray response. The former increases 70 percent from 1 Mev to 14 Mev while the latter increases 135 percent over this energy range. (auth)

  3. Dilaton vs Higgs: Nearly Conformal Physics

    Science.gov (United States)

    Kozlov, G. A.

    2016-04-01

    We consider the model in which the conformal symmetry can be broken spontaneously, and a light scalar dilaton could emerge in the low-energy spectrum. The contribution of the dark photon production relevant to two photons decays of a Higgs boson/dilaton is discussed.

  4. Application of an excited state LDA exchange energy functional for the calculation of transition energy of atoms within time-independent density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Shamim, Md; Harbola, Manoj K, E-mail: sami@iitk.ac.i, E-mail: mkh@iitk.ac.i [Department of Physics, Indian Institute of Technology, Kanpur 208 016 (India)

    2010-11-14

    Transition energies of a new class of excited states (two-gap systems) of various atoms are calculated in time-independent density functional formalism by using a recently proposed local density approximation exchange energy functional for excited states. It is shown that the excitation energies calculated with this functional compare well with those calculated with exact exchange theories.

  5. Application of an excited state LDA exchange energy functional for the calculation of transition energy of atoms within time-independent density functional theory

    International Nuclear Information System (INIS)

    Shamim, Md; Harbola, Manoj K

    2010-01-01

    Transition energies of a new class of excited states (two-gap systems) of various atoms are calculated in time-independent density functional formalism by using a recently proposed local density approximation exchange energy functional for excited states. It is shown that the excitation energies calculated with this functional compare well with those calculated with exact exchange theories.

  6. 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.

  7. Calorific energy deposited by gamma radiations in a test reactor. Calorimetric measurements and calculations

    International Nuclear Information System (INIS)

    Mecheri, K.-F.

    1977-01-01

    The purpose of this work was to determine the calorific energy deposited by gamma radiations in the experimental devices irradiated in the test reactors of the Grenoble Nuclear Study Centre. A theoretical study briefly recalls to mind the various sorts of nuclear reactions that occur in a reactor, from the special angle of their ability to deposit calorific energy in the materials. A special study with the help of a graphite calorimeter made it possible to show the possible effect of the various parameters intervening in this energy absorption: the nature of the materials, their geometry, the spectrum of the incident gamma rays and the fact that the variation of this spectrum is due to the position of the measuring point with respect to the reactor core or to the presence of structures around the measuring instrument. The results of the calculations made with the help of the Mercury IV and ANISN codes are compared with those of the determinations in order to ascertain that very are adapted to the forecasts of energy deposition in the various materials. The conclusion was reached that in order to calculate with accuracy the depositifs of gamma energy in the experimental devices, it is necessary either to introduce the build-up calculation for the low energy photons, in the Mercury IV calculation code or to associate the DOT code to the ANISN calculation code [fr

  8. Calculation of the fifth atomic energy research dynamic benchmark with APROS

    International Nuclear Information System (INIS)

    Puska Eija Karita; Kontio Harii

    1998-01-01

    The band-out presents the model used for calculation of the fifth atomic energy research dynamic benchmark with APROS code. In the calculation of the fifth atomic energy research dynamic benchmark the three-dimensional neutronics model of APROS was used. The core was divided axially into 20 nodes according to the specifications of the benchmark and each six identical fuel assemblies were placed into one one-dimensional thermal hydraulic channel. The five-equation thermal hydraulic model was used in the benchmark. The plant process and automation was described with a generic WWER-440 plant model created by IVO Power Engineering Ltd. - Finland. (Author)

  9. Microscopic calculations of λ single particle energies

    International Nuclear Information System (INIS)

    Usmani, Q. N.

    1998-01-01

    Λ binding energy data for total baryon number A ≤ 208 and for Λ angular momenta ell Λ ≤ 3 are analyzed in terms of phenomenological (but generally consistent with meson-exchange) ΛN and ΛNN potentials. The Fermi-Hypernetted-Chain technique is used to calculate the expectation values for the Λ binding to nuclear matter. Accurate effective ΛN and ΛNN potentials are obtained which are folded with the core nucleus nucleon densities to calculate the Λ single particle potential U Λ (r). We use a dispersive ΛNN potential but also include an explicit ρ dependence to allow for reduced repulsion in the surface, and the best fits have a large ρ dependence giving consistency with the variational Monte Carlo calculations for Λ 5 He. The exchange fraction of the ΛN space-exchange potential is found to be 0.2-0.3 corresponding to m Λ * ≅ (0.74-0.82)m Λ . Charge symmetry breaking is found to be significant for heavy hypernuclei with a large neutron excess, with a strength consistent with that obtained from the A = 4 hypernuclei

  10. Astrophysical Tests of Kinematical Conformal Cosmology in Fourth-Order Conformal Weyl Gravity

    Directory of Open Access Journals (Sweden)

    Gabriele U. Varieschi

    2014-12-01

    Full Text Available In this work we analyze kinematical conformal cosmology (KCC, an alternative cosmological model based on conformal Weyl gravity (CG, and test it against current type Ia supernova (SNIa luminosity data and other astrophysical observations. Expanding upon previous work on the subject, we revise the analysis of SNIa data, confirming that KCC can explain the evidence for an accelerating expansion of the Universe without using dark energy or other exotic components. We obtain an independent evaluation of the Hubble constant, H0 = 67:53 kms-1 Mpc-1, very close to the current best estimates. The main KCC and CG parameters are re-evaluated and their revised values are found to be close to previous estimates. We also show that available data for the Hubble parameter as a function of redshift can be fitted using KCC and that this model does not suffer from any apparent age problem. Overall,

  11. 4He binding energy calculation including full tensor-force effects

    Science.gov (United States)

    Fonseca, A. C.

    1989-09-01

    The four-body equations of Alt, Grassberger, and Sandhas are solved in the version where the (2)+(2) subamplitudes are treated exactly by convolution, using one-term separable Yamaguchy nucleon-nucleon potentials in the 1S0 and 3S1-3D1 channels. The resulting jp=1/2+ and (3/2+ three-body subamplitudes are represented in a separable form using the energy-dependent pole expansion. Converged bound-state results are calculated for the first time using the full interaction, and are compared with those obtained from a simplified treatment of the tensor force. The Tjon line that correlates three-nucleon and four-nucleon binding energies is shown using different nucleon-nucleon potentials. In all calculations the Coulomb force has been neglected.

  12. 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.

  13. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Jin; He, Jianfeng, E-mail: Antti.Niemi@physics.uu.se, E-mail: hjf@bit.edu.cn [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se, E-mail: hjf@bit.edu.cn [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours (France)

    2016-07-28

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

  14. Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

    International Nuclear Information System (INIS)

    Dai, Jin; He, Jianfeng; Niemi, Antti J.

    2016-01-01

    The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

  15. Perspectives on electrostatics and conformational motions in enzyme catalysis.

    Science.gov (United States)

    Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

    2015-02-17

    CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

  16. Variable-temperature NMR and conformational analysis of Oenothein B

    International Nuclear Information System (INIS)

    Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de

    2014-01-01

    Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

  17. Variable-temperature NMR and conformational analysis of Oenothein B

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de, [Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Instituto de Quimica

    2014-02-15

    Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

  18. Flow equation, conformal symmetry, and anti-de Sitter geometry

    Science.gov (United States)

    Aoki, Sinya; Yokoyama, Shuichi

    2018-03-01

    We argue that the anti-de Sitter (AdS) geometry in d+1 dimensions naturally emerges from an arbitrary conformal field theory in d dimensions using the free flow equation. We first show that an induced metric defined from the flowed field generally corresponds to the quantum information metric, called the Bures or Helstrom metric, if the flowed field is normalized appropriately. We next verify that the induced metric computed explicitly with the free flow equation always becomes the AdS metric when the theory is conformal. We finally prove that the conformal symmetry in d dimensions converts to the AdS isometry in d+1 dimensions after d-dimensional quantum averaging. This guarantees the emergence of AdS geometry without explicit calculation.

  19. Conformal house

    DEFF Research Database (Denmark)

    Ryttov, Thomas Aaby; Sannino, Francesco

    2010-01-01

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

  20. Monte Carlo conformal treatment planning as an independent assessment

    International Nuclear Information System (INIS)

    Rincon, M.; Leal, A.; Perucha, M.; Carrasco, E.; Sanchez-Doblado, F.; Hospital Univ. Virgen Macarena, Sevilla; Arrans, R.; Sanchez-Calzado, J.A.; Errazquin, L.; Medrano, J.C.

    2001-01-01

    The wide range of possibilities available in Radiotherapy with conformal fields cannot be covered experimentally. For this reason, dosimetrical and planning procedures are based on approximate algorithms or systematic measurements. Dose distribution calculations based on Monte Carlo (MC) simulations can be used to check results. In this work, two examples of conformal field treatments are shown: A prostate carcinoma and an ocular lymphoma. The dose distributions obtained with a conventional Planning System and with MC have been compared. Some significant differences have been found. (orig.)

  1. Calculation of energy costs of composite biomass stirring at biogas stations

    Science.gov (United States)

    Suslov, D. Yu; Temnikov, D. O.

    2018-03-01

    The paper is devoted to the study of the equipment to produce biogas fuel from organic wastes. The bioreactor equipped with a combined stirring system ensuring mechanical and bubbling stirring is designed. The method of energy cost calculation of the combined stirring system with original design is suggested. The received expressions were used in the calculation of the stirring system installed in the 10 m3 bioreactor: power consumed by the mixer during the start-up period made Nz =9.03 kW, operating power of the mixer made NE =1.406 kW, compressor power for bubbling stirring made NC =18.5 kW. Taking into account the operating mode of single elements of the stirring system, the energy cost made 4.38% of the total energy received by the biogas station.

  2. Learning Approach on the Ground State Energy Calculation of Helium Atom

    International Nuclear Information System (INIS)

    Shah, Syed Naseem Hussain

    2010-01-01

    This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function.The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.

  3. Conformational Preferences of Glycerol in the Gas Phase and in Water

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Keun Hong [Korea Military Academy, Seoul (Korea, Republic of); Byun, Byung Jin; Kang, Young Kee [Chungbuk National University, Cheongju (Korea, Republic of)

    2012-03-15

    The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two C{sub 5} hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory

  4. Towards accurate free energy calculations in ligand protein-binding studies.

    Science.gov (United States)

    Steinbrecher, Thomas; Labahn, Andreas

    2010-01-01

    Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties of biomolecule binding, would be invaluable in the study of biological systems. In addition, as the mode of action of many pharmaceuticals is based upon their inhibition or activation of biomolecule targets, predictive models of small molecule receptor binding are very helpful tools in rational drug design. Since the goal here is normally to design a new compound with a high inhibition strength, one of the most important thermodynamic properties is the binding free energy DeltaG(0). The prediction of binding constants has always been one of the major goals in the field of computational chemistry, because the ability to reliably assess a hypothetical compound's binding properties without having to synthesize it first would save a tremendous amount of work. The different approaches to this question range from fast and simple empirical descriptor methods to elaborate simulation protocols aimed at putting the computation of free energies onto a solid foundation of statistical thermodynamics. While the later methods are still not suited for the screenings of thousands of compounds that are routinely performed in computational drug design studies, they are increasingly put to use for the detailed study of protein ligand interactions. This review will focus on molecular mechanics force field based free energy calculations and their application to the study of protein ligand interactions. After a brief overview of other popular methods for the calculation of free energies, we will describe recent advances in methodology and a variety of exemplary studies of molecular dynamics

  5. Conformal mapping calculation of railgun skin inductance

    International Nuclear Information System (INIS)

    Huerta, M.A.; Nearing, J.C.

    1991-01-01

    This paper considers the common rail arrangement consisting of two long, parallel, rectangular rails. The authors calculate the inductance per unit length L' in the short flight time limit where the skin depth is much smaller than any rail dimensions, the current is all on the rail surface, and the magnetic field does not penetrate the rails. The authors give the solution based on the Schwartz-Christoffel transformation that maps the boundaries of the problem into a simpler shape

  6. Enhanced conformational sampling using enveloping distribution sampling.

    Science.gov (United States)

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2013-10-14

    To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

  7. The normal conformal Cartan connection and the Bach tensor

    International Nuclear Information System (INIS)

    Korzynski, Mikolaj; Lewandowski, Jerzy

    2003-01-01

    The goal of this paper is to express the Bach tensor of a four-dimensional conformal geometry of an arbitrary signature by the Cartan normal conformal (CNC) connection. We show that the Bach tensor can be identified with the Yang-Mills current of the connection. It follows from that result that a conformal geometry whose CNC connection is reducible in an appropriate way has a degenerate Bach tensor. As an example we study the case of a CNC connection which admits a twisting covariantly constant twistor field. This class of conformal geometries of this property is known as given by the Fefferman metric tensors. We use our result to calculate the Bach tensor of an arbitrary Fefferman metric and show that it is proportional to the tensorial square of the four-fold eigenvector of the Weyl tensor. Finally, we solve the Yang-Mills equations imposed on the CNC connection for all the homogeneous Fefferman metrics. The only solution is the Nurowski-Plebanski metric

  8. A calculation of Zsub(eff) for low-energy positron-hydrogen-molecule scattering

    International Nuclear Information System (INIS)

    Armour, E.A.G.; Baker, D.J.

    1985-01-01

    The value of Zsub(eff), the effective number of electrons per molecule available to the positron for annihilation, is calculated for low-energy positron-hydrogen-molecule scattering using the scattering wavefunctions obtained in recent detailed ab initio calculations. The results are higher than those obtained in previous calculations but much lower than the experimental value. (author)

  9. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    Science.gov (United States)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  10. Monte Carlo calculation of the energy deposited in the KASCADE GRANDE detectors

    International Nuclear Information System (INIS)

    Mihai, Constantin

    2004-01-01

    The energy deposited by protons, electrons and positrons in the KASCADE GRANDE detectors is calculated with a simple and fast Monte Carlo method. The KASCADE GRANDE experiment (Forschungszentrum Karlsruhe, Germany), based on an array of plastic scintillation detectors, has the aim to study the energy spectrum of the primary cosmic rays around and above the 'knee' region of the spectrum. The reconstruction of the primary spectrum is achieved by comparing the data collected by the detectors with simulations of the development of the extensive air shower initiated by the primary particle combined with detailed simulations of the detector response. The simulation of the air shower development is carried out with the CORSIKA Monte Carlo code. The output file produced by CORSIKA is further processed with a program that estimates the energy deposited in the detectors by the particles of the shower. The standard method to calculate the energy deposit in the detectors is based on the Geant package from the CERN library. A new method that calculates the energy deposit by fitting the Geant based distributions with simpler functions is proposed in this work. In comparison with the method based on the Geant package this method is substantially faster. The time saving is important because the number of particles involved is large. (author)

  11. First calculation of the deuteron binding energy

    International Nuclear Information System (INIS)

    Schaegger, B.

    2012-01-01

    No universal constant characterizing the nuclear force has yet been found as for gravity and electromagnetism. The neutron is globally neutral with a zero net charge. The charges contained in a neutron may be separated by the electric field of a nearby proton and therefore being attracted by electrostatic induction in the same way as a rubbed plastic pen attracts small pieces of paper. There is also a magnetic force that may repel the nucleons like magnets in the proper relative orientation. In the deuteron, the heavy hydrogen nucleus, the induced electrostatic attraction is equilibrated by the magnetic repulsion between the opposite and colinear moments of the nucleons. Equilibrium is calculated by minimizing the electromagnetic interaction potential, giving a binding energy of 1.6 MeV, not much lower than the experimental value, 2.2 MeV. No fitting parameter is used: it is a true ab initio calculation

  12. New conformity indices based on the calculation of distances between the target volume and the volume of reference isodose

    Science.gov (United States)

    Park, J M; Park, S-Y; Ye, S-J; Kim, J H; Carlson, J

    2014-01-01

    Objective: To present conformity indices (CIs) based on the distance differences between the target volume (TV) and the volume of reference isodose (VRI). Methods: The points on the three-dimensional surfaces of the TV and the VRI were generated. Then, the averaged distances between the points on the TV and the VRI were calculated (CIdistance). The performance of the presented CIs were evaluated by analysing six situations, which were a perfect match, an expansion and a reduction of the distance from the centroid to the VRI compared with the distance from the centroid to the TV by 10%, a lateral shift of the VRI by 3 cm, a rotation of the VRI by 45° and a spherical-shaped VRI having the same volume as the TV. The presented CIs were applied to the clinical prostate and head and neck (H&N) plans. Results: For the perfect match, CIdistance was 0 with 0 as the standard deviation (SD). When expanding and reducing, CIdistance was 10 and −10 with SDs 11. The average value of the CIdistance in the prostate and H&N plans was 0.13 ± 7.44 and 6.04 ± 23.27, respectively. Conclusion: The performance of the CIdistance was equal or better than those of the conventional CIs. Advances in knowledge: The evaluation of target conformity by the distances between the surface of the TV and the VRI could be more accurate than evaluation with volume information. PMID:25225915

  13. Influence of simulation assumptions and input parameters on energy balance calculations of residential buildings

    International Nuclear Information System (INIS)

    Dodoo, Ambrose; Tettey, Uniben Yao Ayikoe; Gustavsson, Leif

    2017-01-01

    In this study, we modelled the influence of different simulation assumptions on energy balances of two variants of a residential building, comprising the building in its existing state and with energy-efficient improvements. We explored how selected parameter combinations and variations affect the energy balances of the building configurations. The selected parameters encompass outdoor microclimate, building thermal envelope and household electrical equipment including technical installations. Our modelling takes into account hourly as well as seasonal profiles of different internal heat gains. The results suggest that the impact of parameter interactions on calculated space heating of buildings is somewhat small and relatively more noticeable for an energy-efficient building in contrast to a conventional building. We find that the influence of parameters combinations is more apparent as more individual parameters are varied. The simulations show that a building's calculated space heating demand is significantly influenced by how heat gains from electrical equipment are modelled. For the analyzed building versions, calculated final energy for space heating differs by 9–14 kWh/m"2 depending on the assumed energy efficiency level for electrical equipment. The influence of electrical equipment on calculated final space heating is proportionally more significant for an energy-efficient building compared to a conventional building. This study shows the influence of different simulation assumptions and parameter combinations when varied simultaneously. - Highlights: • Energy balances are modelled for conventional and efficient variants of a building. • Influence of assumptions and parameter combinations and variations are explored. • Parameter interactions influence is apparent as more single parameters are varied. • Calculated space heating demand is notably affected by how heat gains are modelled.

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

    Science.gov (United States)

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

    2016-03-18

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

  15. New insights on mu/delta selectivity of opioid peptides: conformational analysis of deltorphin analogues.

    Science.gov (United States)

    Tancredi, T; Temussi, P A; Picone, D; Amodeo, P; Tomatis, R; Salvadori, S; Marastoni, M; Santagada, V; Balboni, G

    1991-05-01

    The message domain of dermorphin (Tyr-D-Ala-Phe), a natural mu-opioid heptapeptide, has long been considered the main cause of the high mu selectivity of this peptide and of its analogues. The recent discovery, in the skin of Phyllomedusa sauvagei (i.e., the same natural source of dermorphin) and of Phyllomedusa bicolor of deltorphins, challenges this belief. Deltorphins, in fact, are three heptapeptides characterized by a message domain typical of mu-selective peptides, but endowed of an extremely high delta selectivity, the highest of all natural opioid peptides. A conformational analysis of dermorphin and deltorphins, based on nmr studies in DMSO and cryoprotective mixtures and internal energy calculations, showed that the enormous differences in receptor selectivity can be interpreted on the basis of receptor models for mu and delta opioids that recognize the same beta-turn in the N-terminal part, but discriminate for the conformation and polarity of the C-terminal part. Here we present the synthesis, biological activity, and conformational analysis in solution of three deltorphin analogues with very similar constitution, but with different net charge, different location of negative residues, or even without negative residues, which confirm these hypotheses and show that His4 can play a specific structural role.

  16. Fluorine substitution and nonconventional OH...pi intramolecular bond: high-resolution UV spectroscopy and ab initio calculations of 2-(p-fluorophenyl)ethanol.

    Science.gov (United States)

    Karaminkov, Rosen; Chervenkov, Sotir; Neusser, Hans J

    2008-05-21

    The para-fluorinated flexible neurotransmitter analogue 2-phenylethanol has been investigated by highly resolved resonance-enhanced two-photon ionisation two-colour UV laser spectroscopy with mass resolution and ab initio structural optimisations and energy calculations. Two stable conformations, gauche and anti, separated by a high potential barrier have been identified in the cold molecular beam by rotational analysis of the vibronic band structures. The theoretically predicted higher-lying conformations most likely relax to these two structures during the adiabatic expansion. The lowest-energy gauche conformer is stabilised by an intramolecular nonconventional OH...pi-type hydrogen bond between the terminal OH group of the side chain and the pi electrons of the phenyl ring. The good agreement between the experimental and theoretical results demonstrates that even the substitution with a strongly electronegative atom of 2-phenylethanol at the para position has no noticeable effect on the strength and orientation of the OH...pi bond.

  17. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    , the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows...... conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

  18. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D......, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

  19. Causality Constraints in Conformal Field Theory

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d-dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂φ)4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinni...

  20. Causality constraints in conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, Thomas; Jain, Sachin; Kundu, Sandipan [Department of Physics, Cornell University,Ithaca, New York (United States)

    2016-05-17

    Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂ϕ){sup 4} coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators.

  1. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

    Directory of Open Access Journals (Sweden)

    M Olivia Kim

    2015-10-01

    Full Text Available BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.

  2. A theoretical study on 2-chloro-5-(2-hydroxyethyl-4-methoxy-6-methylpyrimidine by DFT/ab initio calculations

    Directory of Open Access Journals (Sweden)

    Gümüs Hacer Pir

    2015-06-01

    Full Text Available Quantum chemical calculations have been performed to study the molecular geometry, 1H and 13C NMR chemical shifts, conformational, natural bond orbital (NBO and nonlinear optical (NLO properties of the 2-chloro-5-(2-hydroxyethyl-4- methoxy-6-methylpyrimidine molecule in the ground state using DFT and HF methods with 6-311++G(d,p basis set. The optimized geometric parameters and 1H and 13C NMR chemical shifts have been compared with the experimental values of the title molecule. The results of the calculations show excellent agreement between the experimental and calculated frequencies at B3LYP/6-311++G(d,p level. In order to provide a full understanding of the properties of the title molecule in the context of molecular orbital picture, the highest occupied molecular energy level (EHOMO, the lowest unoccupied molecular energy level (ELUMO, the energy difference (DE between EHOMO and ELUMO, electronegativity (χ, hardness (η and softness (S have been calculated using B3LYP/6-311++G(d,p and HF/6-311++G(d,p levels. The calculated HOMO and LUMO energies show that the charge transfer occurs within the title molecule.

  3. Graphical Calculation of Estimated Energy Expenditure in Burn Patients.

    Science.gov (United States)

    Egro, Francesco M; Manders, Ernest C; Manders, Ernest K

    2018-03-01

    Historically, estimated energy expenditure (EEE) has been related to the percent of body surface area burned. Subsequent evaluations of these estimates have indicated that the earlier formulas may overestimate the amount of caloric support necessary for burn-injured patients. Ireton-Jones et al derived 2 equations for determining the EEE required to support burn patients, 1 for ventilator-dependent patients and 1 for spontaneously breathing patients. Evidence has proved their reliability, but they remain challenging to apply in a clinical setting given the difficult and cumbersome mathematics involved. This study aims to introduce a graphical calculation of EEE in burn patients that can be easily used in the clinical setting. The multivariant linear regression analysis from Ireton-Jones et al yielded equations that were rearranged into the form of a simple linear equation of the type y = mx + b. By choosing an energy expenditure and the age of the subject, the weight was calculated. The endpoints were then calculated, and a graph was mapped by means of Adobe FrameMaker. A graphical representation of Ireton-Jones et al's equations was obtained by plotting the weight (kg) on the y axis, the age (years) on the x axis, and a series of parallel lines representing the EEE in burn patients. The EEE has been displayed graphically on a grid to allow rapid determination of the EEE needed for a given patient of a designated weight and age. Two graphs were plotted: 1 for ventilator-dependent patients and 1 for spontaneously breathing patients. Correction factors for sex, the presence of additional trauma, and obesity are indicated on the graphical calculators. We propose a graphical tool to calculate caloric requirements in a fast, easy, and portable manner.

  4. User guide – COE Calculation Tool for Wave Energy Converters

    DEFF Research Database (Denmark)

    Chozas, Julia Fernandez; Kofoed, Jens Peter; Jensen, Niels Ejner Helstrup

    Aalborg University together with Energinet.dk and Julia F. Chozas Consulting Engineer, have released a freely available online spreadsheet to evaluate the Levelised Cost of Energy (LCOE) for wave energy projects. The open-access tool calculates the LCOE based on the power production of a Wave...... Energy Converter (WEC) at a particular location. Production data may derive from laboratory testing, numerical modelling or from sea trials. The tool has been developed as a transparent and simple model that evaluates WEC’s economic feasibility in a range of locations, while scaling WEC’s features...

  5. Daily conformity drinking motivations are associated with increased odds of consuming alcohol mixed with energy drinks.

    Science.gov (United States)

    Linden-Carmichael, Ashley N; Lau-Barraco, Cathy

    2018-04-01

    Recent research indicates that individuals drank more heavily and experienced more harms on days they consumed alcohol mixed with energy drinks (AmEDs). Limited research, thus far, has examined predictors of AmED use on a daily level. Drinking motives, or reasons for drinking, are shown to discern AmED users from non-users, but the extent to which daily drinking motives covary with AmED use has not been tested. The current study used a daily diary design to determine how motives differ between AmED and other drinking occasions. Participants included 122 college students (73.8% women) with a mean age of 20.39years. Participants completed up to 14 daily surveys, resulting in 389 drinking days (40days involved AmED use). Participants reported on their drinking motives at baseline as well as on each drinking day. Multilevel models revealed that, after controlling for other motives, AmED use was more likely on days where conformity motives were higher than usual and was less likely when enhancement motives were higher. Daily social and coping motives as well as all motives measured at baseline were unassociated with AmED use. Our findings suggest that conformity motives, or drinking to fit in with others, are the most salient drinking motive predicting AmED use on a drinking day. Given that conformity motives are often less associated with alcohol use outcomes in general, these findings highlight AmEDs as a unique alcoholic beverage. Clinicians and interventionists working with frequent AmED users should consider the unique conditions under which AmEDs are consumed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Conformal invariance and pion wave functions of nonleading twist

    International Nuclear Information System (INIS)

    Braun, V.M.; Filyanov, I.E.

    1989-01-01

    The restrictions are studied for the general structure of pion wave functions of twist 3 and twist 4 imposed by the conformal symmetry and the equations of motion. A systematic expansion of wave functions in the conformal spin is built and the first order corrections to asymptotic formulae are calculated by the QCD sum rule method. In particular, we have found a multiplicatively renormalizable contribution into the two-particle wave function of twist 4 which cannot be expanded in a finite set of Gegenbauer polynomials. 19 refs.; 5 figs

  7. QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

    Science.gov (United States)

    Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

    2017-05-05

    Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

  8. The correlation of cathodic peak potentials of vitamin K(3) derivatives and their calculated electron affinities. The role of hydrogen bonding and conformational changes.

    Science.gov (United States)

    Nasiri, Hamid Reza; Panisch, Robin; Madej, M Gregor; Bats, Jan W; Lancaster, C Roy D; Schwalbe, Harald

    2009-06-01

    2-methyl-1,4-naphtoquinone 1 (vitamin K(3), menadione) derivatives with different substituents at the 3-position were synthesized to tune their electrochemical properties. The thermodynamic midpoint potential (E(1/2)) of the naphthoquinone derivatives yielding a semi radical naphthoquinone anion were measured by cyclic voltammetry in the aprotic solvent dimethoxyethane (DME). Using quantum chemical methods, a clear correlation was found between the thermodynamic midpoint potentials and the calculated electron affinities (E(A)). Comparison of calculated and experimental values allowed delineation of additional factors such as the conformational dependence of quinone substituents and hydrogen bonding which can influence the electron affinities (E(A)) of the quinone. This information can be used as a model to gain insight into enzyme-cofactor interactions, particularly for enzyme quinone binding modes and the electrochemical adjustment of the quinone motif.

  9. Sustainable manufacturing by calculating the energy demand during turning of AISI 1045 steel

    Science.gov (United States)

    Nur, R.; Nasrullah, B.; Suyuti, M. A.; Apollo

    2018-01-01

    Sustainable development will become important issues for many fields, including production, industry, and manufacturing. In order to achieve sustainable development, industry should be able to perform of sustainable production processes and environmentally friendly. Therefore, there is need to minimize the energy demand in the machining process. This paper presents a calculation method of energy consumption in the machining process, especially turning process which calculated by summing the number of energy consumption, such as the electric energy consumed during the machining preparation, the electrical energy during the cutting processes, and the electrical energy to produce a cutting tool. A case study was performed on dry turning of mild carbon steel using coated carbide. This approach can be used to determine the total amount of electrical energy consumed in the specific machining process. It concluded that the energy consumption will be an increase for using the high cutting speed as well as for the feed rate was increased.

  10. Universality of fast quenches from the conformal perturbation theory

    Science.gov (United States)

    Dymarsky, Anatoly; Smolkin, Michael

    2018-01-01

    We consider global quantum quenches, a protocol when a continuous field theoretic system in the ground state is driven by a homogeneous time-dependent external interaction. When the typical inverse time scale of the interaction is much larger than all relevant scales except for the UV-cutoff the system's response exhibits universal scaling behavior. We provide both qualitative and quantitative explanations of this universality and argue that physics of the response during and shortly after the quench is governed by the conformal perturbation theory around the UV fixed point. We proceed to calculate the response of one and two-point correlation functions confirming and generalizing universal scalings found previously. Finally, we discuss late time behavior after the quench and argue that all local quantities will equilibrate to their thermal values specified by an excess energy acquired by the system during the quench.

  11. Approximate calculation of electronic energy levels of axially symmetric quantum dot and quantum ring by using energy dependent effective mass

    International Nuclear Information System (INIS)

    Yu-Min, Liu; Zhong-Yuan, Yu; Xiao-Min, Ren

    2009-01-01

    Calculations of electronic structures about the semiconductor quantum dot and the semiconductor quantum ring are presented in this paper. To reduce the calculation costs, for the quantum dot and the quantum ring, their simplified axially symmetric shapes are utilized in our analysis. The energy dependent effective mass is taken into account in solving the Schrödinger equations in the single band effective mass approximation. The calculated results show that the energy dependent effective mass should be considered only for relatively small volume quantum dots or small quantum rings. For large size quantum materials, both the energy dependent effective mass and the parabolic effective mass can give the same results. The energy states and the effective masses of the quantum dot and the quantum ring as a function of geometric parameters are also discussed in detail. (general)

  12. Development of nuclear models for higher energy calculations

    International Nuclear Information System (INIS)

    Bozoian, M.; Siciliano, E.R.; Smith, R.D.

    1988-01-01

    Two nuclear models for higher energy calculations have been developed in the regions of high and low energy transfer, respectively. In the former, a relativistic hybrid-type preequilibrium model is compared with data ranging from 60 to 800 MeV. Also, the GNASH exciton preequilibrium-model code with higher energy improvements is compared with data at 200 and 318 MeV. In the region of low energy transfer, nucleon-nucleus scattering is predominately a direct reaction involving quasi-elastic collisions with one or more target nucleons. We discuss various aspects of quasi-elastic scattering which are important in understanding features of cross sections and spin observables. These include (1) contributions from multi-step processes; (2) damping of the continuum response from 2p-2h excitations; (3) the ''optimal'' choice of frame in which to evaluate the nucleon-nucleon amplitudes; and (4) the effect of optical and spin-orbit distortions, which are included in a model based on the RPA the DWIA and the eikonal approximation. 33 refs., 15 figs

  13. Quantum effects and elimination of the conformal anomaly in anisotropic space-time

    International Nuclear Information System (INIS)

    Grib, A.A.; Nesteruk, A.V.

    1988-01-01

    In homogeneous anisotropic space-time the connection between the problem of the elimination of infrared divergences and the conformal anomaly of the regularized energy-momentum tensor is studied. It is shown that removal of the infrared divergence by means of a cutoff leads to the absence of a conformal anomaly. A physical interpretation of the infrared cutoff as a shift in the particle-energy spectrum by an amount equal to the effective temperature of the gravitational field is proposed

  14. High energy physics signatures from inflation and conformal symmetry of de Sitter

    International Nuclear Information System (INIS)

    Kehagias, A.; Riotto, A.

    2015-01-01

    During inflation, the geometry of spacetime is described by a (quasi-)de Sitter phase. Inflationary observables are determined by the underlying (softly broken) de Sitter isometry group SO(1, 4) which acts like a conformal group on R 3 : when the fluctuations are on super-Hubble scales, the correlators of the scalar fields are constrained by conformal invariance. Heavy fields with mass m larger than the Hubble rate H correspond to operators with imaginary dimensions in the dual Euclidean three-dimensional conformal field theory. By making use of the dS/CFT correspondence we show that, besides the Boltzmann suppression expected from the thermal properties of de Sitter space, the generic effect of heavy fields in the inflationary correlators of the light fields is to introduce power-law suppressed corrections of the form O(H 2 / m 2 ). This can be seen, for instance, at the level of the four-point correlator for which we provide the correction due to a massive scalar field exchange. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  15. Spectroscopic [FT-IR and FT-Raman] and molecular modeling (MM) study of benzene sulfonamide molecule using quantum chemical calculations

    Science.gov (United States)

    Vinod, K. S.; Periandy, S.; Govindarajan, M.

    2016-07-01

    The spectroscopic and molecular modeling (MM) study includes, FT-IR, FT-Raman and 13C NMR and 1H NMR spectra of the Benzene sulfonamide were recorded for the analysis. The observed experimental and theoretical frequencies (IR and Raman) were assigned according to their distinctive region. The present study of this title molecule have been carried out by hybrid computational calculations of HF and DFT (B3LYP) methods with 6-311+G(d,p) and 6-311++G(d,p) basis sets and the corresponding results are tabulated. The structural modifications of the compound due to the substitutions of NH2 and SO2 were investigated. The minimum energy conformers of the compound were studied using conformational analysis. The alternations of the vibrational pattern of the base structure related to the substitutions were analyzed. The thermodynamic parameters (such as zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment) of Benzene sulfonamide have been calculated. The donor acceptor interactions of the compound and the corresponding UV transitions are found out using NBO analysis. The NMR spectra were simulated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts related to TMS were compared. A quantum computational study on the electronic and optical properties absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The energy gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand group. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase and

  16. On holography for (pseudo-)conformal cosmology

    CERN Document Server

    Libanov, M.; Sibiryakov, S.

    2015-01-01

    We propose a holographic dual for (pseudo-)conformal cosmological scenario, with a scalar field that forms a moving domain wall in adS_5. The domain wall separates two vacua with unequal energy densities. Unlike in the existing construction, the 5d solution is regular in the relevant space-time domain.

  17. Quality control, mean glandular dose estimate and room shielding calculation in mammography

    International Nuclear Information System (INIS)

    Rakotomalala, H.M.

    2014-01-01

    This study focuses in the importance of Radiation Protection in mammography. A good control of the radiological risk depends on the dose optimization, room shielding calculation and the quality of equipment. The work was carried out in the three private medical centers called A, B, and C. Dosimetry estimates were made on the equipment of the three centers. Values has been compared with the Diagnostic Reference Levels established by the International Atomic Energy Agency (IAEA). Conformity control of the radiological devices has also been done with the Mammographic Quality Control Kit of the INSTN-Madagascar. Verifications of shields of the room containing the mammography equipment were done by theoretical calculations using the method provided by NCRP 147. [fr

  18. Conformally covariant composite operators in quantum chromodynamics

    International Nuclear Information System (INIS)

    Craigie, N.S.; Dobrev, V.K.; Todorov, I.T.

    1983-03-01

    Conformal covariance is shown to determine renormalization properties of composite operators in QCD and in the C 6 3 -model at the one-loop level. Its relevance to higher order (renormalization group improved) perturbative calculations in the short distance limit is also discussed. Light cone operator product expansions and spectral representations for wave functions in QCD are derived. (author)

  19. Free-Energy Calculations. A Mathematical Perspective

    Science.gov (United States)

    Pohorille, Andrzej

    2015-01-01

    conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

  20. Universality of sparse d>2 conformal field theory at large N

    Energy Technology Data Exchange (ETDEWEB)

    Belin, Alexandre; Boer, Jan de; Kruthoff, Jorrit [Institute for Theoretical Physics Amsterdam and Delta Institute for Theoretical Physics,University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The (Netherlands); Michel, Ben; Shaghoulian, Edgar; Shyani, Milind [Department of Physics, University of California,Santa Barbara, CA, 93106 (United States)

    2017-03-13

    We derive necessary and sufficient conditions for large N conformal field theories to have a universal free energy and an extended range of validity of the higher-dimensional Cardy formula. These constraints are much tighter than in two dimensions and must be satisfied by any conformal field theory dual to Einstein gravity. We construct and analyze symmetric product orbifold theories on T{sup d} and show that they only realize the necessary phase structure and extended range of validity if the seed theory is assumed to have a universal vacuum energy.

  1. A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments.

    Science.gov (United States)

    Sellers, Benjamin D; James, Natalie C; Gobbi, Alberto

    2017-06-26

    Reducing internal strain energy in small molecules is critical for designing potent drugs. Quantum mechanical (QM) and molecular mechanical (MM) methods are often used to estimate these energies. In an effort to determine which methods offer an optimal balance in accuracy and performance, we have carried out torsion scan analyses on 62 fragments. We compared nine QM and four MM methods to reference energies calculated at a higher level of theory: CCSD(T)/CBS single point energies (coupled cluster with single, double, and perturbative triple excitations at the complete basis set limit) calculated on optimized geometries using MP2/6-311+G**. The results show that both the more recent MP2.X perturbation method as well as MP2/CBS perform quite well. In addition, combining a Hartree-Fock geometry optimization with a MP2/CBS single point energy calculation offers a fast and accurate compromise when dispersion is not a key energy component. Among MM methods, the OPLS3 force field accurately reproduces CCSD(T)/CBS torsion energies on more test cases than the MMFF94s or Amber12:EHT force fields, which struggle with aryl-amide and aryl-aryl torsions. Using experimental conformations from the Cambridge Structural Database, we highlight three example structures for which OPLS3 significantly overestimates the strain. The energies and conformations presented should enable scientists to estimate the expected error for the methods described and we hope will spur further research into QM and MM methods.

  2. On calculations of the ground state energy in quantum mechanics

    International Nuclear Information System (INIS)

    Efimov, G.V.

    1991-02-01

    In nonrelativistic quantum mechanics the Wick-ordering method called the oscillator representation suggested to calculate the ground-state energy for a wide class of potentials allowing the existence of a bound state. The following examples are considered: the orbital excitations of the ground-state in the Coulomb plus linear potential, the Schroedinger equation with a ''relativistic'' kinetic energy √p 2 +m 2 , the Coulomb three-body problem. (author). 22 refs, 2 tabs

  3. THE CALCULATION OF THE ENERGY RECOVERY ELECTRIFIED URBAN TRANSPORT DURING THE INSTALLATION DRIVE FOR TRACTION SUBSTATION

    Directory of Open Access Journals (Sweden)

    A. A. Sulim

    2014-01-01

    Full Text Available At present a great attention is paid to increasing of energy efficiency at operated electrified urban transport. Perspective direction for increasing energy efficiency at that type of transport is the application of regenerative braking. For additional increasing of energy efficiency there were suggested the use of capacitive drive on tires of traction substation. One of the main task is the analysis of energy recovery application  with drive and without it.These analysis demonstrated that the calculation algorithms don’t allow in the full volume to carry out calculations of amount and cost of energy recovery without drive and with it. That is why we see the current interest to this topic. The purpose of work is to create methods of algorithms calculation for definite amount and cost of consumed, redundant and recovery energy of electrified urban transport due to definite regime of motion on wayside. There is algorithm developed, which allow to calculate amount and cost of consumed, redundant and recovery energy of electrified urban transport on wayside during the installation capacitive drive at traction substation. On the basis of developed algorithm for the definite regime of wagon motion of subway there were fulfilled the example of energy recovery amount and its cost calculation, among them with limited energy intensity drive, when there are 4 trains on wayside simultaneously.

  4. Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    ⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bondinteraction evidenced by a significantly blue......-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported...... by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformationalenergy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins....

  5. Continuous Energy, Multi-Dimensional Transport Calculations for Problem Dependent Resonance Self-Shielding

    International Nuclear Information System (INIS)

    Downar, T.

    2009-01-01

    The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system. The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multidimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system. Specifically, the methods here utilize the existing continuous energy SCALE5 module, CENTRM, and the multi-dimensional discrete ordinates solver, NEWT to develop a new code, CENTRM( ) NEWT. The work here addresses specific theoretical limitations in existing CENTRM resonance treatment, as well as investigates advanced numerical and parallel computing algorithms for CENTRM and NEWT in order to reduce the computational burden. The result of the work here will be a new computer code capable of performing problem dependent self-shielding analysis for both existing and proposed GENIV fuel designs. The objective of the work was to have an immediate impact on the safety analysis of existing reactors through improvements in the calculation of fuel temperature effects, as well as on the analysis of more sophisticated GENIV/NGNP systems through improvements in the depletion/transmutation of actinides for Advanced Fuel Cycle Initiatives.

  6. Watching Conformations of Biomolecules: a Microwave Spectroscopy Approach

    Science.gov (United States)

    Lopez, J. C.

    2011-06-01

    The combination of laser ablation with Fourier transform microwave spectroscopy in supersonic jets (LA-MB-FTMW) has made possible the gas-phase study of solid biomolecules with high melting points. In the experiment, solids are efficiently vaporized by a high-energy laser pulse, supersonically expanded into a evacuated Fabry-Perot cavity and characterised by their rotational spectra. Recent improvements such as the use of picosecond pulse lasers, new ablation nozzles and the extension of the range of the spectrometers to low frequecy have notably increased the sensitivity of our experimental setup. To date different α-, β- and γ-amino acids have been studied using this technique, making possible the characterization of their preferred conformations and gaining insight in the role of intramolecular interactions. Even in conformationally challenging systems the different rotamers of such biomolecules can be identified by rotational spectroscopy as can be illustrated by the assignment of six low-energy conformers in cysteine and aspartic acid, seven in serine and threonine,^a and nine in γ-amino butyric acid (GABA). In all cases the low-energy conformers have been conclusive identified from their experimental rotational and 14N quadrupole coupling constants. The spectra of neurotransmitters and of the nucleic acid bases uracil, thymine, cytosine and guanine have also been studied and their preferred conformers or tautomeric forms determined. The complexes between amino acids and nucleic acid bases with water have also been investigated to obtain information on the possible changes induced in the conformational or tautomeric preferences by the addition of solvent molecules. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11, 617-627 (2009) and references therein M. E. Sanz, J. C. López, J. L. Alonso, Phys. Chem. Chem. Phys., 12, 3573-3578 (2010) S. Blanco, J. C. López, S. Mata and J. L. Alonso, Angew. Chem. Int. Ed. 49, 9187

  7. Calculations for nuclear data evaluation for Nb, Zr and W in the high energy region

    Energy Technology Data Exchange (ETDEWEB)

    Kitsuki, Hirohiko; Maruyama, Shin-ichi; Ishibashi, Kenji [Kyushu Univ., Fukuoka (Japan)

    1998-03-01

    Neutron total cross sections on Nb, Zr and W were calculated in the high energy region. In this calculation, we used the neutron optical-model potentials derived from those for proton incidence with introducing the symmetry term. Proton-induced activation yields for Nb and Zr was calculated by means of HETC/KFA2 and QMD plus SDM at incident energies up to 5 GeV. (author)

  8. 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.

  9. On holography for (pseudo-)conformal cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Libanov, M. [Institute for Nuclear Research of the Russian Academy of Sciences, 60th October Anniversary Prospect, 7a, 117312, Moscow (Russian Federation); Moscow Institute of Physics and Technology, Institutskii per., 9, 141700, Dolgoprudny, Moscow Region (Russian Federation); Rubakov, V. [Institute for Nuclear Research of the Russian Academy of Sciences, 60th October Anniversary Prospect, 7a, 117312, Moscow (Russian Federation); Department of Particle Physics and Cosmology, Physics Faculty, Moscow State University, Vorobjevy Gory, 119991, Moscow (Russian Federation); Sibiryakov, S., E-mail: sibir@ms2.inr.ac.ru [Institute for Nuclear Research of the Russian Academy of Sciences, 60th October Anniversary Prospect, 7a, 117312, Moscow (Russian Federation); Theory Group, Physics Department, CERN, CH-1211 Geneva 23 (Switzerland); FSB/ITP/LPPC, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne (Switzerland)

    2015-02-04

    We propose a holographic dual for (pseudo-)conformal cosmological scenario, with a scalar field that forms a moving domain wall in adS{sub 5}. The domain wall separates two vacua with unequal energy densities. Unlike in the existing construction, the 5d solution is regular in the relevant space–time domain.

  10. Computer calculations of activation energy for pyrolysis from thermogravimetric curves

    International Nuclear Information System (INIS)

    Hussain, R.

    1994-01-01

    A BASIC programme to determine energy of activation for the degradation of polymers has been described. The calculations are based on the results of thermogravimetric curves. This method is applicable for those polymers which produce volatile products upon thermal degradation. (author)

  11. 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...

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-15

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

  14. Calculation of Activation Energy by OIT Method for aging evaluation of NPP cable

    International Nuclear Information System (INIS)

    Park, Kyung-Heun; Kim, Jong-Seog; Cho, Bok-Gee

    2006-01-01

    Extending the lifetime of nuclear power plant is one of the most important concerns in the world nuclear industry. Cables are one of the long live items which have not been considered to be replaced during the design life of NPP. In order to simulate the natural aging in nuclear power plant, a study on accelerated aging needs to be conducted and to carry out the accelerated aging test, we must calculate the activation energy of the cable if we don't have the activation energy information. The activation energy is the most important element and it can be calculated by indentor modulus and elongation data and so on. But there is often only a limited quantity of material available in the deposit for testing, so it is important the samples for any destructive test are conserved as much as possible. But if there is only a limited quantity of the material, OIT(Oxidation Induction Time) is very useful with calculating activation energy and evaluation of the cable lifetime

  15. The calculation of surface free energy based on embedded atom method for solid nickel

    International Nuclear Information System (INIS)

    Luo Wenhua; Hu Wangyu; Su Kalin; Liu Fusheng

    2013-01-01

    Highlights: ► A new solution for accurate prediction of surface free energy based on embedded atom method was proposed. ► The temperature dependent anisotropic surface energy of solid nickel was obtained. ► In isotropic environment, the approach does not change most predictions of bulk material properties. - Abstract: Accurate prediction of surface free energy of crystalline metals is a challenging task. The theory calculations based on embedded atom method potentials often underestimate surface free energy of metals. With an analytical charge density correction to the argument of the embedding energy of embedded atom method, an approach to improve the prediction for surface free energy is presented. This approach is applied to calculate the temperature dependent anisotropic surface energy of bulk nickel and surface energies of nickel nanoparticles, and the obtained results are in good agreement with available experimental data.

  16. Major conformations of the ligand skeleton of a tetranuclear dysprosium (3) tartrate complex

    International Nuclear Information System (INIS)

    Chevela, V.V.; Semenov, V.Eh.; Bezryadin, S.G.; Savitskaya, T.V.; Kolesar, I.R.; Matveev, S.N.; Shamov, G.A.

    1999-01-01

    By the molecular mechanics method (MIND program, stoichiometry was studied and basic conformations of ligand frame of dysprosium (3) tetranuclear complex bis-(d-tartrato) bis-(l-tartrato)tetradysprosiate (3) - anion Dy 4 (d-L) 2 (l-L) 2 4- (1) (d-H 4 L = d-tartaric acid, l-H 4 L = l - tartaric acid) were revealed. It is shown that theoretically calculated mP τ constants for so-called compact conformations of 1, where tartratoligands are in gosh conformation, agree with experimentally obtained constant of paramagnetic birefringence (mP e ) of complex 1 [ru

  17. Wave packet methods for the direct calculation of energy-transfer moments in molecular collisions

    International Nuclear Information System (INIS)

    Bradley, K.S.; Schatz, G.C.; Balint-Kurti, G.G.

    1999-01-01

    The authors present a new wave packet based theory for the direct calculation of energy-transfer moments in molecular collision processes. This theory does not contain any explicit reference to final state information associated with the collision dynamics, thereby avoiding the need for determining vibration-rotation bound states (other than the initial state) for the molecules undergoing collision and also avoiding the calculation of state-to-state transition probabilities. The theory applies to energy-transfer moments of any order, and it generates moments for a wide range of translational energies in a single calculation. Two applications of the theory are made that demonstrate its viability; one is to collinear He + H 2 and the other to collinear He + CS 2 (with two active vibrational modes in CS 2 ). The results of these applications agree well with earlier results based on explicit calculation of transition probabilities

  18. 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.

  19. Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

    Science.gov (United States)

    Chong, Song-Ho; Ham, Sihyun

    2015-10-01

    Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components. We find that the change in configurational entropy upon folding is dominated by the conformational entropy despite the fact that the magnitude of the vibrational entropy is the significantly larger component in each of the folded and unfolded states, which is in accord with the previous empirical estimations. The straightforward applicability of our method to unfolded proteins promises a wide range of applications, including those related to intrinsically disordered proteins.

  20. Quantum Fluctuations and the Unruh effect in strongly-coupled conformal field theories

    Science.gov (United States)

    Cáceres, Elena; Chernicoff, Mariano; Güijosa, Alberto; Pedraza, Juan F.

    2010-06-01

    Through the AdS/CFT correspondence, we study a uniformly accelerated quark in the vacuum of strongly-coupled conformal field theories in various dimensions, and determine the resulting stochastic fluctuations of the quark trajectory. From the perspective of an inertial observer, these are quantum fluctuations induced by the gluonic radiation emitted by the accelerated quark. From the point of view of the quark itself, they originate from the thermal medium predicted by the Unruh effect. We scrutinize the relation between these two descriptions in the gravity side of the correspondence, and show in particular that upon transforming the conformal field theory from Rindler space to the open Einstein universe, the acceleration horizon disappears from the boundary theory but is preserved in the bulk. This transformation allows us to directly connect our calculation of radiation-induced fluctuations in vacuum with the analysis by de Boer et al. of the Brownian motion of a quark that is on average static within a thermal medium. Combining this same bulk transformation with previous results of Emparan, we are also able to compute the stress-energy tensor of the Unruh thermal medium.