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Mode Analysis (mode + analysis)
Kinds of Mode Analysis Selected AbstractsLinear and Nonlinear Viscoelasticity of a Model Unentangled Polymer Melt: Molecular Dynamics and Rouse Modes AnalysisMACROMOLECULAR THEORY AND SIMULATIONS, Issue 3 2006Mihail Vladkov Abstract Summary: Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli and viscosity, including Green-Kubo and nonequilibrium molecular dynamics (NEMD). An alternative approach, based on the use of the Rouse modes, is also discussed. This approach could be used to assess local viscoelastic properties in inhomogeneous systems. We also focus on the contributions of different interactions to the viscoelastic moduli and explain the microscopic mechanisms involved in the mechanical response of the melt to external solicitation. [source] Performance analysis of optically preamplified DC-coupled burst mode receiversEUROPEAN TRANSACTIONS ON TELECOMMUNICATIONS, Issue 3 2009T. J. Zuo Bit error rate and threshold acquisition penalty evaluation is performed for an optically preamplified DC-coupled burst mode receiver using a moment generating function (MGF) description of the signal plus noise. The threshold itself is a random variable and is also described using an appropriate MGF. Chernoff bound (CB), modified Chernoff bound (MCB) and the saddle-point approximation (SPA) techniques make use of the MGF to provide the performance analyses. This represents the first time that these widely used approaches to receiver performance evaluation have been applied to an optically preamplified burst mode receiver and it is shown that they give threshold acquisition penalty results in good agreement with a prior existing approach, whilst having the facility to incorporate arbitrary receiver filtering, receiver thermal noise and non-ideal extinction ratio. A traditional Gaussian approximation (GA) is also calculated and comparison shows that it is clearly less accurate (it exceeds the upper bounds provided by CB and MCB) in the realistic cases examined. It is deduced, in common with the equivalent continuous mode analysis, that the MCB is the most sensible approach. Copyright © 2009 John Wiley & Sons, Ltd. [source] Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysisFEBS JOURNAL, Issue 4 2010Dimitar Kenanov In the present study, we investigated lipid biosynthesis in the bacterium Escherichia coli by mathematical modeling. In particular, we studied the interaction between the subsystems producing unsaturated and saturated fatty acids, phospholipids, lipid A, and cardiolipin. The present analysis was carried out both for the wild-type and for several in silico knockout mutants, using the concept of elementary flux modes. Our results confirm that, in the wild type, there are four main products: L1-phosphatidylethanolamine, lipid A, lipid A (cold-adapted), and cardiolipin. We found that each of these compounds is produced on several different routes, indicating a high redundancy of the system under study. By analysis of the elementary flux modes remaining after the knockout of genes of lipid biosynthesis, and comparison with publicly available data on single-gene knockouts in vivo, we were able to determine the metabolites essential for the survival of the cell. Furthermore, we analyzed a set of mutations that occur in a cell wall-free mutant of Escherichia coli W1655F+. We postulate that the mutant is not capable of producing both forms of lipid A, when the combination of mutations is considered to make a nonfunctional pathway. This is in contrast to gene essentiality data showing that lipid A synthesis is indispensable for the survival of the cell. The loss of the outer membrane in the cell wall-free mutant, however, shows that lipid A is dispensable as the main component of the outer surface structure in this particular E. coli strain. [source] Merging formation and current amplification of field-reversed configurationIEEJ TRANSACTIONS ON ELECTRICAL AND ELECTRONIC ENGINEERING, Issue 4 2007Michiaki Inomoto Member Abstract The merging formation of the field-reversed configuration (FRC) has been developed in the TS-3 merging experiment, leading us to a new scenario of FRC slow formation, heating and current amplification. Two force-free spheromaks with opposing toroidal fields were merged together in the axial direction to form a high-, FRC with higher efficiency than the conventional field-reversed theta-pinch method. This unique relaxation from the force-free (, , 0.05 , 0.1) spheromaks to the high-, (, , 0.7 , 1) FRC is attributed to the conversion of toroidal magnetic energy into ion thermal energy through the reconnection outflow. A central ohmic heating (OH) coil worked successfully to amplify the FRC plasma current by a factor of 2. Toroidal mode analysis of magnetic structure indicated that the tilting stability of the oblate FRC was provided by an ion kinetic effect. This oblate FRC is also useful as an initial equilibrium to produce a high-,p spherical tokamak (ST) with diamagnetic toroidal magnetic field, suggesting the close relationship between FRCs and high-,p STs in the second stable region of the ballooning mode. © 2007 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc. [source] The blending of narrative and argument in the generic texture of newspaper editorialsINTERNATIONAL JOURNAL OF APPLIED LINGUISTICS, Issue 1 2000Mike Reynolds This paper is a study in textural mode analysis (TMA). It examines the generic discourse texture of a set of editorials from the London Times and Guardian, on the topic of the British General Election of May 1997. It describes how the texture of the set can be accounted for in terms of just three representational textural modes, narrative, description and argument , and shows how argument predominates in the editorial genre. Toulmin's influential rhetorical model of argumentation, consisting of grounds, claims and warrants, is used and related to the realisation of argument mode through a number of functions, namely hypotheses, predictions, evaluations and assertions. The last of these frequently perform an ideological role in editorial discourse, via unmodalized assertions. The extremely common blending of textural modes by means of linear and layered blending is brought out, particularly through a ,case study'of one of the editorials. [source] Multiple criticality and staged ignition of methane in the counterflowINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 12 2009Wei Liu The counterflow ignition of methane was investigated, with particular interest in the role of radical versus thermal runaway. Simulation with different kinetic mechanisms showed that the ignition response is qualitatively sensitive to the kinetic mechanism adopted, either exhibiting or not exhibiting two ignition turning points in the S-curve response. For the former situation, ignition could take place in a staged manner with either increasing temperature or decreasing strain rate of the counterflow, characterized by the first ignition event being radical induced with negligible thermal effect and the second ignition event requiring thermal feedback. Sensitivity analysis and a recently developed chemical explosive mode analysis were performed to identify the dominant reactions in the radical runaway stage, revealing the importance of branching pathways involving the HO2 radical. Counterflow experiments were also conducted, yielding useful information on the ignition response. The study identifies items of further research to sharpen the comprehensiveness and accuracy of the methane oxidation mechanism. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 764,776, 2009 [source] Infrared spectra of water molecule encapsulated inside fullerene studied by instantaneous vibrational analysis,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2009Kiyoshi Yagi Abstract Instantaneous vibrational analysis (IVA) is proposed for computing the infrared spectrum of dynamically fluctuating system, and applied to a water molecule encapsulated into fullerene (H2O@C60). A molecular dynamics simulation is first carried out to generate an ensemble of configurations averaging the rotational and translational motion of H2O inside fullerene. At each configuration, instantaneous vibrational frequencies of the water molecule are computed by the vibrational configuration interaction method, which are then employed to construct the line-shape of the spectrum. The vibrational spectrum in the OH stretching region is computed at a temperature of 10 and 100 K based on a direct potential energy surface incorporating the electronic structure theory. It is found that the vibrational frequency of the symmetric stretching mode is blue-shifted compared to that of isolated water, whereas that of the asymmetric stretching mode exhibits no shift in average. The relation between IVA and instantaneous normal mode analysis is presented, and their performances are compared. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Symplectic molecular dynamics integration using normal mode analysisINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001anka Jane Abstract The split integration symplectic method (SISM) for molecular dynamics (MD) integration using normal mode analysis based on a factorization of the Liouville propagator is presented. This approach is quite distinct from others that use fractional-step methods, owing to the analytical treatment of high-frequency motions. The method involves splitting the total Hamiltonian of the system into a harmonic part and the remaining part. Then the Hamilton equations are solved using a second-order generalized leapfrog integration scheme in which the purely harmonic Hamiltonian (which represents the main contribution of the chemical bonds and angles) is treated analytically, i.e., independent of the step size of integration, by a normal mode analysis that is carried out only once, at the beginning of calculation. The whole integration step combines analytical evolution of the harmonic part of the Hamiltonian with a correction arising from the remaining part. The proposed algorithm requires only one force evaluation per integration step. The algorithm was tested on a simple system of linear chain molecules. Results demonstrate the method makes possible the integration of the MD equations over larger time steps without loss of stability while being economical in computer time. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 2,12, 2001 [source] Metabolism of the mesoionic compound (MI-D) by mouse liver microsome, detection of its metabolite In Vivo, and acute toxicity in miceJOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 6 2009Silvia Romão Abstract The mesoionic derivative 4-phenyl-5-[4-nitrocinnamoyl]-1,3,4-thiadiazolyl-2-phenylamine chloride (MI-D) has antitumoral and anti-inflammatory effects. In this study, we present aspects of its metabolism and toxicity in mice. MI-D was metabolized in vitro by liver microsome, generating a main product with a much shorter retention time than MI-D in high-performance liquid chromatography (HPLC) analysis but with a spectrum similar to that of the original molecule. Mass spectrometry with electrospray ionization in positive mode analysis of the purified compound by HPLC indicated that the product of metabolism has four additional hydroxyl groups (m/z = 465) compared with MI-D (m/z = 401). The HPLC analyses of plasma and urine samples from mice treated with MI-D showed the presence of the metabolite product. The kinetic parameters Km (19.5 ± 4.5 ,M) and Vmax [1.5 ± 0.4 units of fluorescence/(100 ,g of microsomal protein/mL/s)] were estimated, confirming the metabolism of MI-D and indicating that the reaction follows Michaelis-Menten kinetics. Acute toxicity was established on the basis of an estimation of mean lethal dose (LD-50; 181.2 mg/kg) and histopathological analysis of animals that survived the LD-50 test. Abdominal adhesions, inflammatory foci, and formation of granulomas were observed. Altogether, the results contribute to the advancement of research in support of MI-D as a future chemotherapeutic drug. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:394,405, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20303 [source] Converging free energy estimates: MM-PB(GB)SA studies on the protein,protein complex Ras,RafJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Holger Gohlke Abstract Estimating protein,protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute,solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson,Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras,Raf obtained in this study of ,8.3 kcal mol,1 is in good agreement with the experimental result of ,9.6 kcal mol,1, however, further probing the transferability of the applied protocol that led to this result is necessary. © 2003 Wiley Periodicals, Inc. J Comput Chem 2: 238,250, 2003 [source] Vibrational analysis of Ni(II)- and Cu(II)-octamethylchlorin by polarized resonance Raman and Fourier transform infrared spectroscopyJOURNAL OF RAMAN SPECTROSCOPY, Issue 6-7 2001Robert J. Lipski We measured the polarized resonance Raman spectra of Cu(II)-2,2,7,8,12,13,17,18-octamethylchlorin in CS2 at various excitation wavenumbers in a spectral region covering the Qy, Qx and Bx optical absorption bands. Additionally, we measured the FTIR-Raman spectrum of the highly overcrowded spectral region between 1300 and 1450 cm,1. The spectral decomposition was carried out by a self-consistent global fit to all spectra obtained. The thus identified Raman and IR lines were assigned by comparison with the resonance Raman spectra of Cu(II)-octaethylporphyrin, by utilizing their depolarization ratio dispersions and by a normal mode analysis. The latter was based on a modified transferable molecular mechanics force field of Ni(II)-octaethylporphyrin [E. Unger, M. Beck, R.J. Lipski, W. Dreybrodt, C.J. Medforth, K.M. Smith and R. Schweitzer-Stenner, J. Phys. Chem. B103, 10229 (1999)]. A comparison of normal mode patterns obtained for Cu(II)-octamethylchlorin and Cu(II)-octaethylporphyrin revealed that some modes are significantly distorted by the reduction of the pyrrole ring, in accordance with results which Boldt et al. reported earlier for Ni(II)-octaethylchlorin [N.J. Boldt, F.J. Donohoe, R.R. Birge and D.F. Bocian, J. Am. Chem. Soc.109, 2284 (1987)]. In contrast to conclusions drawn from this study, however, the results of our vibrational analysis and several further lines of evidence suggest that the normal modes of corresponding chlorines and porphyrins are still comparable, because they display contributions from the same local coordinates. Thus, the classical normal mode classification developed for metalloporphyrins is also applicable to metallochlorins. Finally, we performed a preliminary analysis of the absorption spectrum and the resonance excitation profiles and depolarization ratio dispersions of some Raman lines. The results show that the electronic properties of Cu(II)-octamethylchlorin can still be described in terms of Gouterman's four orbital model [M. Gouterman, J. Chem. Phys.30, 1139 (1959)]. In regions of the Q bands, Raman scattering of A1 modes is determined by interferences between Franck, Condon coupling and interstate Herzberg, Teller coupling between Qx(Qy) and Bx(By) states. The B2 modes are resonance enhanced by Herzberg, Teller coupling between Qx and Qy and between Qx(Qy) and By(Bx). Franck, Condon coupling of A1 modes with large contributions from C,Cm stretching vibrations is comparatively strong for Qx. This is interpreted as reflecting the expansion of the chlorin macrocycle by an electronic transition into this excited state. Copyright © 2001 John Wiley & Sons, Ltd. [source] Backward-wave directional coupler with complete coupling and broadband using conventional microstrip and 1D mushroom structureMICROWAVE AND OPTICAL TECHNOLOGY LETTERS, Issue 7 2006Jae-Gon Lee Abstract A new type of backward-wave coupled-line directional coupler with complete coupling and broadband, which is composed of a conventional microstrip and a 1D mushroom structure, is proposed. The 1D mushroom structure is employed for a double negative (DNG) transmission line. The coupler exhibits unusual characteristics such as complex propagation. The complex propagation constant of the coupled mode enables strong coupling due to exponential field decay. The performance of the proposed coupler is verified by c- and ,-mode analysis, full-wave simulation, and measurement. The measured coupling level of ,0.5 dB with 3-dB fractional bandwidth of 35% and high directivity of 30 dB is achieved. © 2006 Wiley Periodicals, Inc. Microwave Opt Technol Lett 48: 1293,1296, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.21622 [source] Collective Dynamics of Large Proteins from Mixed Coarse-Grained Elastic Network ModelMOLECULAR INFORMATICS, Issue 4 2005Ozge Kurkcuoglu Abstract Elastic network model- a coarse-grained normal mode analysis- is widely used to investigate the functionally important collective motions of proteins and their complexes. Mixed coarse-graining approach has been recently introduced to the elastic network model, so that the protein's native conformation can be modeled with regions of low and high resolution. In the mixed resolution model, each node of the elastic network may represent either a single atom (high-resolution) or a residue (low-resolution), and close-neighboring nodes are connected by harmonic springs. Here, the high-resolution parts constitute the interesting parts of the protein, such as the active site, while the rest of the structure is retained at lower resolution. By performing normal mode analysis of the resulting network, the collective dynamics (low-frequency modes) and consequent conformational changes can be analyzed even for supramolecular assemblages with reasonable computational efficiency, which may serve as a means of incorporating protein flexibility into docking algorithms and drug design. In this study, the mixed coarse-graining methodology is applied to analyze the functional motions of an important enzyme, triosephosphate isomerase. [source] Structure,property correlation over five phases and four transitions in Pb5Al3F19ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2003S. C. Abrahams The calorimetric and dielectric properties of Pb5Al3F19 in the five phases stable under ambient pressure are correlated with structure for fuller characterization of each phase. The first-order transition between ferroelectric phase V and antiferroelectric phase IV at TV,IV = 260,(5),K exhibits a thermal hysteresis of 135,(5),K on heating, with a maximum atomic displacement ,(xyz)max = 1.21,(6),Å; the transition from phase IV to ferroelastic phase III at 315,(5),K is also first order but with a thermal hysteresis of 10,(5),K and ,(xyz)max = 0.92,(7) ,Å; that from phase III to paraelastic phase II at 360,(5),K is second order without hysteresis and has ,(xyz)max = 0.69,(4),Å; and the transition from phase II to paraelectric phase I at 670,(5),K is second or higher order, with ,(xyz)max = 0.7,(4),Å. The measured entropy change ,S at TV,IV agrees well with ,S as derived from the increased configurational energy by Stirling's approximation. For all other phase transitions, 0.5 ,,S > 0,J,mol,1,K,1 is consistent with an entropy change caused primarily by the changes in the vibrational energy. The structure of phase III is determined both by group theoretical/normal mode analysis and by consideration of the structures of phases II, IV and V reported previously; refinement is by simultaneous Rietveld analysis of the X-ray and neutron diffraction powder profiles. The structure of prototypic phase I is predicted on the basis of the atomic arrangement in phases II, III, IV and V. The introduction of 3d electrons into the Pb5Al3F19 lattice disturbs the structural equilibrium, the addition of 0.04% Cr3+ causing significant changes in atomic positions and increasing TIV,III by ,15,K. Substitution of Al3+ by 20% or more Cr3+ eliminates the potential minima that otherwise stabilize phases IV, III and II. [source] X-ray diffraction study of the phase transition of K2Mn2(BeF4)3: a new type of low-temperature structure for langbeinitesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001A. Guelylah The potassium manganese tetrafluoroberyllate langbeinite compound has been studied in the temperature range 100,300,K. Using DSC measurements, a phase transition has been detected at 213,K. The space group of the low-temperature phase was determined to be P1121 using X-ray diffraction experiments and optical observations of the domain structure. The b axis is doubled with respect to the prototypic P213 cubic phase. Lattice parameters were determined by powder diffraction data [a = 10.0690,(8), b = 20.136,(2), c = 10.0329,(4),Å, , = 90.01,(1)°]. A precise analysis of the BeF4 tetrahedra in the low-temperature phase shows that two independent tetrahedra rotate in opposite directions along the doubled crystallographic axis. A symmetry mode analysis of the monoclinic distortion is also reported. This is the first report of the existence of such a phase transition in K2Mn2(BeF4)3 and also of a new type of low-temperature structure for langbeinite compounds. [source] Analysis of a regularized, time-staggered discretization applied to a vertical slice model,ATMOSPHERIC SCIENCE LETTERS, Issue 4 2006Mark Dubal Abstract A regularized and time-staggered discretization of the two-dimensional, vertical slice Euler equation set is described and analysed. A linear normal mode analysis of the time-discrete system indicates that unconditional stability is obtained, for appropriate values of the regularization parameters, for both the hydrostatic and non-hydrostatic cases. Furthermore, when these parameters take their optimal values, the stability behaviour of the normal modes is identical to that obtained from a semi-implicit discretization of the unregularized equations. © Crown Copyright 2006. Reproduced with the permission of the Controller of HMSO. Published by John Wiley & Sons, Ltd. [source] Multiscale modeling of nucleic acids: Insights into DNA flexibilityBIOPOLYMERS, Issue 9 2008Yannick J. Bomble Abstract The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 722,731, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Vibrations-determined properties of green fluorescent proteinBIOPOLYMERS, Issue 3 2005Veera Krasnenko Abstract The physicochemical characteristics of the green fluorescent protein (GFP), including the thermodynamic properties (entropy, enthalpy, Gibbs' free energy, heat capacity), normal mode vibrations, and atomic fluctuations, were investigated. The Gaussian 03 computational chemistry program was employed for normal mode analysis using the AMBER force field. The thermodynamic parameters and atomic fluctuations were then calculated from the vibrational eigenvalues (frequencies) and eigenvectors. The regions of highest rigidity were shown to be the ,-sheet barrel with the central ,-helix, which bears the chromophore. The most flexible parts of the GFP molecule were the outlying loops that cover the top and bottom of the ,-barrel. This way, the balance between rigidity and flexibility is maintained, which is the optimal relationship for protein stability in terms of Gibbs' free energy. This dual-schemed structure satisfies the requirements for GFP function. In this sense, the structure of GFP resembles a nanoscale drum: a stiff cylinder with flexible vibrating end(s). © 2005 Wiley Periodicals, Inc. Biopolymers 78: 140,146, 2005 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Ribosome motions modulate electrostatic propertiesBIOPOLYMERS, Issue 6 2004Joanna Trylska Abstract The electrostatic properties of the 70S ribosome of Thermus thermophilus were studied qualitatively by solving the Poisson,Boltzmann (PB) equation in aqueous solution and with physiological ionic strength. The electrostatic potential was calculated for conformations of the ribosome derived by recent normal mode analysis (Tama, F., et al. Proc Natl Acad Sci USA 2003 100, 9319,9323) of the ratchet-like reorganization that occurs during translocation (Frank, J.; Agrawal, R. K. Nature 2000 406, 318,322). To solve the PB equation, effective parameters (charges and radii), applicable to a highly charged backbone model of the ribosome, were developed. Regions of positive potential were found at the binding site of the elongation factors G and Tu, as well as where the release factors bind. Large positive potential areas are especially pronounced around the L11 and L6 proteins. The region around the L1 protein is also positively charged, supporting the idea that L1 may interact with the E-site tRNA during its release from the ribosome after translocation. Functional rearrangement of the ribosome leads to electrostatic changes which may help the translocation of the tRNAs during the elongation stage. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] Observation of Protein Domain Motions by Neutron SpectroscopyCHEMPHYSCHEM, Issue 6 2010Michael Monkenbusch Dr. Abstract High-resolution inelastic neutron scattering, which is available with neutron spin-echo spectroscopy (NSE) is introduced as a tool for the analysis of biomolecule ,exibility. Coherent scattering in a range where it is sensitive to length scales of nanometers and covering a time range from picoseconds to several 100 ns makes the motion of larger subdomains within proteins visible. We show that and how the internal domain motion within a protein in solution can be measured. Comparison with displacement patterns from normal mode analysis provides further insight into the nature of the geometry of the motions that lead to the oberved dynamic signature. The NSE experiment on alcohol dehydrogenase (ADH) is used as example to illustrate the general principles of the method. [source] Reaction Mechanism and Dynamic Investigations of Poly-channel Decomposition Reactions of o -Pyridyl RadicalCHINESE JOURNAL OF CHEMISTRY, Issue 8 2005Cheng Xue-Li Abstract Utilizing Gaussian94 program package, all species involved in decomposition reactions of o -pyridyl radical were optimized fully at B3LYP/6-311++G** level. Intrinsic reaction coordinate calculations were employed to confirm the connections of the transition states and products, and transition states were ascertained by the number of imaginary frequency (0 or 1). The reaction mechanism was elucidated by the vibrational mode analysis and electronic population analysis, and the reaction rate constants were calculated with transition state theory. [source] A VCD robust mode analysis of induced chirality: The case of pulegone in chloroform,CHIRALITY, Issue 1E 2009Valentin Paul Nicu Abstract Vibrational modes in an achiral molecule may acquire rotational strength by complexation to a chiral molecule, as happens for achiral solvent molecules complexed to a chiral solute. We investigate this transfer of chirality in vibrational circular dichroism for the pulegone molecule in CDCl3 solvent from the point of view of the robustness concept introduced recently. It turns out that the transfer of chirality yields nonrobust modes, which means that, although they are observed in vibrational circular dichroism (VCD) experiments, the sign of these modes cannot be predicted reliably with standard (Density Functional Theory) VCD calculations. This limits the usefulness of the induced chirality phenomenon for obtaining information on the intermolecular interactions that give rise to it. Chirality 21:E287,E297, 2009. © 2010 Wiley-Liss, Inc. [source] An extremely miniaturized microstrip branch-line couplerMICROWAVE AND OPTICAL TECHNOLOGY LETTERS, Issue 6 2009Mehdi Nosrati Abstract In this letter, an extremely miniaturized branch-line coupler (BLC) operating at 0.9 GHz is analyzed, designed, and introduced to enhance the bandwidth accompanied by highly size reduction without via-holes, multilayered technique, and air-bridged. A combination of a simple low-pass and band-stop filters is proposed to increase isolation between BLC's ports. This model is equaled by a quarter-wavelength line and necessary equations are obtained using even and odd modes analysis. A compact BLC is designed and tested using this technique. It is shown that the proposed BLC works as well as conventional ones though with size reduction of about 74% and 4.5% enhancement in bandwidth in analogy with recent branch-line coupler. The measurement results are in good agreement with the theoretical. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1403,1406, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24365 [source] | ||||||||||||||||