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Sample records for all-atom normal mode

  1. All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method.

    PubMed

    Kaledin, Alexey L; Kaledin, Martina; Bowman, Joel M

    2006-01-01

    Conventional normal-mode analysis of molecular vibrations requires computation and storage of the Hessian matrix. For a typical biological system such storage can reach several gigabytes posing difficulties for straightforward implementation. In this work we discuss an iterative block method to carry out full diagonalization of the Hessian while only storing a few vectors in memory. The iterative approach is based on the conjugate gradient formulation of the Davidson algorithm for simultaneous optimization of L roots, where in our case 10 < L < 300. The procedure is modified further by automatically adding a new vector into the search space for each locked (converged) root and keeping the new vector orthogonal to the eigenvectors previously determined. The higher excited states are then converged with the orthonormality constraint to the locked roots by applying a projector which is carried out using a read-rewind step done once per iteration. This allows for convergence of as many roots as desired without increasing the computer memory. The required Hessian-vector products are calculated on the fly as follows, Kp = dgp/dt, where K is the mass weighted Hessian, and gp is the gradient along p. The method has been implemented into the TINKER suite of molecular design codes. Preliminary results are presented for the normal modes of bacteriorhodopsin (bR) up to 300 cm(-)(1) and for the high frequency range between 2840 and 3680 cm(-)(1). There is evidence of a highly localized, noncollective mode at ∼1.4 cm(-)(1), caused by long-range interactions acting between the cytoplasmic and extracellular domains of bR.

  2. Anomalous normal mode oscillations in semiconductor microcavities

    SciTech Connect

    Wang, H.; Hou, H.Q.; Hammons, B.E.

    1997-04-01

    Semiconductor microcavities as a composite exciton-cavity system can be characterized by two normal modes. Under an impulsive excitation by a short laser pulse, optical polarizations associated with the two normal modes have a {pi} phase difference. The total induced optical polarization is then expected to exhibit a sin{sup 2}({Omega}t)-like oscillation where 2{Omega} is the normal mode splitting, reflecting a coherent energy exchange between the exciton and cavity. In this paper the authors present experimental studies of normal mode oscillations using three-pulse transient four wave mixing (FWM). The result reveals surprisingly that when the cavity is tuned far below the exciton resonance, normal mode oscillation in the polarization is cos{sup 2}({Omega}t)-like, in contrast to what is expected form the simple normal mode model. This anomalous normal mode oscillation reflects the important role of virtual excitation of electronic states in semiconductor microcavities.

  3. Normal modes of a small gamelan gong.

    PubMed

    Perrin, Robert; Elford, Daniel P; Chalmers, Luke; Swallowe, Gerry M; Moore, Thomas R; Hamdan, Sinin; Halkon, Benjamin J

    2014-10-01

    Studies have been made of the normal modes of a 20.7 cm diameter steel gamelan gong. A finite-element model has been constructed and its predictions for normal modes compared with experimental results obtained using electronic speckle pattern interferometry. Agreement was reasonable in view of the lack of precision in the manufacture of the instrument. The results agree with expectations for an axially symmetric system subject to small symmetry breaking. The extent to which the results obey Chladni's law is discussed. Comparison with vibrational and acoustical spectra enabled the identification of the small number of modes responsible for the sound output when played normally. Evidence of non-linear behavior was found, mainly in the form of subharmonics of true modes. Experiments using scanning laser Doppler vibrometry gave satisfactory agreement with the other methods.

  4. Normal Modes of Black Hole Accretion Disks

    SciTech Connect

    Ortega-Rodriguez, Manuel; Silbergleit, Alexander S.; Wagoner, Robert V.; /Stanford U., Phys. Dept. /KIPAC, Menlo Park

    2006-11-07

    This paper studies the hydrodynamical problem of normal modes of small adiabatic oscillations of relativistic barotropic thin accretion disks around black holes (and compact weakly magnetic neutron stars). Employing WKB techniques, we obtain the eigen frequencies and eigenfunctions of the modes for different values of the mass and angular momentum of the central black hole. We discuss the properties of the various types of modes and examine the role of viscosity, as it appears to render some of the modes unstable to rapid growth.

  5. Terahertz normal mode relaxation in pentaerythritol tetranitrate.

    PubMed

    Pereverzev, Andrey; Sewell, Thomas D

    2011-01-07

    Normal vibrational modes for a three-dimensional defect-free crystal of the high explosive pentaerythritol tetranitrate were obtained in the framework of classical mechanics using a previously published unreactive potential-energy surface [J. Phys. Chem. B 112, 734 (2008)]. Using these results the vibrational density of states was obtained for the entire vibrational frequency range. Relaxation of selectively excited terahertz-active modes was studied using isochoric-isoergic (NVE) molecular dynamics simulations for energy and density conditions corresponding to room temperature and atmospheric pressure. Dependence of the relaxation time on the initial modal excitation was considered for five excitation energies between 10 and 500 kT and shown to be relatively weak. The terahertz absorption spectrum was constructed directly using linewidths obtained from the relaxation times of the excited modes for the case of 10 kT excitation. The spectrum shows reasonably good agreement with experimental results. Dynamics of redistribution of the excited mode energy among the other normal modes was also studied. The results indicate that, for the four terahertz-active initially excited modes considered, there is a small subset of zero wave vector (k = 0) modes that preferentially absorb the energy on a few-picosecond time scale. The majority of the excitation energy, however, is transferred nonspecifically to the bath modes of the system.

  6. Normal modes of confined cold ionic systems

    SciTech Connect

    Schiffer, J.P.; Dubin, D.H.

    1995-08-01

    The normal modes of a cloud of confined ions forming a strongly-correlated plasma were investigated. The results of molecular-dynamics simulations were compared to predictions of a cold fluid mode. Mode frequencies are observed to shift slightly compared to the cold fluid predictions, and the modes are also observed to damp in time. Simulations also reveal a set of torsional oscillations which have no counterpart in cold fluid theory. The frequency shift, damping, and torsional effects are compared to a model that treats trapped plasmas as a visco-elastic spheroid. It may be possible to measure high-frequency bulk and shear moduli of a strongly-correlated plasma from mode excitation experiments on trapped non-neutral plasmas. An example of the results of the calculation is presented.

  7. Normal modes and mode transformation of pure electron vortex beams

    NASA Astrophysics Data System (ADS)

    Thirunavukkarasu, G.; Mousley, M.; Babiker, M.; Yuan, J.

    2017-02-01

    Electron vortex beams constitute the first class of matter vortex beams which are currently routinely produced in the laboratory. Here, we briefly review the progress of this nascent field and put forward a natural quantum basis set which we show is suitable for the description of electron vortex beams. The normal modes are truncated Bessel beams (TBBs) defined in the aperture plane or the Fourier transform of the transverse structure of the TBBs (FT-TBBs) in the focal plane of a lens with the said aperture. As these modes are eigenfunctions of the axial orbital angular momentum operator, they can provide a complete description of the two-dimensional transverse distribution of the wave function of any electron vortex beam in such a system, in analogy with the prominent role Laguerre-Gaussian (LG) beams played in the description of optical vortex beams. The characteristics of the normal modes of TBBs and FT-TBBs are described, including the quantized orbital angular momentum (in terms of the winding number l) and the radial index p>0. We present the experimental realization of such beams using computer-generated holograms. The mode analysis can be carried out using astigmatic transformation optics, demonstrating close analogy with the astigmatic mode transformation between LG and Hermite-Gaussian beams. This article is part of the themed issue 'Optical orbital angular momentum'.

  8. Normal Modes Expose Active Sites in Enzymes

    PubMed Central

    Glantz-Gashai, Yitav; Samson, Abraham O.

    2016-01-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

  9. Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.

    PubMed

    Zhou, Lei; Siegelbaum, Steven A

    2008-05-01

    Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics.

  10. Modeling seismic noise by normal mode summation

    NASA Astrophysics Data System (ADS)

    Gualtieri, L.; Stutzmann, E.; Capdeville, Y.; Ardhuin, F.; Schimmel, M.; Mangeney, A.; Morelli, A.

    2012-12-01

    Cross-correlation of ambient seismic noise plays a fundamental role to extract and better understand seismic properties of the Earth. The knowledge of the distribution of noise sources and the theory behind the seismic noise generation turns out to be of fundamental importance in the study of seismic noise cross-correlation. To improve these knowledge, we model the secondary microseismic noise, i.e. the period band 5-12 s, using normal mode summation and focus our attention on the noise sources distribution varying both in space and in time. Longuet-Higgins (1950) showed that the sources of the secondary microseismic noise are due to the pressure fluctuations that are generated by the interaction of ocean waves either in deep ocean or close by the coast and due to coastal reflection. Considering a recent ocean wave model (Ardhuin et al., 2011) that takes into account coastal reflection, we compute the vertical force due to the pressure fluctuation that has to be applied at the surface of the ocean. Noise sources are discretized in a spherical grid with constant resolution of 50 km and they are used to compute synthetic seismograms and spectra by normal mode summation. We show that we retrieve the maximum force amplitude for periods of 6-7 s which is consistent with the position of the maximum peak in the spectra and that, for long period in the secondary microseismic band, i.e. around 12 s, mostly the sources generated by coastal reflection have a strong influence on the microseism generation. We also show that the displacement of the ground is amplified in relation with the ocean bathymetry in agreement with Longuet-Higgins' theory and that the ocean site amplification can be computed using normal modes. We investigate also the role of the attenuation considering sources at regional scale. We are able to reproduce seasonal variations and to identify the noise sources having the main contribution in the spectra. We obtain a good agreement between synthetic and real

  11. Normal mode study of the earth's rigid body motions

    NASA Technical Reports Server (NTRS)

    Chao, B. F.

    1983-01-01

    In this paper it is shown that the earth's rigid body (rb) motions can be represented by an analytical set of eigensolutions to the equation of motion for elastic-gravitational free oscillations. Thus each degree of freedom in the rb motion is associated with a rb normal mode. Cases of both nonrotating and rotating earth models are studied, and it is shown that the rb modes do incorporate neatly into the earth's system of normal modes of free oscillation. The excitation formula for the rb modes are also obtained, based on normal mode theory. Physical implications of the results are summarized and the fundamental differences between rb modes and seismic modes are emphasized. In particular, it is ascertained that the Chandler wobble, being one of the rb modes belonging to the rotating earth, can be studied using the established theory of normal modes.

  12. Modeling seismic noise by normal mode summation

    NASA Astrophysics Data System (ADS)

    Gualtieri, L.; Stutzmann, E.; Capdeville, Y.; Ardhuin, F.; Schimmel, M.; Mangeney, A.; Morelli, A.

    2012-04-01

    Microseismic noise is the continuous oscillation of the ground in the period band 5-20 s. We observe seasonal variations of this noise that are stable over the last 20 years. Microseism spectra display 2 peaks, and the strongest peak, in the period band 5-12 s, correspond to the so called secondary microseism. Longuet-Higgins (1950) showed that the corresponding sources are pressure fluctuations that are generated by the interaction of ocean waves either in deep ocean or due to coastal reflection. Considering an ocean wave model that takes into account coastal reflection, we compute the pressure fluctuation as a vertical force applied at the surface of the ocean. The sources are discretized in a spherical grid with constant grid spacing of 50 km. We then compute the synthetic spectra by normal mode summation in a realistic Earth model. We show that the maximum force amplitude is for periods 6-7 s which is consistent with the period of the seismic spectra maximum peak and that, for periods around 12 s, only the sources generated by coastal reflection have a strong influence for the microseism generation. We also show that the displacement of the ground is amplified in relation with the ocean bathymetry in agreement with Longuet-Higgins' theory. We obtain a good agreement between synthetic and real seismic spectra in the period band 5-12sec. Modeling seismic noise is a useful tool for selecting particular noise data such as the strongest peaks and further investigating the corresponding sources. These noise sources may then be used for tomography.

  13. Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches.

    PubMed

    Mozolewska, Magdalena A; Krupa, Paweł; Scheraga, Harold A; Liwo, Adam

    2015-08-01

    The iron-sulfur protein 1 (Isu1) and the J-type co-chaperone Jac1 from yeast are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ-shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105 , L109 , and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1-12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N(95), T(98), P(102), H(112), V(159), L(167), and A(170) of Jac1, not yet tested experimentally, were also found to be important in binding.

  14. Molecular modeling of the binding modes of the Iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

    PubMed Central

    Mozolewska, Magdalena A.; Krupa, Paweł; Scheraga, Harold A.; Liwo, Adam

    2015-01-01

    The Iron sulfur protein 1 (Isu1) from yeast, and the J-type co-chaperone Jac1, are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the “Γ” shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105, L109, and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J. Mol. Biol. 2012, 417, 1–12). These residues were also found, by UNRES/MD simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N95, T98, P102, H112, V159, L167 and A170 of Jac1, not yet tested experimentally, were also found important in binding. PMID:25973573

  15. Normal mode sound field of a directional radiator

    NASA Astrophysics Data System (ADS)

    Zhang, R.; Zhu, B.

    1987-12-01

    In this paper, the sound field of a general type of directional radiator in a stratified medium is treated, and the concept of directivity is applied to calculation of the normal modes. The result shows that the normal mode field of a directional radiator can be obtained by supplementing the normal mode expression of an omnidirectional point source with the directional excitation function, which is dependent on the position and directivity of the radiator. In addition, the normal mode fields of radiators with vertical-symmetrical, vertical-antisymmetrical, single-sided and sharp directivities are calculated, respectively. For a vertical line array in a homogeneous water layer, if the source distribution is proportional to the eigenfunction of some normal mode, the zeros of the directional excitation function correspond precisely to the directions of the eigenrays of other normal modes.

  16. Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry.

    PubMed

    van Vlijmen, Herman W T; Karplus, Martin

    2005-07-15

    The study of the dynamics and thermodynamics of small icosahedral virus capsids is an active field of research. Normal mode analysis is one of the computational tools that can provide important insights into the conformational changes of the virus associated with cell entry or caused by changing of the physicochemical environment. Normal mode analysis of virus capsids has been limited due to the size of these systems, which often exceed 50,000 residues. Here we present the first normal mode calculation with full dihedral flexibility of several virus capsids, including poliovirus, rhinovirus, and cowpea chlorotic mottle virus. The calculations were made possible by applying group theoretical methods, which greatly simplified the calculations without any approximation beyond the all-atom force field representations in general use for smaller protein systems. Since a full Cartesian basis set was too large to be handled by the available computer memory, we used a basis set that includes all internal dihedral angles of the system with the exception of the peptide bonds, which were assumed rigid. The fluctuations of the normal modes are shown to correlate well with crystallographic temperature factors. The motions of the first several normal modes of each symmetry type are described. A hinge bending motion in poliovirus was found that may be involved in the mechanism by which bound small molecules inhibit conformational changes of the capsid. Fully flexible normal mode calculations of virus capsids are expected to increase our understanding of virus dynamics and thermodynamics, and can be useful in the refinement of cryo-electron microscopy structures of viruses.

  17. Atmospheric Excitation of Planetary Normal Modes

    NASA Technical Reports Server (NTRS)

    Tanimoto, Toshiro

    2001-01-01

    The objectives of this study were to: (1) understand the phenomenon of continuous free oscillations of the Earth and (2) examine the idea of using this phenomenon for planetary seismology. We first describe the results on (1) and present our evaluations of the idea (2) in the final section. In 1997, after almost forty years since the initial attempt by Benioff et al, continuous free oscillations of the Earth were discovered. Spheroidal fundamental modes between 2 and 7 millihertz are excited continuously with acceleration amplitudes of about 0.3-0.5 nanogals. The signal is now commonly found in virtually all data recorded by STS-1 type broadband seismometers at quiet sites. Seasonal variation in amplitude and the existence of two coupled modes between the atmosphere and the solid Earth support that these oscillations are excited by the atmosphere. Stochastic excitation due to atmospheric turbulence is a favored mechanism, providing a good match between theory and data. The atmosphere has ample energy to support this theory because excitation of these modes require only 500-10000 W whereas the atmosphere contains about 117 W of kinetic energy. An application of this phenomenon includes planetary seismology, because other planets may be oscillating due to atmospheric excitation. The interior structure of planets could be learned by determining the eigenfrequencies in the continuous free oscillations. It is especially attractive to pursue this idea for tectonically quiet planets, since quakes may be too infrequent to be recorded by seismic instruments.

  18. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    PubMed

    Na, Hyuntae; Jernigan, Robert L; Song, Guang

    2015-10-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  19. A normal-mode approach to Jovian atmospheric dynamic

    NASA Technical Reports Server (NTRS)

    Achterberg, Richard K.; Ingersoll, Andrew P.

    1989-01-01

    A nonlinear, quasi-geostrophic, baroclinic model of Jovian atmospheric dynamics is proposed, in which vertical variations of velocity are represented by a truncated sum over a complete set of orthogonal functions obtained by a separation of variables of the linearized quasi-geostrophic potential vorticity equation. A set of equations for the time variation of the mode amplitudes in the nonlinear case is then derived. It is shown that, for a planet with a neutrally stable, fluid interior instead of a solid lower boundary, the barotropic mode represents motions in the interior, and is not affected by the baroclinic modes. One consequence of this is that a normal-mode model with one baroclinic mode is dynamically equivalent to a one-layer model with solid lower topography. It is also shown that, for motions in Jupiter's cloudy lower troposphere, the stratosphere behaves nearly as a rigid lid, so that the normal-mode is applicable to Jupiter. The accuracy of the normal-mode model for Jupiter is tested using the following simple problems: (1) forced, vertically propagating Rossby waves, using two and three baroclinic modes, and (2) baroclinic instability, using two baroclinic modes. It is found that the normal-mode model provides qualitatively correct results, even with only a very limited number of vertical degrees of freedom.

  20. Instantaneous Normal Modes and the Protein Glass Transition

    SciTech Connect

    Schultz, Roland; Krishnan, Marimuthu; Daidone, Isabella; Smith, Jeremy C

    2009-01-01

    In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.

  1. Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations.

    PubMed

    Park, Jun-Koo; Jernigan, Robert; Wu, Zhijun

    2013-01-01

    We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C(α), C, N, and C(β) are considered. Combinations of some of these atoms are also tested. The force constants between the representative atoms are extracted from the Hessian matrix of the energy function and served as the force constants between the corresponding residues. The residue mean-square-fluctuations and their correlations with the experimental B-factors are calculated for a large set of proteins. The results are compared with all-atom normal mode analysis and the residue-level Gaussian Network Model. The coarse-grained methods perform more efficiently than all-atom normal mode analysis, while their B-factor correlations are also higher. Their B-factor correlations are comparable with those estimated by the Gaussian Network Model and in many cases better. The extracted force constants are surveyed for different pairs of residues with different numbers of separation residues in sequence. The statistical averages are used to build a refined Gaussian Network Model, which is able to predict residue-level structural fluctuations significantly better than the conventional Gaussian Network Model in many test cases.

  2. Normal-Mode Force APPROPRIATION—THEORY and Application

    NASA Astrophysics Data System (ADS)

    Wright, J. R.; Cooper, J. E.; Desforges, M. J.

    1999-03-01

    Normal-mode force appropriation is a method of physically exciting and measuring the undamped natural frequencies and normal-mode shapes of a structure which is distinct from the more common phase separation approaches. In this paper, the theory of normal modes and force appropriation is reviewed and a comparison made of a number of common force appropriation techniques. Both simulated and experimental data are used to highlight the relative merits of the different approaches, and comparisons to phase separation results are presented. Further advancements and applications of normal-mode testing—to non-proportionally damped structures, non-linear structures and consideration of the optimal exciter placement problem—are also discussed.

  3. Relating normal vibrational modes to local vibrational modes with the help of an adiabatic connection scheme.

    PubMed

    Zou, Wenli; Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2012-08-28

    Information on the electronic structure of a molecule and its chemical bonds is encoded in the molecular normal vibrational modes. However, normal vibrational modes result from a coupling of local vibrational modes, which means that only the latter can provide detailed insight into bonding and other structural features. In this work, it is proven that the adiabatic internal coordinate vibrational modes of Konkoli and Cremer [Int. J. Quantum Chem. 67, 29 (1998)] represent a unique set of local modes that is directly related to the normal vibrational modes. The missing link between these two sets of modes are the compliance constants of Decius, which turn out to be the reciprocals of the local mode force constants of Konkoli and Cremer. Using the compliance constants matrix, the local mode frequencies of any molecule can be converted into its normal mode frequencies with the help of an adiabatic connection scheme that defines the coupling of the local modes in terms of coupling frequencies and reveals how avoided crossings between the local modes lead to changes in the character of the normal modes.

  4. High-Frequency Normal Mode Propagation in Aluminum Cylinders

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2009-01-01

    Acoustic measurements made using compressional-wave (P-wave) and shear-wave (S-wave) transducers in aluminum cylinders reveal waveform features with high amplitudes and with velocities that depend on the feature's dominant frequency. In a given waveform, high-frequency features generally arrive earlier than low-frequency features, typical for normal mode propagation. To analyze these waveforms, the elastic equation is solved in a cylindrical coordinate system for the high-frequency case in which the acoustic wavelength is small compared to the cylinder geometry, and the surrounding medium is air. Dispersive P- and S-wave normal mode propagations are predicted to exist, but owing to complex interference patterns inside a cylinder, the phase and group velocities are not smooth functions of frequency. To assess the normal mode group velocities and relative amplitudes, approximate dispersion relations are derived using Bessel functions. The utility of the normal mode theory and approximations from a theoretical and experimental standpoint are demonstrated by showing how the sequence of P- and S-wave normal mode arrivals can vary between samples of different size, and how fundamental normal modes can be mistaken for the faster, but significantly smaller amplitude, P- and S-body waves from which P- and S-wave speeds are calculated.

  5. Universal spectrum of normal modes in low-temperature glasses

    PubMed Central

    Franz, Silvio; Parisi, Giorgio; Urbani, Pierfrancesco; Zamponi, Francesco

    2015-01-01

    We report an analytical study of the vibrational spectrum of the simplest model of jamming, the soft perceptron. We identify two distinct classes of soft modes. The first kind of modes are related to isostaticity and appear only in the close vicinity of the jamming transition. The second kind of modes instead are present everywhere in the glass phase and are related to the hierarchical structure of the potential energy landscape. Our results highlight the universality of the spectrum of normal modes in disordered systems, and open the way toward a detailed analytical understanding of the vibrational spectrum of low-temperature glasses. PMID:26561585

  6. Normal mode Rossby waves observed in the upper stratosphere

    NASA Technical Reports Server (NTRS)

    Hirooka, T.; Hirota, I.

    1985-01-01

    In recent years, observational evidence has been obtained for westward traveling planetary waves in the middle atmosphere with the aid of global data from satellites. There is no doubt that the fair portion of the observed traveling waves can be understood as the manifestation of the normal mode Rossby waves which are theoretically derived from the tidal theory. Some observational aspects of the structure and behavior of the normal model Rossby waves in the upper stratosphere are reported. The data used are the global stratospheric geopotential thickness and height analyses which are derived mainly from the Stratospheric Sounding Units (SSUs) on board TIROS-N and NOAA satellites. A clear example of the influence of the normal mode Rossby wave on the mean flow is reported. The mechanism considered is interference between the normal mode Rossby wave and the quasi-stationary wave.

  7. Quasi-Normal Modes of Stars and Black Holes.

    PubMed

    Kokkotas, Kostas D; Schmidt, Bernd G

    1999-01-01

    Perturbations of stars and black holes have been one of the main topics of relativistic astrophysics for the last few decades. They are of particular importance today, because of their relevance to gravitational wave astronomy. In this review we present the theory of quasi-normal modes of compact objects from both the mathematical and astrophysical points of view. The discussion includes perturbations of black holes (Schwarzschild, Reissner-Nordström, Kerr and Kerr-Newman) and relativistic stars (non-rotating and slowly-rotating). The properties of the various families of quasi-normal modes are described, and numerical techniques for calculating quasi-normal modes reviewed. The successes, as well as the limits, of perturbation theory are presented, and its role in the emerging era of numerical relativity and supercomputers is discussed.

  8. Mean flow generation mechanism by inertial waves and normal modes

    NASA Astrophysics Data System (ADS)

    Will, Andreas; Ghasemi, Abouzar

    2016-04-01

    The mean flow generation mechanism by nonlinearity of the inertial normal modes and inertial wave beams in a rotating annular cavity with longitudinally librating walls in stable regime is discussed. Inertial normal modes (standing waves) are excited when libration frequency matches eigenfrequencies of the system. Inertial wave beams are produced by Ekman pumping and suction in a rotating cylinder and form periodic orbits or periodic ray trajectories at selected frequencies. Inertial wave beams emerge as concentrated shear layers in a librating annular cavity, while normal modes appear as global recirculation cells. Both (inertial wave beam and mode) are helical and thus intrinsically non-linear flow structures. No second mode or wave is necessary for non-linearity. We considered the low order normal modes (1,1), (2,1) and (2,2) which are expected to be excited in the planetary objects and investigate the mean flow generation mechanism using two independent solutions: 1) analytical solution (Borcia 2012) and 2) the wave component of the flow (ω0 component) obtained from the direct numerical simulation (DNS). It is well known that a retrograde bulk mean flow is generated by the Ekman boundary layer and E1/4-Stewartson layer close to the outer cylinder side wall due to libration. At and around the normal mode resonant frequencies we found additionally a prograde azimuthal mean flow (Inertial Normal Mode Mean Flow: INMMF) in the bulk of the fluid. The fluid in the bulk is in geostrophic balance in the absence of the inertial normal modes. However, when INMMF is excited, we found that the geostrophic balance does not hold in the region occupied by INMMF. We hypothesize that INMMF is generated by the nonlinearity of the normal modes or by second order effects. Expanding the velocity {V}(u_r,u_θ,u_z) and pressure (p) in a power series in ɛ (libration amplitude), the Navier-Stokes equations are segregated into the linear and nonlinear parts at orders ɛ1 and ɛ^2

  9. Nonlinear normal modes modal interactions and isolated resonance curves

    SciTech Connect

    Kuether, Robert J.; Renson, L.; Detroux, T.; Grappasonni, C.; Kerschen, G.; Allen, M. S.

    2015-05-21

    The objective of the present study is to explore the connection between the nonlinear normal modes of an undamped and unforced nonlinear system and the isolated resonance curves that may appear in the damped response of the forced system. To this end, an energy balance technique is used to predict the amplitude of the harmonic forcing that is necessary to excite a specific nonlinear normal mode. A cantilever beam with a nonlinear spring at its tip serves to illustrate the developments. Furthermore, the practical implications of isolated resonance curves are also discussed by computing the beam response to sine sweep excitations of increasing amplitudes.

  10. Nonlinear normal modes modal interactions and isolated resonance curves

    DOE PAGES

    Kuether, Robert J.; Renson, L.; Detroux, T.; ...

    2015-05-21

    The objective of the present study is to explore the connection between the nonlinear normal modes of an undamped and unforced nonlinear system and the isolated resonance curves that may appear in the damped response of the forced system. To this end, an energy balance technique is used to predict the amplitude of the harmonic forcing that is necessary to excite a specific nonlinear normal mode. A cantilever beam with a nonlinear spring at its tip serves to illustrate the developments. Furthermore, the practical implications of isolated resonance curves are also discussed by computing the beam response to sine sweepmore » excitations of increasing amplitudes.« less

  11. Instantaneous normal mode analysis of melting of finite dust clusters.

    PubMed

    Melzer, André; Schella, André; Schablinski, Jan; Block, Dietmar; Piel, Alexander

    2012-06-01

    The experimental melting transition of finite two-dimensional dust clusters in a dusty plasma is analyzed using the method of instantaneous normal modes. In the experiment, dust clusters are heated in a thermodynamic equilibrium from a solid to a liquid state using a four-axis laser manipulation system. The fluid properties of the dust cluster, such as the diffusion constant, are measured from the instantaneous normal mode analysis. Thereby, the phase transition of these finite clusters is approached from the liquid phase. From the diffusion constants, unique melting temperatures have been assigned to dust clusters of various sizes that very well reflect their dynamical stability properties.

  12. Modelling secondary microseismic noise by normal mode summation

    NASA Astrophysics Data System (ADS)

    Gualtieri, L.; Stutzmann, E.; Capdeville, Y.; Ardhuin, F.; Schimmel, M.; Mangeney, A.; Morelli, A.

    2013-06-01

    Secondary microseisms recorded by seismic stations are generated in the ocean by the interaction of ocean gravity waves. We present here the theory for modelling secondary microseismic noise by normal mode summation. We show that the noise sources can be modelled by vertical forces and how to derive them from a realistic ocean wave model. We then show how to compute bathymetry excitation effect in a realistic earth model by using normal modes and a comparison with Longuet-Higgins approach. The strongest excitation areas in the oceans depends on the bathymetry and period and are different for each seismic mode. Seismic noise is then modelled by normal mode summation considering varying bathymetry. We derive an attenuation model that enables to fit well the vertical component spectra whatever the station location. We show that the fundamental mode of Rayleigh waves is the dominant signal in seismic noise. There is a discrepancy between real and synthetic spectra on the horizontal components that enables to estimate the amount of Love waves for which a different source mechanism is needed. Finally, we investigate noise generated in all the oceans around Africa and show that most of noise recorded in Algeria (TAM station) is generated in the Northern Atlantic and that there is a seasonal variability of the contribution of each ocean and sea.

  13. Numerical computation of nonlinear normal modes in mechanical engineering

    NASA Astrophysics Data System (ADS)

    Renson, L.; Kerschen, G.; Cochelin, B.

    2016-03-01

    This paper reviews the recent advances in computational methods for nonlinear normal modes (NNMs). Different algorithms for the computation of undamped and damped NNMs are presented, and their respective advantages and limitations are discussed. The methods are illustrated using various applications ranging from low-dimensional weakly nonlinear systems to strongly nonlinear industrial structures.

  14. A theory for protein dynamics: Global anisotropy and a normal mode approach to local complexity

    NASA Astrophysics Data System (ADS)

    Copperman, Jeremy; Romano, Pablo; Guenza, Marina

    2014-03-01

    We propose a novel Langevin equation description for the dynamics of biological macromolecules by projecting the solvent and all atomic degrees of freedom onto a set of coarse-grained sites at the single residue level. We utilize a multi-scale approach where molecular dynamic simulations are performed to obtain equilibrium structural correlations input to a modified Rouse-Zimm description which can be solved analytically. The normal mode solution provides a minimal basis set to account for important properties of biological polymers such as the anisotropic global structure, and internal motion on a complex free-energy surface. This multi-scale modeling method predicts the dynamics of both global rotational diffusion and constrained internal motion from the picosecond to the nanosecond regime, and is quantitative when compared to both simulation trajectory and NMR relaxation times. Utilizing non-equilibrium sampling techniques and an explicit treatment of the free-energy barriers in the mode coordinates, the model is extended to include biologically important fluctuations in the microsecond regime, such as bubble and fork formation in nucleic acids, and protein domain motion. This work supported by the NSF under the Graduate STEM Fellows in K-12 Education (GK-12) program, grant DGE-0742540 and NSF grant DMR-0804145, computational support from XSEDE and ACISS.

  15. User's manual for the coupled mode version of the normal modes rotor aeroelastic analysis computer program

    NASA Technical Reports Server (NTRS)

    Bergquist, R. R.; Carlson, R. G.; Landgrebe, A. J.; Egolf, T. A.

    1974-01-01

    This User's Manual was prepared to provide the engineer with the information required to run the coupled mode version of the Normal Modes Rotor Aeroelastic Analysis Computer Program. The manual provides a full set of instructions for running the program, including calculation of blade modes, calculations of variable induced velocity distribution and the calculation of the time history of the response for either a single blade or a complete rotor with an airframe (the latter with constant inflow).

  16. Resolving nanophotonic spectra with quasi-normal modes (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Powell, David A.

    2016-09-01

    Many nanophotonic systems are strongly coupled to radiating waves, or suffer significant dissipative losses. Furthermore, they may have complex shapes which are not amenable to closed form calculations. This makes it challenging to determine their modes without resorting to quasi-static or point dipole approximations. To solve this problem, the quasi-normal modes (QNMs) are found from an integral equation model of the particle. These give complex frequencies where excitation can be supported without any incident field. The corresponding eigenvectors yield the modal distributions, which are non-orthogonal due to the non-Hermitian nature of the system. The model based on quasi-normal modes is applied to plasmonic and dielectric particles, and compared with a spherical multipole decomposition. Only with the QNMs is it possible to resolve all features of the extinction spectrum, as each peak in the spectrum can be attributed to a particular mode. In contrast, many of the multipole coefficient have multiple peaks and dips. Furthermore, by performing a multipolar decomposition of each QNM, the spectrum of multipole coefficients is explained in terms of destructive interference between modes of the same multipole order.

  17. Relationships between nonlinear normal modes and response to random inputs

    NASA Astrophysics Data System (ADS)

    Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

    2017-02-01

    The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). This work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing. Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.

  18. Relationships between nonlinear normal modes and response to random inputs

    DOE PAGES

    Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

    2016-07-25

    The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). Here, this work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing.more » Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.« less

  19. Relationships between nonlinear normal modes and response to random inputs

    SciTech Connect

    Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

    2016-07-25

    The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). Here, this work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing. Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.

  20. Elastic Pekeris waveguide normal mode solution comparisons against laboratory data.

    PubMed

    Schneiderwind, Joseph D; Collis, Jon M; Simpson, Harry J

    2012-09-01

    Following the derivation presented by Press and Ewing [Geophysics 15, 426-446 (1950)], a normal mode solution for the Pekeris waveguide problem with an elastic bottom is outlined. The analytic solution is benchmarked against data collected in an experiment performed at the Naval Research Laboratory [Collis et al., J. Acoust. Soc. Am. 122, 1987-1993 (2007)]. Comparisons reveal a close match between the analytic solution and experimental data. Results are strongly dependent on the accuracy of the horizontal wavenumbers for the modes, and horizontal wavenumber spectra are compared against those from the experimental data.

  1. S-Wave Normal Mode Propagation in Aluminum Cylinders

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2010-01-01

    Large amplitude waveform features have been identified in pulse-transmission shear-wave measurements through cylinders that are long relative to the acoustic wavelength. The arrival times and amplitudes of these features do not follow the predicted behavior of well-known bar waves, but instead they appear to propagate with group velocities that increase as the waveform feature's dominant frequency increases. To identify these anomalous features, the wave equation is solved in a cylindrical coordinate system using an infinitely long cylinder with a free surface boundary condition. The solution indicates that large amplitude normal-mode propagations exist. Using the high-frequency approximation of the Bessel function, an approximate dispersion relation is derived. The predicted amplitude and group velocities using the approximate dispersion relation qualitatively agree with measured values at high frequencies, but the exact dispersion relation should be used to analyze normal modes for full ranges of frequency of interest, particularly at lower frequencies.

  2. NOLB : Non-linear rigid block normal mode analysis method.

    PubMed

    Hoffmann, Alexandre; Grudinin, Sergei

    2017-04-05

    We present a new conceptually simple and computationally efficient method for non-linear normal mode analysis called NOLB. It relies on the rotations-translations of blocks (RTB) theoretical basis developed by Y.-H. Sanejouand and colleagues. We demonstrate how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a non-linear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a pure rotation about a certain center. We demonstrate the motions produced with the NOLB method on three different molecular systems and show that some of the lowest frequency normal modes correspond to the biologically relevant motions. For example, NOLB detects the spiral sliding motion of the TALE protein, which is capable of rapid diffusion along its target DNA. Overall, our method produces better structures compared to the standard approach, especially at large deformation amplitudes, as we demonstrate by visual inspection, energy and topology analyses, and also by the MolProbity service validation. Finally, our method is scalable and can be applied to very large molecular systems, such as ribosomes. Standalone executables of the NOLB normal mode analysis method are available at https://team.inria.fr/nano-d/software/nolb-normal-modes. A graphical user interfaces created for the SAMSON software platform will be made available at https: //www.samson-connect.net.

  3. Normal Modes of Magnetized Finite Two-Dimensional Yukawa Crystals

    NASA Astrophysics Data System (ADS)

    Marleau, Gabriel-Dominique; Kaehlert, Hanno; Bonitz, Michael

    2009-11-01

    The normal modes of a finite two-dimensional dusty plasma in an isotropic parabolic confinement, including the simultaneous effects of friction and an external magnetic field, are studied. The ground states are found from molecular dynamics simulations with simulated annealing, and the influence of screening, friction, and magnetic field on the mode frequencies is investigated in detail. The two-particle problem is solved analytically and the limiting cases of weak and strong magnetic fields are discussed.[4pt] [1] C. Henning, H. K"ahlert, P. Ludwig, A. Melzer, and M.Bonitz. J. Phys. A 42, 214023 (2009)[2] B. Farokhi, M. Shahmansouri, and P. K. Shukla. Phys.Plasmas 16, 063703 (2009)[3] L. Cândido, J.-P. Rino, N. Studart, and F. M. Peeters. J. Phys.: Condens. Matter 10, 11627--11644 (1998)

  4. Modeling secondary microseismic noise by normal mode summation

    NASA Astrophysics Data System (ADS)

    Gualtieri, Lucia; Stutzmann, Eleonore; Capdeville, Yann; Ardhuin, Fabrice; Schimmel, Martin; Mangenay, Anne; Morelli, Andrea

    2013-04-01

    Seismic noise is the continuous oscillation of the ground recorded by seismic stations in the period band 5-20s. In particular, secondary microseisms occur in the period band 5-12s and are generated in the ocean by the interaction of ocean gravity waves. We present the theory for modeling secondary microseismic noise by normal mode summation. We show that the noise sources can be modeled by vertical forces and how to derive them from a realistic ocean wave model. During the computation we take into account the bathymetry. We show how to compute bathymetry excitation effect in a realistic Earth model using normal modes and a comparison with Longuet-Higgins (1950) approach. The strongest excitation areas in the oceans depends on the bathymetry and period and are different for each seismic mode. We derive an attenuation model than enables to fit well the vertical component spectra whatever the station location. We show that the fundamental mode of Rayleigh wave is the dominant signal in seismic noise and it is sufficient to reproduce the main features of noise spectra amplitude. We also model horizontal components. There is a discrepancy between real and synthetic spectra on the horizontal components that enables to estimate the amount of Love waves for which a different source mechanism is needed. Finally, we investigate noise generated in all the oceans around Africa and show that most of noise recorded in Algeria (TAM station) is generated in the Northern Atlantic and that there is a seasonal variability of the contribution of each ocean and sea. Moreover, we also show that the Mediterranean Sea contributes significantly to the short period noise in winter.

  5. The normal modes of lattice vibrations of ice XI

    PubMed Central

    Zhang, Peng; Wang, Zhe; Lu, Ying-Bo; Ding, Zheng-Wen

    2016-01-01

    The vibrational spectrum of ice XI at thermal wavelengths using the CASTEP code, a first-principles simulation method, is investigated. A dual-track approach is constructed to verify the validity for the computational phonon spectrum: collate the simulated spectrum with inelastic neutron scattering experiments and assign the photon scattering peaks according to the calculated normal vibration frequencies. The 33 optical normal vibrations at the Brillouin center are illustrated definitely from the ab initio outcomes. The depolarizing field effect of the hydrogen bond vibrations at frequencies of 229 cm−1 and 310 cm−1 is found to agree well with the LST relationship. It is a convincing evidence to manifest the LO-TO splitting of hydrogen bonds in ice crystal. We attribute the two hydrogen bond peaks to the depolarization effect and apply this viewpoint to ordinary ice phase, ice Ih, which is difficult to analyse their vibration modes due to proton disorder. PMID:27375199

  6. Relating normal vibrational modes to local vibrational modes: benzene and naphthalene.

    PubMed

    Zou, Wenli; Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2013-07-01

    Local vibrational modes can be directly derived from normal vibrational modes using the method of Konkoli and Cremer (Int J Quant Chem 67:29, 1998). This implies the calculation of the harmonic force constant matrix F (q) (expressed in internal coordinates q) from the corresponding Cartesian force constant matrix f (x) with the help of the transformation matrix U = WB (†)(BWB (†))(-1) (B: Wilson's B-matrix). It is proven that the local vibrational modes are independent of the choice of the matrix W. However, the choice W = M (-1) (M: mass matrix) has numerical advantages with regard to the choice W = I (I: identity matrix), where the latter is frequently used in spectroscopy. The local vibrational modes can be related to the normal vibrational modes in the form of an adiabatic connection scheme (ACS) after rewriting the Wilson equation with the help of the compliance matrix. The ACSs of benzene and naphthalene based on experimental vibrational frequencies are discussed as nontrivial examples. It is demonstrated that the local-mode stretching force constants provide a quantitative measure for the C-H and C-C bond strength.

  7. Kelvin waves in ECMWF analysis: normal-mode diagnostics

    NASA Astrophysics Data System (ADS)

    Blaauw, Marten; Zagar, Nedjeljka

    2013-04-01

    Equatorial Kelvin waves show a large spread in spatial and temporal variability similar to their source of tropical convective forcing. Once decoupled from their source, Kelvin waves are modulated during their ascent by changes in the background wind and stability. In this presentation, we focus on the seasonal and interannual variability of Kelvin waves in relation with variability of (i) tropical convection and (ii) background zonal wind and static stability. Global data is extracted from ECMWF operational analysis from January 2007 till May 2011 on 91 model levels (top level at 0.01 hPa) and ~ 25 km horizontal resolution. Using three-dimensional orthogonal normal-mode expansions, we project input mass and wind data simultaneously onto balanced rotational modes and unbalanced inertia-gravity modes including Kelvin modes. Next, an inverse transformation of Kelvin modes to physical space is performed under the linearity assumption, allowing a study on the spatial and temporal variability of Kelvin wave zonal wind and temperature. Results show an annual cycle in KW zonal wind in agreement with other studies. Minima resp. maxima in zonal wind amplitudes are found in the Indian ocean resp. Western Pacific and are most pronounced in the tropical tropopause at 150 hPa in January and 100 hPa in July. The annual cycle is enhanced (reduced) through interaction with a descending westerly QBO phase and enhanced (reduced) convective forcing. We also note a gradual eastward shift of KW zonal wind maxima till January 2010 in correspondence with an eastward shift of tropical convection.

  8. Nonlinear normal modes and localization in two bubble oscillators.

    PubMed

    Sugita, Naohiro; Sugiura, Toshihiko

    2017-02-01

    We investigated a bifurcation structure of coupled nonlinear oscillation of two spherical gas bubbles subject to a stationary sound field by means of nonlinear modal analysis. The goal of this paper is to describe an energy localization phenomenon of coupled two-bubble oscillators, resulting from symmetry-breaking bifurcation of the steady-state oscillation. Approximate asymptotic solutions of nonlinear normal modes (NNMs) and steady state oscillation are obtained based on the method of multiple scales. It is found that localized oscillation arises in a neighborhood of the localized normal modes. The analytical solutions of the amplitude and the phase shift of the steady-state oscillation are compared to numerical results and found to be in good agreement within the limit of small-amplitude oscillation. For larger amplitude oscillation, a bifurcation diagram of the localized solution as a function of the driving frequency and the separation distance between the bubbles is provided in the presence of the thermal damping. The numerical results show that the localized oscillation can occur for a fairly typical parameter range used in practical experiments and simulations in the early literatures.

  9. Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations.

    PubMed

    Strom, Alexander M; Fehling, Samuel C; Bhattacharyya, Sudeep; Hati, Sanchita

    2014-05-01

    Coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. To evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-tRNA synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-tRNA synthetases--Escherichia coli methionyl-tRNA synthetase, Thermus thermophilus leucyl-tRNA synthetase, and Enterococcus faecium prolyl-tRNA synthetase. In the present study, comparison of predicted dynamics based on B-factor and overlap calculations revealed that coarse-grained methods are comparable to the all-atom simulations in depicting the intrinsic global dynamics of the three enzymes. However, the principal component analyses of the motions obtained from the all-atom molecular dynamics simulations provide a superior description of the local fluctuations of these enzymes. In particular, the all-atom model was able to capture the functionally relevant substrate-induced dynamical changes in prolyl-tRNA synthetase. The alteration in the coupled dynamics between the catalytically important proline-binding loop and its neighboring structural elements due to substrate binding has been characterized and reported for the first time. Taken together, the study portrays comparable and contrasting situations in studying the functional dynamics of large multi-domain aminoacyl-tRNA synthetases using coarse-grained and all-atom simulation methods.

  10. [Raman, FTIR spectra and normal mode analysis of acetanilide].

    PubMed

    Liang, Hui-Qin; Tao, Ya-Ping; Han, Li-Gang; Han, Yun-Xia; Mo, Yu-Jun

    2012-10-01

    The Raman and FTIR spectra of acetanilide (ACN) were measured experimentally in the regions of 3 500-50 and 3 500-600 cm(-1) respectively. The equilibrium geometry and vibration frequencies of ACN were calculated based on density functional theory (DFT) method (B3LYP/6-311G(d, p)). The results showed that the theoretical calculation of molecular structure parameters are in good agreement with previous report and better than the ones calculated based on 6-31G(d), and the calculated frequencies agree well with the experimental ones. Potential energy distribution of each frequency was worked out by normal mode analysis, and based on this, a detailed and accurate vibration frequency assignment of ACN was obtained.

  11. iMODS: internal coordinates normal mode analysis server

    PubMed Central

    López-Blanco, José Ramón; Aliaga, José I.; Quintana-Ortí, Enrique S.; Chacón, Pablo

    2014-01-01

    Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org. PMID:24771341

  12. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  13. An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

    PubMed Central

    Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

    2012-01-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  14. "Good Vibrations": A workshop on oscillations and normal modes

    NASA Astrophysics Data System (ADS)

    Barbieri, Sara; Carpineti, Marina; Giliberti, Marco; Rigon, Enrico; Stellato, Marco; Tamborini, Marina

    2016-05-01

    We describe some theatrical strategies adopted in a two hour workshop in order to show some meaningful experiments and the underlying useful ideas to describe a secondary school path on oscillations, that develops from harmonic motion to normal modes of oscillations, and makes extensive use of video analysis, data logging, slow motions and applet simulations. Theatre is an extremely useful tool to stimulate motivation starting from positive emotions. That is the reason why the theatrical approach to the presentation of physical themes has been explored by the group "Lo spettacolo della Fisica" (http://spettacolo.fisica.unimi.it) of the Physics Department of University of Milano for the last ten years (Carpineti et al., JCOM, 10 (2011) 1; Nuovo Cimento B, 121 (2006) 901) and has been inserted also in the European FP7 Project TEMI (Teaching Enquiry with Mysteries Incorporated, see http://teachingmysteries.eu/en) which involves 13 different partners coming from 11 European countries, among which the Italian (Milan) group. According to the TEMI guidelines, this workshop has a written script based on emotionally engaging activities of presenting mysteries to be solved while participants have been involved in nice experiments following the developed path.

  15. Approach to calculate normal modes by decomposing the dyadic Green's function.

    PubMed

    Yu, Wenhai; Yue, Wencheng; Yao, Peijun; Lu, Yonghua; Liu, Wen

    2014-11-03

    Normal mode is a very fundamental notion in quantum and classical optics. In this paper, we present a method to calculate normal modes by decomposing dyadic Green's function, where the modes are excited by dipoles. The modes obtained by our method can be directly normalized and their degeneracies can be easily removed. This method can be applied to many theoretical descriptions of cavity electrodynamics and is of interest to nanophotonics.

  16. On the nonlinear normal modes of free vibration of piecewise linear systems

    NASA Astrophysics Data System (ADS)

    Uspensky, B. V.; Avramov, K. V.

    2014-07-01

    A modification of the Shaw-Pierre nonlinear normal modes is suggested in order to analyze the vibrations of a piecewise linear mechanical systems with finite degrees of freedom. The use of this approach allows one to reduce to twice the dimension of the nonlinear algebraic equations system for nonlinear normal modes calculations in comparison with systems obtained by previous researchers. Two degrees of freedom and fifteen degrees of freedom nonlinear dynamical systems are investigated numerically by using nonlinear normal modes.

  17. Normal modes of a defected linear system of beaded springs

    NASA Astrophysics Data System (ADS)

    Aghamohammadi, Amir; Foulaadvand, M. Ebrahim; Yaghoubi, Mohammad Hassan; Mousavi, Amir Hossein

    2017-03-01

    A model of a one-dimensional mass-spring chain with mass or spring defects is investigated. With a mass defect, all oscillators except the central one have the same mass, and with a spring defect, all the springs except those connected to the central oscillator have the same stiffness constant. The motion is assumed to be one-dimensional and frictionless, and both ends of the chain are assumed to be fixed. The system vibrational modes are obtained analytically, and it is shown that if the defective mass is lighter than the others, then a high frequency mode appears in which the amplitudes decrease exponentially with the distance from the defect. In this sense, the mode is localized in space. If the defect mass is greater than the others, then there will be no localized mode and all modes are extended throughout the system. Analogously, for some values of the defective spring constant, there may be one or two localized modes. If the two defected spring constants are less than that of the others, there is no localized mode.

  18. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    NASA Astrophysics Data System (ADS)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  19. Empirical orthogonal functions and normal modes. [for atmospheric data studies

    NASA Technical Reports Server (NTRS)

    North, G. R.

    1984-01-01

    An attempt to provide physical insight into the empirical orthogonal function (EOF) representation of data fields by the study of fields generated by linear stochastic models is presented in this paper. In a large class of these models, the EOFs at individual Fourier frequencies coincide with the orthogonal mechanical modes of the system - provided they exist. The precise mathematical criteria for this coincidence are derived and a physical interpretation is provided. A scheme possibly useful in forecasting is formally constructed for representing any stochastic field by a linear Hermitian model forced by noise.

  20. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.

    PubMed

    Euston, Stephen R

    2010-10-11

    The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

  1. Comparison of Non-Neutral Plasma Normal Modes with Calculation

    NASA Astrophysics Data System (ADS)

    Tobler, Samuel K.; Peterson, Bryan G.; Hart, Grant W.; Spencer, Ross L.

    2004-10-01

    We have measured the diocotron and Trivelpiece-Gould mode frequencies, radial density profile and central temperature in a long (0.6 m), cylindrical Malmberg-Penning electron trap at four different magnetic field strengths. The total particle count varied by a factor of 10 and the magnetic field varied by a factor of 3.5. The temperatures were fairly constant. Using an equilibrium code (EQUILSOR), a 2-D particle-in-cell code (RATTLE), and a 3-D particle-in-cell code (INFERNO) we have calculated the frequencies corresponding to the experimental conditions. We will discuss the limitations of the codes and the conditions in which they agree with experimental results.

  2. A new technique in demodulation of normal modes

    NASA Astrophysics Data System (ADS)

    Nawab, Ramin; L´, Philippe

    1994-07-01

    Lateral heterogeneities of the Earth produce amplitude modulations of the so-called unresolved multiplets. A spectral fitting technique based on the polynomial interpolation of Hermite allows the retrieval of these slowly varying modulation functions. No restrictive hypothesis on coupling among multiplets is necessary. Modulation functions are constrained in time within a Q-cycle for data with typical signal-to-noise ratios. Sensitivity to noise is reduced by the introduction of cosine tapers and by a priori information on the modulation functions. The method then damps rapid oscillations caused by noise and becomes stable. These amplitude modulations can be used in a first stage for inversions where both phase and amplitude are necessary, and generalize basic mode observables such as the local frequency.

  3. Synthetic Tsunami Waveform and Character of Tsunami Sources in Japan Sea, a Normal Mode Approach

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Satake, K.

    2015-12-01

    Normal mode method is widely used in seismology. Although some possibilities of applying normal mode to tsunami researches are already pointed out, the potential power of this method still remains. One advantage of normal mode method is that, once the mode solution is obtained and stored in the computer, we can synthesize tsunami waveforms as superposition of normal modes (Satake and Shimazaki, 1987). Although this theory is scientifically sound and there are some simple numerical tests, it has never been applied to a real case, due to computational difficulty. Recently, Wu and Satake (2014) developed a faster method to calculate normal mode based on Loomis (1975) method, and then obtained high resolution normal mode solution of Japan Sea, which contains 4000 modes (down to period of about 10 min). This makes it possible to verify the theory using real earthquake source parameter. With the source parameter of the Mw 7.7 1983 Japan Sea earthquake, we succeeded to synthesize tsunami waveforms by normal mode method for the first time. Comparisons with computed waveform based on finite different method (FDM) show good fit, thus proved the goodness of this idea. Unlike FDM, the calculation time does not depend on the duration for computation. Another merit of normal mode method is that the weight of excited tsunami due to an earthquake source may give us some direct information about the feature of tsunami generated by that source. In this study, we also calculated the excitation weight of 60 potential submarine faults in Japan Sea proposed by MLIT (2014). From these obtained weights, we can clearly see, for example, that when the source is located at shallower part or with larger magnitude, the generated weight will usually be larger.

  4. Electromagnetic fluctuations and normal modes of a drifting relativistic plasma

    SciTech Connect

    Ruyer, C.; Gremillet, L.; Bénisti, D.; Bonnaud, G.

    2013-11-15

    We present an exact calculation of the power spectrum of the electromagnetic fluctuations in a relativistic equilibrium plasma described by Maxwell-Jüttner distribution functions. We consider the cases of wave vectors parallel or normal to the plasma mean velocity. The relative contributions of the subluminal and supraluminal fluctuations are evaluated. Analytical expressions of the spatial fluctuation spectra are derived in each case. These theoretical results are compared to particle-in-cell simulations, showing a good reproduction of the subluminal fluctuation spectra.

  5. Molecular structure, natural bond analysis, vibrational and electronic spectra, surface enhanced Raman scattering and Mulliken atomic charges of the normal modes of [Mn(DDTC)2] complex.

    PubMed

    Téllez S, Claudio A; Costa, Anilton C; Mondragón, M A; Ferreira, Glaucio B; Versiane, O; Rangel, J L; Lima, G Müller; Martin, A A

    2016-12-05

    Theoretical and experimental bands have been assigned for the Fourier Transform Infrared and Raman spectra of the bis(diethyldithiocarbamate)Mn(II) complex, [Mn(DDTC)2]. The calculations have been based on the DFT/B3LYP method, second derivative spectra and band deconvolution analysis. The UV-vis experimental spectra were measured in acetonitrile solution, and the calculated electronic spectrum was obtained using the TD/B3LYP method with 6-311G(d, p) basis set for all atoms. Charge transfer bands and those d-d spin forbidden were assigned in the UV-vis spectrum. The natural bond orbital analysis was carried out using the DFT/B3LYP method and the Mn(II) hybridization leading to the planar geometry of the framework was discussed. Surface enhanced Raman scattering (SERS) was also performed. Mulliken charges of the normal modes were obtained and related to the SERS enhanced bands.

  6. Molecular structure, natural bond analysis, vibrational and electronic spectra, surface enhanced Raman scattering and Mulliken atomic charges of the normal modes of [Mn(DDTC)2] complex

    NASA Astrophysics Data System (ADS)

    Téllez S., Claudio A.; Costa, Anilton C.; Mondragón, M. A.; Ferreira, Glaucio B.; Versiane, O.; Rangel, J. L.; Lima, G. Müller; Martin, A. A.

    2016-12-01

    Theoretical and experimental bands have been assigned for the Fourier Transform Infrared and Raman spectra of the bis(diethyldithiocarbamate)Mn(II) complex, [Mn(DDTC)2]. The calculations have been based on the DFT/B3LYP method, second derivative spectra and band deconvolution analysis. The UV-vis experimental spectra were measured in acetonitrile solution, and the calculated electronic spectrum was obtained using the TD/B3LYP method with 6-311G(d, p) basis set for all atoms. Charge transfer bands and those d-d spin forbidden were assigned in the UV-vis spectrum. The natural bond orbital analysis was carried out using the DFT/B3LYP method and the Mn(II) hybridization leading to the planar geometry of the framework was discussed. Surface enhanced Raman scattering (SERS) was also performed. Mulliken charges of the normal modes were obtained and related to the SERS enhanced bands.

  7. Normal force for static and steady shear mode in magnetorheological fluid

    NASA Astrophysics Data System (ADS)

    Liu, Xuhui; Ye, Dun; Gao, Xiaoli; Li, Fang; Sun, Meng; Zhang, Hui; Tu, Tiangang; Yu, Hao

    2016-01-01

    This paper presents the normal force phenomena for static and steady shear mode in magnetorheological (MR) fluid. The results of the study show that, in the static mode, with the magnetic flux density increasing, the normal force will increase until the maximum, and then reduce to a steady value, and during the increasing stage, it can be expressed as FN=4667*B2.48 approximately; however, in the steady shear mode, only when the magnetic flux density achieves a certain value, the normal force phenomena will be observed clearly, and with the increasing of magnetic field, the normal force reaches the maximum, and then also decreases to a steady value. Besides, by defining the time parameters of dynamic response, the dynamic response of normal force is studied. If the shear plate is stationary, from the magnetic field on to a stable normal force produced, the response time is about 25.11 ms.

  8. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.

  9. Energetics analysis of the observed and simulated general circulation using three-dimensional normal mode expansions

    NASA Technical Reports Server (NTRS)

    Tanaka, Hiroshi; Kung, Ernest C.; Baker, Wayman E.

    1986-01-01

    The energetics characteristics of the observed and simulated general circulation are analyzed using three-dimensional normal mode expansions. The data sets involved are the Goddard Laboratory for Atmospheres (GLA) analysis and simulation data and the Geophysical Fluid Dynamics Laboratory (GFDL) analysis data. The spectral energy properties of the Rossby and gravity modes and energy transformations are presented. Significant influences of model characteristics and the assimilation techniques are observed in the barotropic energy spectrum, particularly for the gravity mode. Energy transformations of the zonal mean field in the GLA analysis and simulation are similar, but distinctly different from that in the GFDL analysis. However, overall, the energy generation in the baroclinic mode is largely balanced by the sink in the barotropic mode. The present study may demonstrate utilities of the three-dimensional normal mode energetics in the analysis of the general circulation.

  10. Characterization of Non-Linearized Spacecraft Relative Motion using Nonlinear Normal Modes

    DTIC Science & Technology

    2016-04-20

    AFRL-RV-PS- AFRL-RV-PS- TR-2015-0182 TR-2015-0182 CHARACTERIZATION OF NON-LINEARIZED SPACECRAFT RELATIVE MOTION USING NONLINEAR NORMAL MODES Eric...Non-Linearized Spacecraft Relative Motion using Nonlinear Normal Modes 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 62601F...public release; distribution is unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT Characterize the nonlinear dynamics for large amplitude relative motion

  11. Investigation and Analysis of Current Writing Teaching Mode among English Majors in Normal Universities in China

    ERIC Educational Resources Information Center

    Zeng, Hang-li

    2010-01-01

    This paper has made an investigation on the current writing teaching mode among English majors in normal universities in China, by means of questionnaire, interview and class observation. The study finds out that the current writing teaching mode is not purely product approach or process approach. In fact, the two approaches to writing co-exist in…

  12. Computational aspects of the nonlinear normal mode initialization of the GLAS 4th order GCM

    NASA Technical Reports Server (NTRS)

    Navon, I. M.; Bloom, S. C.; Takacs, L.

    1984-01-01

    Using the normal modes of the GLAS 4th Order Model, a Machenhauer nonlinear normal mode initialization (NLNMI) was carried out for the external vertical mode using the GLAS 4th Order shallow water equations model for an equivalent depth corresponding to that associated with the external vertical mode. A simple procedure was devised which was directed at identifying computational modes by following the rate of increase of BAL sub M, the partial (with respect to the zonal wavenumber m) sum of squares of the time change of the normal mode coefficients (for fixed vertical mode index) varying over the latitude index L of symmetric or antisymmetric gravity waves. A working algorithm is presented which speeds up the convergence of the iterative Machenhauer NLNMI. A 24 h integration using the NLNMI state was carried out using both Matsuno and leap-frog time-integration schemes; these runs were then compared to a 24 h integration starting from a non-initialized state. The maximal impact of the nonlinear normal mode initialization was found to occur 6-10 hours after the initial time.

  13. Normal forms for linear mode conversion and Landau-Zener transitions in one dimension

    SciTech Connect

    Flynn, W.G.; Littlejohn, R.G.

    1994-09-01

    Standard eikonal methods for the asymptotic analysis of coupled linear wave equations may fail when two eigenvalues of a matrix (the dispersion matrix) associated with the wave operator are both small in the same region of wave phase space. In this region the two eikonal modes associated with the two small eigenvalues are coupled, leading to a process called linear mode conversion or Landau-Zener coupling. A theory of linear mode conversion is presented in which geometric structure is emphasized. This theory is then used to identify the most generic type of mode conversion which occurs in one dimension. Finally, a general solution for this generic mode conversion problem is derived by transforming an arbitrary equation exhibiting generic mode conversion into an easily solvable normal form. This solution is given as a connection rule, with which one may continue standard eikonal wave solutions through mode conversion regions. 51 refs., 13 figs.

  14. A Study of Saturn's Normal Mode Oscillations and Their Forcing of Density Waves in the Rings

    NASA Astrophysics Data System (ADS)

    Friedson, Andrew James; Cao, Lyra

    2016-10-01

    Analysis of Cassini Visual and Infrared Mapping Spectrometer (VIMS) ring occultation profiles has revealed the presence of spiral density waves in Saturn's C ring that are consistent with being driven by gravitational perturbations associated with normal-mode oscillations of the planet [1]. These waves allow the C ring to serve as a sort of seismometer, since their pattern speeds (i.e., azimuthal phase speeds) can in principle be mapped onto the frequencies of the predominant normal oscillations of the planet. The resonant mode frequencies in turn are sensitive to Saturn's internal structure and rotational state. Characterization of the normal modes responsible for the forcing holds the potential to supply important new constraints on Saturn's internal structure and rotation. We perform numerical calculations to determine the resonant frequencies of the normal modes of a uniformly rotating planet for various assumptions regarding its internal stratification and compare the implied pattern speeds to those of density waves observed in the C ring. A question of particular interest that we address is whether quasi-toroidal modes are responsible for exciting a mysterious class of slowly propagating density waves in the ring. We also explore the implications of avoided crossings between modes for explaining observed fine splitting in the pattern speeds of spiral density waves having the same number of spiral arms, and weigh the role that convective overstability may play in exciting large-scale quasi-toroidal modes in Saturn. [1] Hedman, M.M. and Nicholson, P.D. 2014. MNRAS 444, 1369.

  15. Normal modes of the world's oceans: A numerical investigation using Proudman functions

    NASA Technical Reports Server (NTRS)

    Sanchez, Braulio V.; Morrow, Dennis

    1993-01-01

    The numerical modeling of the normal modes of the global oceans is addressed. The results of such modeling could be expected to serve as a guide in the analysis of observations and measurements intended to detect these modes. The numerical computation of normal modes of the global oceans is a field in which several investigations have obtained results during the past 15 years. The results seem to be model-dependent to an unsatisfactory extent. Some modeling areas, such as higher resolution of the bathymetry, inclusion of self-attraction and loading, the role of the Arctic Ocean, and systematic testing by means of diagnostic models are addressed. The results show that the present state of the art is such that a final solution to the normal mode problem still lies in the future. The numerical experiments show where some of the difficulties are and give some insight as to how to proceed in the future.

  16. Rossby normal modes in nonuniform background configurations. I Simple fields. II - Equinox and solstice conditions

    NASA Technical Reports Server (NTRS)

    Salby, M. L.

    1981-01-01

    An investigation is conducted regarding the influence of mean field variations on the realization of planetary normal modes, taking into account the mode response and structure in the presence of simple background nonuniformities. It is found that mean field variations have the combined effect of depressing, shifting, and broadening the characteristic response of Rossby normal modes. While nonuniformities in both the mean wind and temperature fields contribute to the reduction in peak response, the former are primarily responsible for translation and spectral broadening. An investigation is conducted to determine which modes may be realized in actual atmospheric configurations and which may be identified. For both the equinox and solstice configurations, response peaks corresponding to all of the first four modes of wavenumbers 1, 2, and 3 are readily visible above the noise.

  17. Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.

    PubMed

    Farag, Marwa H; Zúñiga, José; Requena, Alberto; Bastida, Adolfo

    2013-05-28

    Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ~85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.

  18. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  19. Isotope effect in normal-to-local transition of acetylene bending modes

    SciTech Connect

    Ma, Jianyi; Xu, Dingguo; Guo, Hua; Tyng, Vivian; Kellman, Michael E.

    2012-01-01

    The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helps to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans and normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.

  20. Isotope effect in normal-to-local transition of acetylene bending modes

    DOE PAGES

    Ma, Jianyi; Xu, Dingguo; Guo, Hua; ...

    2012-01-01

    The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helpsmore » to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans and normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.« less

  1. Normal Mode Splitting and Mechanical Effects of an Optical Lattice in a Ring Cavity

    NASA Astrophysics Data System (ADS)

    Klinner, Julian; Lindholdt, Malik; Nagorny, Boris; Hemmerich, Andreas

    2006-01-01

    A novel regime of atom-cavity physics is explored, arising when large atom samples dispersively interact with high-finesse optical cavities. A stable far-detuned optical lattice of several million rubidium atoms is formed inside an optical ring resonator by coupling equal amounts of laser light to each propagation direction of a longitudinal cavity mode. An adjacent longitudinal mode, detuned by about 3 GHz, is used to perform probe transmission spectroscopy of the system. The atom-cavity coupling for the lattice beams and the probe is dispersive and dissipation results only from the finite photon-storage time. The observation of two well-resolved normal modes demonstrates the regime of strong cooperative coupling. The details of the normal mode spectrum reveal mechanical effects associated with the retroaction of the probe upon the optical lattice.

  2. Normal mode splitting and mechanical effects of an optical lattice in a ring cavity.

    PubMed

    Klinner, Julian; Lindholdt, Malik; Nagorny, Boris; Hemmerich, Andreas

    2006-01-20

    A novel regime of atom-cavity physics is explored, arising when large atom samples dispersively interact with high-finesse optical cavities. A stable far-detuned optical lattice of several million rubidium atoms is formed inside an optical ring resonator by coupling equal amounts of laser light to each propagation direction of a longitudinal cavity mode. An adjacent longitudinal mode, detuned by about 3 GHz, is used to perform probe transmission spectroscopy of the system. The atom-cavity coupling for the lattice beams and the probe is dispersive and dissipation results only from the finite photon-storage time. The observation of two well-resolved normal modes demonstrates the regime of strong cooperative coupling. The details of the normal mode spectrum reveal mechanical effects associated with the retroaction of the probe upon the optical lattice.

  3. Isotope effect in normal-to-local transition of acetylene bending modes.

    PubMed

    Ma, Jianyi; Xu, Dingguo; Guo, Hua; Tyng, Vivian; Kellman, Michael E

    2012-01-07

    The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helps to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans- and cis-normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.

  4. Extended Majorana zero modes in a topological superconducting-normal T-junction

    NASA Astrophysics Data System (ADS)

    Spånslätt, Christian; Ardonne, Eddy

    2017-03-01

    We investigate the sub gap properties of a three terminal Josephson T-junction composed of topologically superconducting wires connected by a normal metal region. This system naturally hosts zero energy Andreev bound states which are of self-conjugate Majorana nature and we show that they are, in contrast to ordinary Majorana zero modes, spatially extended in the normal metal region. If the T-junction respects time-reversal symmetry, we show that a zero mode is distributed only in two out of three arms in the junction and tuning the superconducting phases allows for transfer of the mode between the junction arms. We further provide tunneling conductance calculations showing that these features can be detected in experiments. Our findings suggest an experimental platform for studying the nature of spatially extended Majorana zero modes.

  5. Normal Mode Splitting and Mechanical Effects of an Optical Lattice in a Ring Cavity

    SciTech Connect

    Klinner, Julian; Lindholdt, Malik; Nagorny, Boris; Hemmerich, Andreas

    2006-01-20

    A novel regime of atom-cavity physics is explored, arising when large atom samples dispersively interact with high-finesse optical cavities. A stable far-detuned optical lattice of several million rubidium atoms is formed inside an optical ring resonator by coupling equal amounts of laser light to each propagation direction of a longitudinal cavity mode. An adjacent longitudinal mode, detuned by about 3 GHz, is used to perform probe transmission spectroscopy of the system. The atom-cavity coupling for the lattice beams and the probe is dispersive and dissipation results only from the finite photon-storage time. The observation of two well-resolved normal modes demonstrates the regime of strong cooperative coupling. The details of the normal mode spectrum reveal mechanical effects associated with the retroaction of the probe upon the optical lattice.

  6. a Normal Mode Expansion Method for the Undamped Forced Vibration of Linear Piezoelectric Solid

    NASA Astrophysics Data System (ADS)

    LIU, D.-C.

    2000-06-01

    A normal mode expansion method for the vibrational responses of non-homogeneous linear piezoelectric materials without damping is presented. It can be applied directly to arbitrary piezoelectric composites, which are widely used in vibrational and acoustic sensor/actuator/transmitter applications. In the present article it is shown that if the normal modes are given, the displacement field can be expanded as the linear superposition of normal modes, while the modal coefficients can be represented in terms of surface and volume integrals directly over the six types of distributed excitations without solving the quasi-static solution explicitly. The present treatment is a modification of an earlier work by Liu [11] using a different definition of the so-called quasi-static solution, and the damping effect has been neglected for simplicity. A simple example is given to exemplify the application of the present formulation.

  7. Controllable Bistability and Normal Mode Splitting in an Optomechanical System Assisted by an Atomic Ensemble

    NASA Astrophysics Data System (ADS)

    Wu, Qin; Hu, Yao-Hua; Ma, Peng-Cheng

    2017-02-01

    We consider a system consisting of a standard optomechanical cavity and a trapped atomic ensemble. In such a system, we mainly focus on the features of optomechanical bistability and normal mode splitting with the presence of atomic ensemble. The results show that the energy of laser directly coupling the atomic ensemble can be enhanced effectively, and using this laser is more convenient and easier to realize the bistability and normal mode splitting than the traditional means. Besides, we find that atom-cavity field detuning also has a significant impact on optomechanical bistability, which offers us an important method to adjust and control the cavity mean photon number. At last, the numerical results show that atom-cavity field detuning and atom-cavity field coupling strength have an opposite effect on the normal mode splitting because they have different contributions to the effective cavity field decay rate.

  8. Large-scale Rossby Normal Modes during Some Recent Northern Hemisphere Winters

    DTIC Science & Technology

    2011-01-01

    prescribed climatological background winds and temperatures typical of solstice and equinox. Salby (1981a) also showed that inhomogeneities in the...relatively undisturbed and eastward. The amplitude of the normal modes is substantially biased toward the winter hemisphere near solstice when...modes in nonuniform background configurations. Part II: Equinox and solstice conditions. J. Atmos. Sci., 38, 1827-1840. Salby, M.L., 1984. Transient

  9. Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes

    DOE PAGES

    Kuether, Robert J.; Deaner, Brandon J.; Hollkamp, Joseph J.; ...

    2015-09-15

    Several reduced-order modeling strategies have been developed to create low-order models of geometrically nonlinear structures from detailed finite element models, allowing one to compute the dynamic response of the structure at a dramatically reduced cost. But, the parameters of these reduced-order models are estimated by applying a series of static loads to the finite element model, and the quality of the reduced-order model can be highly sensitive to the amplitudes of the static load cases used and to the type/number of modes used in the basis. Our paper proposes to combine reduced-order modeling and numerical continuation to estimate the nonlinearmore » normal modes of geometrically nonlinear finite element models. Not only does this make it possible to compute the nonlinear normal modes far more quickly than existing approaches, but the nonlinear normal modes are also shown to be an excellent metric by which the quality of the reduced-order model can be assessed. Hence, the second contribution of this work is to demonstrate how nonlinear normal modes can be used as a metric by which nonlinear reduced-order models can be compared. Moreover, various reduced-order models with hardening nonlinearities are compared for two different structures to demonstrate these concepts: a clamped–clamped beam model, and a more complicated finite element model of an exhaust panel cover.« less

  10. Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes

    SciTech Connect

    Kuether, Robert J.; Deaner, Brandon J.; Hollkamp, Joseph J.; Allen, Matthew S.

    2015-09-15

    Several reduced-order modeling strategies have been developed to create low-order models of geometrically nonlinear structures from detailed finite element models, allowing one to compute the dynamic response of the structure at a dramatically reduced cost. But, the parameters of these reduced-order models are estimated by applying a series of static loads to the finite element model, and the quality of the reduced-order model can be highly sensitive to the amplitudes of the static load cases used and to the type/number of modes used in the basis. Our paper proposes to combine reduced-order modeling and numerical continuation to estimate the nonlinear normal modes of geometrically nonlinear finite element models. Not only does this make it possible to compute the nonlinear normal modes far more quickly than existing approaches, but the nonlinear normal modes are also shown to be an excellent metric by which the quality of the reduced-order model can be assessed. Hence, the second contribution of this work is to demonstrate how nonlinear normal modes can be used as a metric by which nonlinear reduced-order models can be compared. Moreover, various reduced-order models with hardening nonlinearities are compared for two different structures to demonstrate these concepts: a clamped–clamped beam model, and a more complicated finite element model of an exhaust panel cover.

  11. NORM2L: An Interactive Computer Program for Acoustic Normal Mode Calculations for the Pekeris Model.

    DTIC Science & Technology

    1980-12-01

    Points concerning the solution of the Schrodinger Equation ", J.Comp.Phys. 1 382-396 (1967) 3. D.D. Ellis and B. Leverman, DREA, work in progress. 4. R...although the formulae for the normal mode equations are scattered throughout the book. Chapter 9 of the newer book by Clay and Medwin [6] contains a...fairly clear introduction to normal mode theory. Only the essential equations are presented here. Note that the formulation ’s in terms of the

  12. Comparative estimation of vibrational entropy changes in proteins through normal modes analysis.

    PubMed

    Carrington, Benjamin J; Mancera, Ricardo L

    2004-10-01

    We compare the vibrational entropy changes of proteins calculated using a full and a number of approximate normal modes analysis methods. The vibrational entropy differences for three conformational changes and three protein binding interactions were computed. In general, the approximate methods yield good estimates of the vibrational entropy change in a fraction of the time required by full normal modes analysis. The absolute entropies are either overestimated or greatly underestimated, but the difference is sufficiently accurate for some methods. This indicates that some of the approximate methods can give reasonable estimates of the associated vibrational entropy changes, making them suitable for inclusion in free energy calculations.

  13. Photoelectron spectra of dihalomethyl anions: Testing the limits of normal mode analysis

    NASA Astrophysics Data System (ADS)

    Vogelhuber, Kristen M.; Wren, Scott W.; McCoy, Anne B.; Ervin, Kent M.; Lineberger, W. Carl

    2011-05-01

    We report the 364-nm negative ion photoelectron spectra of CHX2- and CDX2-, where X = Cl, Br, and I. The pyramidal dihalomethyl anions undergo a large geometry change upon electron photodetachment to become nearly planar, resulting in multiple extended vibrational progressions in the photoelectron spectra. The normal mode analysis that successfully models photoelectron spectra when geometry changes are modest is unable to reproduce qualitatively the experimental data using physically reasonable parameters. Specifically, the harmonic normal mode analysis using Cartesian displacement coordinates results in much more C-H stretch excitation than is observed, leading to a simulated photoelectron spectrum that is much broader than that which is seen experimentally. A (2 + 1)-dimensional anharmonic coupled-mode analysis much better reproduces the observed vibrational structure. We obtain an estimate of the adiabatic electron affinity of each dihalomethyl radical studied. The electron affinity of CHCl2 and CDCl2 is 1.3(2) eV, of CHBr2 and CDBr2 is 1.9(2) eV, and of CHI2 and CDI2 is 1.9(2) eV. Analysis of the experimental spectra illustrates the limits of the conventional normal mode approach and shows the type of analysis required for substantial geometry changes when multiple modes are active upon photodetachment.

  14. Large-amplitude nonlinear normal modes of the discrete sine lattices

    NASA Astrophysics Data System (ADS)

    Smirnov, Valeri V.; Manevitch, Leonid I.

    2017-02-01

    We present an analytical description of the large-amplitude stationary oscillations of the finite discrete system of harmonically coupled pendulums without any restrictions on their amplitudes (excluding a vicinity of π ). Although this model has numerous applications in different fields of physics, it was studied earlier in the infinite limit only. The discrete chain with a finite length can be considered as a well analytical analog of the coarse-grain models of flexible polymers in the molecular dynamics simulations. The developed approach allows to find the dispersion relations for arbitrary amplitudes of the nonlinear normal modes. We emphasize that the long-wavelength approximation, which is described by well-known sine-Gordon equation, leads to an inadequate zone structure for the amplitudes of about π /2 even if the chain is long enough. An extremely complex zone structure at the large amplitudes corresponds to multiple resonances between nonlinear normal modes even with strongly different wave numbers. Due to the complexity of the dispersion relations the modes with shorter wavelengths may have smaller frequencies. The stability of the nonlinear normal modes under condition of the resonant interaction are discussed. It is shown that this interaction of the modes in the vicinity of the long wavelength edge of the spectrum leads to the localization of the oscillations. The thresholds of instability and localization are determined explicitly. The numerical simulation of the dynamics of a finite-length chain is in a good agreement with obtained analytical predictions.

  15. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

    PubMed

    Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

    2012-09-21

    Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity.

  16. Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis.

    PubMed

    Gil, Victor A; Lecina, Daniel; Grebner, Christoph; Guallar, Victor

    2016-10-15

    Normal mode methods are becoming a popular alternative to sample the conformational landscape of proteins. In this study, we describe the implementation of an internal coordinate normal mode analysis method and its application in exploring protein flexibility by using the Monte Carlo method PELE. This new method alternates two different stages, a perturbation of the backbone through the application of torsional normal modes, and a resampling of the side chains. We have evaluated the new approach using two test systems, ubiquitin and c-Src kinase, and the differences to the original ANM method are assessed by comparing both results to reference molecular dynamics simulations. The results suggest that the sampled phase space in the internal coordinate approach is closer to the molecular dynamics phase space than the one coming from a Cartesian coordinate anisotropic network model. In addition, the new method shows a great speedup (∼5-7×), making it a good candidate for future normal mode implementations in Monte Carlo methods.

  17. Quasi-normal modes of extremal BTZ black holes in TMG

    NASA Astrophysics Data System (ADS)

    Afshar, Hamid R.; Alishahiha, Mohsen; Mosaffa, Amir E.

    2010-08-01

    We study the spectrum of tensor perturbations on extremal BTZ black holes in topologically massive gravity for arbitrary values of the coefficient of the Chern-Simons term, μ. Imposing proper boundary conditions at the boundary of the space and at the horizon, we find that the spectrum contains quasi-normal modes.

  18. Global normal-mode Rossby waves observed in stratospheric ozone data

    SciTech Connect

    Randel, W.J. )

    1993-02-01

    Westward-propagating Rossby normal-mode planetary waves are documented in stratospheric ozone data using Solar Backscatter Ultraviolet (SBUV) satellite measurements. These modes are evidenced by enhanced spectral power and near-global coherence for westward-traveling zonal wave 1 oscillations with periods of 5-10 days. The ozone waves have maxima in high latitudes of the middle stratosphere (due to transport) and over midlatitudes in the upper stratosphere (due to photochemistry). These modes are nearly continuous throughout the eight years of SBUV observations, with maximum global coherence during the equinoxes. The upper-stratospheric waves are symmetric (in phase) between hemispheres, even for modes previously identified as antisymmetric in geopotential height. This behavior is due to differing wave vertical structure in each hemisphere: the planetary temperature waves are nearly in phase in the upper stratosphere, even though the height waves are out of phase. The observed ozone waves are furthermore compared to calculations based on linear wave transport and photochemistry, incorporating derived wind and temperature fields. Good agreement is found, showing that normal modes provide an idealized context to study the linear wave behavior of trace constituents in the real atmosphere. 23 refs., 17 figs.

  19. Unstable normal modes of low T /W dynamical instabilities in differentially rotating stars

    NASA Astrophysics Data System (ADS)

    Saijo, Motoyuki; Yoshida, Shin'ichirou

    2016-10-01

    We investigate the nature of low T /W dynamical instabilities in differentially rotating stars by means of linear perturbation. Here, T and W represent rotational kinetic energy and the gravitational binding energy of the star. This is the first attempt to investigate low T /W dynamical instabilities as a complete set of the eigenvalue problem. Our equilibrium configuration has "constant" specific angular momentum distribution, which potentially contains a singular solution in the perturbed enthalpy at a corotation radius in linear perturbation. We find the unstable normal modes of differentially rotating stars by solving the eigenvalue problem along the equatorial plane of the star, imposing the regularity condition on the center and the vanished enthalpy at the oscillating equatorial surface. We find that the existing pulsation modes become unstable due to the existence of the corotation radius inside the star. The feature of the unstable mode eigenfrequency and its eigenfunction in the linear analysis roughly agrees with that in three-dimensional hydrodynamical simulations in Newtonian gravity. Therefore, our normal mode analysis in the equatorial motion proves valid to find the unstable equilibrium stars efficiently. Moreover, the nature of the eigenfunction that oscillates between corotation and the surface radius for unstable stars requires reinterpretation of the pulsation modes in differentially rotating stars.

  20. Free and forced Rossby normal modes in a rectangular gulf of arbitrary orientation

    NASA Astrophysics Data System (ADS)

    Graef, Federico

    2016-09-01

    A free Rossby normal mode in a rectangular gulf of arbitrary orientation is constructed by considering the reflection of a Rossby mode in a channel at the head of the gulf. Therefore, it is the superposition of four Rossby waves in an otherwise unbounded ocean with the same frequency and wavenumbers perpendicular to the gulf axis whose difference is equal to 2mπ/W, where m is a positive integer and W the gulf's width. The lower (or higher) modes with small m (or large m) are oscillatory (evanescent) in the coordinate along the gulf; these are elucidated geometrically. However for oceanographically realistic parameter values, most of the modes are evanescent. When the gulf is forced at the mouth with a single Fourier component, the response is in general an infinite sum of modes that are needed to match the value of the streamfunction at the gulf's entrance. The dominant mode of the response is the resonant one, which corresponds to forcing with a frequency ω and wavenumber normal to the gulf axis η appropriate to a gulf mode: η =- β sin α/(2ω) ± Mπ/W, where α is the angle between the gulf's axis and the eastern direction (+ve clockwise) and M the resonant's mode number. For zonal gulfs ω drops out of the resonance condition. For the special cases η = 0 in which the free surface goes up and down at the mouth with no flow through it, or a flow with a sinusoidal profile, resonant modes can get excited for very specific frequencies (only for non-zonal gulfs in the η = 0 case). The resonant mode is around the annual frequency for a wide range of gulf orientations α ∈ [40°, 130°] or α ∈ [220°, 310°] and gulf widths between 150 and 200 km; these include the Gulf of California and the Adriatic Sea. If η is imaginary, i.e. a flow with an exponential profile, there is no resonance. In general less modes get excited if the gulf is zonally oriented.

  1. Normal incidence filters using symmetry-protected modes in dielectric subwavelength gratings

    PubMed Central

    Cui, Xuan; Tian, Hao; Du, Yan; Shi, Guang; Zhou, Zhongxiang

    2016-01-01

    We investigate narrowband transmission filters based on subwavelength-grating reflectors at normal incidence. Computational results show that the filtering is realized through symmetry-protected mode coupling. The guided mode resonances introduced by the slab layer allow flexible control of the filter frequencies. The quality factor of the filters could exceed 106. Dielectric gratings can be used over the entire range of electromagnetic waves, owing to their scale-invariant operations. Owing to the high refraction index and low index dispersion of semiconductors in the infrared range, these filters can be applied over a broad range from near infrared to terahertz frequencies. PMID:27824049

  2. High-frequency Born synthetic seismograms based on coupled normal modes

    USGS Publications Warehouse

    Pollitz, F.

    2011-01-01

    High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ~4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD). ?? The Author Geophysical Journal International ?? 2011 RAS.

  3. High-frequency Born synthetic seismograms based on coupled normal modes

    USGS Publications Warehouse

    Pollitz, Fred F.

    2011-01-01

    High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ∼4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD).

  4. Finite-time normal mode disturbances and error growth during Southern Hemisphere blocking

    NASA Astrophysics Data System (ADS)

    Wei, Mozheng; Frederiksen, Jorgen S.

    2005-01-01

    The structural organization of initially random errors evolving in a barotropic tangent linear model, with time-dependent basic states taken from analyses, is examined for cases of block development, maturation and decay in the Southern Hemisphere atmosphere during April, November, and December 1989. The statistics of 100 evolved errors are studied for six-day periods and compared with the growth and structures of fast growing normal modes and finite-time normal modes (FTNMs). The amplification factors of most initially random errors are slightly less than those of the fastest growing FTNM for the same time interval. During their evolution, the standard deviations of the error fields become concentrated in the regions of rapid dynamical development, particularly associated with developing and decaying blocks. We have calculated probability distributions and the mean and standard deviations of pattern correlations between each of the 100 evolved error fields and the five fastest growing FTNMs for the same time interval. The mean of the largest pattern correlation, taken over the five fastest growing FTNMs, increases with increasing time interval to a value close to 0.6 or larger after six days. FTNM 1 generally, but not always, gives the largest mean pattern correlation with error fields. Corresponding pattern correlations with the fast growing normal modes of the instantaneous basic state flow are significant but lower than with FTNMs. Mean pattern correlations with fast growing FTNMs increase further when the time interval is increased beyond six days.

  5. Skin pigmentation and texture changes after hair removal with the normal-mode ruby laser.

    PubMed

    Haedersdal, M; Egekvist, H; Efsen, J; Bjerring, P

    1999-11-01

    Promising clinical results have been obtained with the normal mode ruby laser for removal of unwanted hair. Melanin within the hair follicles is thought to act as target for the ruby laser pulses, whereas epidermal melanin is thought to be a competitive chromophore, responsible for potential side effects. This study aimed (i) to objectify postoperative changes in skin pigmentation and texture and (ii) to evaluate the importance of variations in preoperative skin pigmentation for the development of side effects 12 weeks after 1 treatment with the normal-mode ruby laser. A total of 17 volunteers (skin types I-IV) were laser-treated in the hairy pubic region (n = 51 test areas). A shaved test area served as control. Skin reflectance spectroscopical measurements, 3-dimensional surface contour analysis and ultrasonography objectified postoperative changes in skin pigmentation and texture. Blinded clinical assessments revealed postoperative hyperpigmentation (2% of test areas) and hypopigmentation (10%), whereas no textural changes were seen. Reflectance spectroscopically-determined pigmentary changes depended on the degree of preoperative skin pigmentation, fairly pigmented skin types experiencing subclinical hyperpigmentation and darkly pigmented skin types experiencing subclinical hypopigmentation. Three-dimensional surface profilometry documented similar pre- and postoperative surface contour parameters, indicating that the skin surface texture is preserved after laser exposure. Ultrasonography revealed similar skin thicknesses in laser-exposed and untreated control areas. It is concluded that normal-mode ruby laser treatment is safe for hair removal in skin types I-IV.

  6. Terahertz spectra and normal mode analysis of the crystalline VA class dipeptide nanotubes.

    PubMed

    Zhang, Hailiang; Siegrist, Karen; Plusquellic, David F; Gregurick, Susan K

    2008-12-31

    Terahertz (THz) vibrational modes are characterized by nonlocal, collective molecular motions which are relevant to conformational changes and molecular functions in biological systems. We have investigated the THz spectra of a set of small bionanotubes which can serve as very simple models of membrane pores, and have examined the character of the THz modes which can impact transport processes. In this work, THz spectra of the crystalline VA class dipeptide nanotubes were calculated at both the harmonic and vibrational self-consistent field (VSCF) level using the CHARMM22 force field with periodic boundary conditions. Comparison of the calculated THz spectra against the experimental spectra revealed that the VSCF corrections generally improved the predictions in the low-frequency region. The improvements were especially manifested in the overall blue-shifts of the VSCF frequencies relative to the harmonic values, and blue shifts were attributed to the overall positive coupling strengths in all systems. Closer examination of the motions in the most significantly coupled normal mode pairs leads us to propose that, when two similar side-chain squeezing modes are coupled, the rapidly increased van der Waals interactions can lead to a stiffening of the effective potential, which in turn leads to the observed blue-shifts. However, we also noted that when the side-chain atoms become unphysically proximate and the van der Waals repulsion becomes too large, the VSCF calculations tend to deviate in the high frequency region and for the system of l-isoleucyl-l-valine. In addition, normal-mode analysis revealed a series of channel-breathing motions in all systems except l-valyl-l-alanine. We show that the inner products of the backbone vibrations between these channel-breathing motions divided the remaining VA class dipeptide systems into two subgroups. It is suggested that these modes may facilitate a pathway for the guest molecule absorption, substitution and removal in the

  7. Oscillatory reaction cross sections caused by normal mode sampling in quasiclassical trajectory calculations

    SciTech Connect

    Nagy, Tibor; Vikár, Anna; Lendvay, György

    2016-01-07

    The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH{sub 4} + H → CH{sub 3} + H{sub 2} and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C–H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C–H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling.

  8. A global shear velocity model of the mantle from normal modes and surface waves

    NASA Astrophysics Data System (ADS)

    durand, S.; Debayle, E.; Ricard, Y. R.; Lambotte, S.

    2013-12-01

    We present a new global shear wave velocity model of the mantle based on the inversion of all published normal mode splitting functions and the large surface wave dataset measured by Debayle & Ricard (2012). Normal mode splitting functions and surface wave phase velocity maps are sensitive to lateral heterogeneities of elastic parameters (Vs, Vp, xi, phi, eta) and density. We first only consider spheroidal modes and Rayleigh waves and restrict the inversion to Vs, Vp and the density. Although it is well known that Vs is the best resolved parameter, we also investigate whether our dataset allows to extract additional information on density and/or Vp. We check whether the determination of the shear wave velocity is affected by the a priori choice of the crustal model (CRUST2.0 or 3SMAC) or by neglecting/coupling poorly resolved parameters. We include the major discontinuities, at 400 and 670 km. Vertical smoothing is imposed through an a priori gaussian covariance matrix on the model and we discuss the effect of coupling/decoupling the inverted structure above and below the discontinuities. We finally discuss the large scale structure of our model and its geodynamical implications regarding the amount of mass exchange between the upper and lower mantle.

  9. Accretion onto magnetized neutron stars - Normal mode analysis of the interchange instability at the magnetopause

    NASA Technical Reports Server (NTRS)

    Arons, J.; Lea, S. M.

    1976-01-01

    Results are reported for a linearized hydromagnetic stability analysis of the magnetopause of an accreting neutron star. The magnetosphere is assumed to be slowly rotating, and the plasma just outside the magnetopause is assumed to be weakly magnetized. The plasma layer is assumed to be bounded above by a shock wave and to be thin compared with the radius of the magnetosphere. Under these circumstances, the growing modes are shown to be localized in the direction parallel to the zero-order magnetic field, but the structure of the modes is still similar to the flute mode. An expression for the growth rate at each magnetic latitude is obtained in terms of the magnitude of the gravitational acceleration normal to the surface, the azimuthal mode number, the radius of the magnetosphere, the height of the shock above the magnetopause, and the effective Atwood number which embodies the stabilizing effects of favorable curvature and magnetic tension. The effective Atwood number is calculated, and the stabilizing effects of viscosity and aligned flow parallel to the magnetopause are discussed.

  10. Coupling the normal incident light into waveguide modes of DBR mirrors via a diffraction grating

    PubMed Central

    Yang, Wenhong; Sun, Shang; Zhang, Chen; Li, Jiankai; Duan, Zonghui; Song, Qinghai; Xiao, Shumin

    2016-01-01

    Here we numerically and experimentally demonstrate the conversion of normally incident light into the guiding modes of distributed Bragg reflector (DBRs) mirror. By fabricating a gold grating onto a 7.5 pairs TiO2/SiO2 DBR mirror, a series of asymmetrical resonances have been formed at the bandgap range of the DBR mirror. The detailed numerical calculations show that these Fano resonances are attributed to the coupling of incident waves into guiding modes of the DBR mirror. Compared with the other resonances, this coupling mechanism can be simply realized and it has also been revealed to be quite robust to the environmental changes, making the conversion between propagating waves and guiding waves to be practically interesting for many applications. PMID:27958336

  11. Coupling the normal incident light into waveguide modes of DBR mirrors via a diffraction grating

    NASA Astrophysics Data System (ADS)

    Yang, Wenhong; Sun, Shang; Zhang, Chen; Li, Jiankai; Duan, Zonghui; Song, Qinghai; Xiao, Shumin

    2016-12-01

    Here we numerically and experimentally demonstrate the conversion of normally incident light into the guiding modes of distributed Bragg reflector (DBRs) mirror. By fabricating a gold grating onto a 7.5 pairs TiO2/SiO2 DBR mirror, a series of asymmetrical resonances have been formed at the bandgap range of the DBR mirror. The detailed numerical calculations show that these Fano resonances are attributed to the coupling of incident waves into guiding modes of the DBR mirror. Compared with the other resonances, this coupling mechanism can be simply realized and it has also been revealed to be quite robust to the environmental changes, making the conversion between propagating waves and guiding waves to be practically interesting for many applications.

  12. Measurement of Quasi Normal Modes for a population of Binary Black Hole Mergers

    NASA Astrophysics Data System (ADS)

    da Silva Costa, Carlos Filipe; Klimenko, Sergey; Tiwari, Shubhanshu

    2017-01-01

    Perturbed solutions of the Kerr Black Hole (BH) are superimposition of damped sinusoids, named Quasi Normal Modes (QNM). These modes are completely defined by the final black hole parameters, mass and spin. Numerical simulations support that Binary BHs (BBH), after merging, produce a final BH emitting gravitational waves as described by the QNMs. This signal is very weak and hence the extraction of a QNM is quite challenging for the current generation of the ground based detectors. I will present a method for extraction of superimposed QNMs from future multiple observations of BBH merger signals in the advanced interferometers. We show that we can coherently sum up QNMs from the different signals and measure QNM parameters to prove the Kerr nature of a detected BHs population. NSF grant PHY 1505308.

  13. Twisted Gaussian Schell-model beams. I. Symmetry structure and normal-mode spectrum

    SciTech Connect

    Simon, R.; Sundar, K. ); Mukunda, N. )

    1993-09-01

    The authors present a comprehensive normal-mode decomposition analysis for the recently introduced class of twisted Gaussian Schell-model fields in partially coherent beam optics. The formal analogies to quantum mechanics in two dimensions are exploited. The authors also make effective use of a dynamical SU(2) symmetry of these fields to achieve the mode decomposition and to determine the spectrum. The twist phase is nonseparable in nature, rendering it nontrivially two dimensional. The consequences of this, resulting in the need to use Laguerre-Gaussian functions rather than products of Hermite-Gaussians, are carefully analyzed. An important identity involving these sets of special functions is established and is used in deriving the spectrum. 10 refs.

  14. On Quasi-Normal Modes, Area Quantization and Bohr Correspondence Principle

    NASA Astrophysics Data System (ADS)

    Corda, Christian

    2015-10-01

    In (Int. Journ. Mod. Phys. D 14, 181 2005), the author Khriplovich verbatim claims that "the correspondence principle does not dictate any relation between the asymptotics of quasinormal modes and the spectrum of quantized black holes" and that "this belief is in conflict with simple physical arguments". In this paper we analyze Khriplovich's criticisms and realize that they work only for the original proposal by Hod, while they do not work for the improvements suggested by Maggiore and recently finalized by the author and collaborators through a connection between Hawking radiation and black hole (BH) quasi-normal modes (QNMs). This is a model of quantum BH somewhat similar to the historical semi-classical model of the structure of a hydrogen atom introduced by Bohr in 1913. Thus, QNMs can be really interpreted as BH quantum levels (the "electrons" of the "Bohr-like BH model").Our results have also important implications on the BH information puzzle.

  15. Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.

    PubMed

    McCullagh, Peter; Lake, Peter T; McCullagh, Martin

    2016-09-13

    An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.

  16. An instrument for direct observations of seismic and normal-mode rotational oscillations of the Earth.

    PubMed

    Cowsik, R

    2007-04-24

    The rotations around the vertical axis associated with the normal mode oscillations of the Earth and those induced by the seismic and other disturbances have been very difficult to observe directly. Such observations will provide additional information for 3D modeling of the Earth and for understanding earthquakes and other underground explosions. In this paper, we describe the design of an instrument capable of measuring the rotational motions associated with the seismic oscillations of the Earth, including the lowest frequency normal mode at nu approximately 3.7 x 10(-4) Hz. The instrument consists of a torsion balance with a natural frequency of nu(0) approximately 1.6 x 10(-4) Hz, which is observed by an autocollimating optical lever of high angular resolution and dynamic range. Thermal noise limits the sensitivity of the apparatus to amplitudes of approximately 1.5 x 10(-9) rad at the lowest frequency normal mode and the sensitivity improves as nu(-3/2) with increasing frequency. Further improvements in sensitivity by about two orders of magnitude may be achieved by operating the balance at cryogenic temperatures. Alternatively, the instrument can be made more robust with a reduced sensitivity by increasing nu(0) to approximately 10(-2) Hz. This instrument thus complements the ongoing effort by Igel and others to study rotational motions using ring laser gyroscopes and constitutes a positive response to the clarion call for developments in rotation seismology by Igel, Lee, and Todorovska [H. Igel, W.H.K. Lee and M.I. Todorovska, AGU Fall Meeting 2006, Rotational Seismology Sessions: S22A,S23B, Inauguration of the International Working Group on Rotational Seismology (IWGoRS)].

  17. The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

    NASA Astrophysics Data System (ADS)

    Wang, Debby D.; Yan, Hong

    2011-12-01

    Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure. In this paper, we use normal mode analysis to detect significant structural deformations of nucleosomal DNA and investigate the relationship between periodic dinucleotides and DNA motions. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing that they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently.

  18. Normal mode solutions for seismo-acoustic propagation resulting from shear and combined wave point sources.

    PubMed

    Nealy, Jennifer L; Collis, Jon M; Frank, Scott D

    2016-04-01

    Normal mode solutions to range-independent seismo-acoustic problems are benchmarked against elastic parabolic equation solutions and then used to benchmark the shear elastic parabolic equation self-starter [Frank, Odom, and Collis, J. Acoust. Soc. Am. 133, 1358-1367 (2013)]. The Pekeris waveguide with an elastic seafloor is considered for a point source located in the ocean emitting compressional waves, or in the seafloor, emitting both compressional and shear waves. Accurate solutions are obtained when the source is in the seafloor, and when the source is at the interface between the fluid and elastic layers.

  19. Supercontinuum generation by noise-like pulses transmitted through normally dispersive standard single-mode fibers.

    PubMed

    Zaytsev, Alexey; Lin, Chih-Hsuan; You, Yi-Jing; Chung, Chia-Chun; Wang, Chi-Luen; Pan, Ci-Ling

    2013-07-01

    We report generation of broadband supercontinuum (SC) by noise-like pulses (NLPs) with a central wavelength of 1070 nm propagating through a long piece of standard single-mode fibers (~100 meters) in normal dispersion region far from the zero-dispersion point. Theoretical simulations indicate that the physical mechanism of SC generation is due to nonlinear effects in fibers. The cascaded Raman scattering is responsible for significant spectral broadening in the longer wavelength regions whereas the Kerr effect results in smoothing of SC generated spectrum. The SC exhibits low threshold (43 nJ) and a flat spectrum over 1050-1250 nm.

  20. High-Latitude Filtering in a Global Grid-Point Model Using Model Normal Modes

    NASA Technical Reports Server (NTRS)

    Takacs, L. L.; Navon, I. M.; Kalnay, E.

    1985-01-01

    The aim of high-latitude filtering in the vicinity of the poles is to avoid the excessively short time steps imposed on an explicit time-differencing scheme by linear stability due to fast moving inertia-gravity waves near the poles. The model normal mode expansion toward the problem of high-latitude filtering in a global shallow water model using the same philosophy as that used by Daley for the problem for large timesteps in P.E. models with explicit time integration schemes was applied.

  1. Normal-mode analysis of lateral diffusion on a bounded membrane surface.

    PubMed Central

    Koppel, D E

    1985-01-01

    The normal-mode analysis of fluorescence redistribution after photobleaching, introduced for the characterization of lateral diffusion on spherical membrane surfaces, has been generalized and extended to other surface geometries. Theoretical expressions are derived for the characteristic values and orthogonal characteristic functions of the diffusion equations for cylindrical surfaces, ellipsoids of revolution and dimpled discoidal surfaces. On the basis of these results, a simple analytical function is proposed as an empirical solution for the analysis of photobleaching data on a variety of discoidal surfaces. Special experimental and computational methods for determining the surface-diffusion coefficient are described, and demonstrated with data for lipid diffusion in erythrocyte membranes. PMID:3978205

  2. Deviation from the Normal Mode Expansion in a Coupled Graphene-Nanomechanical System

    NASA Astrophysics Data System (ADS)

    Schwarz, Cornelia; Pigeau, Benjamin; Mercier de Lépinay, Laure; Kuhn, Aurélien G.; Kalita, Dipankar; Bendiab, Nedjma; Marty, Laëtitia; Bouchiat, Vincent; Arcizet, Olivier

    2016-12-01

    A significant deviation from the normal mode expansion is observed in the optomechanically measured thermal noise of a graphene membrane suspended on a silicon nitride nanoresonator. This deviation is due to the heterogeneous character of mechanical dissipation over the spatial extent of coupled eigenmodes, which is tuned through an avoided anticrossing. We demonstrate that the fluctuation-dissipation theorem permits a proper evaluation of the thermal noise of the coupled nanomechanical system. Since a good spatial homogeneity is delicate to ensure at the nanoscale, this approach is fundamental to correctly describing the thermal noise of nanomechanical systems which ultimately impact their sensing capacity.

  3. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    PubMed

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  4. Experimental and numerical studies of mode-locked fiber laser with large normal and anomalous dispersion.

    PubMed

    Zhang, Lei; El-Damak, A R; Feng, Yan; Gu, Xijia

    2013-05-20

    An ytterbium-doped mode-locked fiber laser was demonstrated with a chirped fiber Bragg grating for dispersion management. The cavity net dispersion could be changed from large normal dispersion (2.4 ps(2)) to large anomalous dispersion (-2.0 ps(2)), depending on the direction of the chirped Bragg grating in laser cavity. The proposed fiber lasers with large normal dispersion generated stable pulses with a pulse width of <1.1 ns and a pulse energy of 1.5 nJ. The laser with large anomalous dispersion generated wavelength-tunable soliton with a pulse width of 2.7 ps and pulse energy of 0.13 nJ. A theoretical model was established and used to verify the experimental observations.

  5. Numerical investigations with a hybrid isentropic-sigma model. I - Normal-mode characteristics. II - The inclusion of moist processes

    NASA Technical Reports Server (NTRS)

    Pierce, R. B.; Johnson, Donald R.; Reames, Fred M.; Zapotocny, Tom H.; Wolf, Bart J.

    1991-01-01

    The normal-mode characteristics of baroclinically amplifying disturbances were numerically investigated in a series of adiabatic simulations by a hybrid isentropic-sigma model, demonstrating the effect of coupling an isentropic-coordinate free atmospheric domain with a sigma-coordinate PBL on the normal-mode characteristics. Next, the normal-mode model was modified by including a transport equation for water vapor and adiabatic heating by condensation. Simulations with and without a hydrological component showed that the overall effect of latent heat release is to markedly enhance cyclogenesis and frontogenesis.

  6. Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk.

    PubMed Central

    Simonson, T; Perahia, D

    1992-01-01

    We use group theoretical methods to study the molecular dynamics of symmetric protein multimers in the harmonic or quasiharmonic approximation. The method explicitly includes the long-range correlations between protein subunits. It can thus address collective dynamic effects, such as cooperativity between subunits. The n lowest-frequency normal modes of each individual subunit are combined into symmetry coordinates for the entire multimer. The Hessian of the potential energy is thereby reduced to a series of blocks of order n or 2n. In the quasiharmonic approximation, the covariance matrix of the atomic oscillations is reduced to the same block structure by an analogous set of symmetry coordinates. The method is applied to one layer of the tobacco mosaic virus protein disk in vacuo, to gain insight into the role of conformational fluctuations and electrostatics in tobacco mosaic virus assembly. The system has 78,000 classical, positional, degrees of freedom, yet the calculation is reduced by symmetry to a problem of order 4,600. Normal modes in the 0-100 cm-1 range were calculated. The calculated correlations extend mainly from each subunit to its nearest neighbors. The network of core helices has weak correlations with the rest of the structure. Similarly, the inner loops 90-108 are uncorrelated with the rest of the structure. Thus, the model predicts that the dielectric response in the RNA-binding region is mainly due to the loops alone. Images FIGURE 1 FIGURE 3 FIGURE 5 FIGURE 7 FIGURE 8 PMID:1547329

  7. Application of Normal Mode Expansion to AE Waves in Finite Plates

    NASA Technical Reports Server (NTRS)

    Gorman, M. R.; Prosser, W. H.

    1997-01-01

    Breckenridge et al. (1975), Hsu (1985) and Pao (1978) adapted approaches from seismology to calculate the response at the surface of an infinite half-space and an infinite plate. These approaches have found use in calibrating acoustic emission (AE) transducers. However, it is difficult to extend this theoretical approach to AE testing of practical structures. Weaver and Pao (1982) considered a normal mode solution to the Lamb equations. Hutchinson (1983) pointed out the potential relevance of Mindlin's plate theory (1951) to AE. Pao (1982) reviewed Medick s (1961) classical plate theory for a point source, but rejected it as useful for AE and no one seems to have investigated its relevance to AE any further. Herein, a normal mode solution to the classical plate bending equation was investigated for its applicability to AE. The same source-time function chosen by Weaver and Pao is considered. However, arbitrary source and receiver positions are chosen relative to the boundaries of the plate. This is another advantage of the plate theory treatment in addition to its simplicity. The source does not have to be at the center of the plate as in the axisymmetric treatment. The plate is allowed to remain finite and reflections are predicted. The importance of this theory to AE is that it can handle finite plates, realistic boundary conditions, and can be extended to composite materials.

  8. Stress-dependent normal-mode frequencies from the effective mass of granular matter.

    PubMed

    Hu, Yanqing; Johnson, David L; Valenza, John J; Santibanez, Francisco; Makse, Hernán A

    2014-06-01

    A zero-temperature critical point has been invoked to control the anomalous behavior of granular matter as it approaches jamming or mechanical arrest. Criticality manifests itself in an anomalous spectrum of low-frequency normal modes and scaling behavior near the jamming transition. The critical point may explain the peculiar mechanical properties of dissimilar systems such as glasses and granular materials. Here we study the critical scenario via an experimental measurement of the normal modes frequencies of granular matter under stress from a pole decomposition analysis of the effective mass. We extract a complex-valued characteristic frequency which displays scaling |ω (σ)| ∼ σΩ' with vanishing stress σ for a variety of granular systems. The critical exponent is smaller than that predicted by mean-field theory opening new challenges to explain the exponent for frictional and dissipative granular matter. Our results shed light on the anomalous behavior of stress-dependent acoustics and attenuation in granular materials near the jamming transition.

  9. The normal mode analysis shape detection method for automated shape determination of lung nodules.

    PubMed

    Stember, Joseph N

    2015-04-01

    Surface morphology and shape in general are important predictors for the behavior of solid-type lung nodules detected on CT. More broadly, shape analysis is useful in many areas of computer-aided diagnosis and essentially all scientific and engineering disciplines. Automated methods for shape detection have all previously, to the author's knowledge, relied on some sort of geometric measure. I introduce Normal Mode Analysis Shape Detection (NMA-SD), an approach that measures shape indirectly via the motion it would undergo if one imagined the shape to be a pseudomolecule. NMA-SD allows users to visualize internal movements in the imaging object and thereby develop an intuition for which motions are important, and which geometric features give rise to them. This can guide the identification of appropriate classification features to distinguish among classes of interest. I employ normal mode analysis (NMA) to animate pseudomolecules representing simulated lung nodules. Doing so, I am able to assign a testing set of nodules into the classes circular, elliptical, and irregular with roughly 97 % accuracy. This represents a proof-of-principle that one can obtain shape information by treating voxels as pseudoatoms in a pseudomolecule, and analyzing the pseudomolecule's predicted motion.

  10. Modeling the effect of anisotropic pressure on tokamak plasmas normal modes and continuum using fluid approaches

    NASA Astrophysics Data System (ADS)

    Qu, Z. S.; Hole, M. J.; Fitzgerald, M.

    2015-09-01

    Extending the ideal MHD stability code MISHKA, a new code, MISHKA-A, is developed to study the impact of pressure anisotropy on plasma stability. Based on full anisotropic equilibrium and geometry, the code can provide normal mode analysis with three fluid closure models: the single adiabatic model (SA), the double adiabatic model (CGL) and the incompressible model. A study on the plasma continuous spectrum shows that in low beta, large aspect ratio plasma, the main impact of anisotropy lies in the modification of the BAE gap and the sound frequency, if the q profile is conserved. The SA model preserves the BAE gap structure as ideal MHD, while in CGL the lowest frequency branch does not touch zero frequency at the resonant flux surface where m   +   nq   =   0, inducing a gap at very low frequency. Also, the BAE gap frequency with bi-Maxwellian distribution in both model becomes higher if {{p}\\bot} \\gt {{p}\\parallel} with a q profile dependency. As a benchmark of the code, we study the m/n   =   1/1 internal kink mode. Numerical calculation of the marginal stability boundary with bi-Maxwellian distribution shows a good agreement with the generalized incompressible Bussac criterion (Mikhailovskii 1983 Sov. J. Plasma Phys. 9 190): the mode is stabilized(destabilized) if {{p}\\parallel}\\lt {{p}\\bot} ({{p}\\parallel}\\gt{{p}\\bot} ).

  11. Analytical description of quasi-normal mode in resonant plasmonic nano cavities

    NASA Astrophysics Data System (ADS)

    Yang, Fan; Liu, Haitao; Jia, Hongwei; Zhong, Ying

    2016-03-01

    We propose an analytical model of quasi-normal mode (QNM) for resonant plasmonic nano cavities formed by sub wavelength grooves in metallic substrate. The QNM has shown great advantages in understanding and calculating the frequency response of resonant nano-structures. With our model we show that the QNM originates from a resonance of the fundamental mode in every individual groove and its interaction via surface waves. Analytical expression for the complex eigenfrequency as well as the field distribution of the QNM can be derived from the model. With the analytical model and a few assumptions on the scattered field, the legitimacy of the expansion of scattered field with QNMs under external illuminations is justified with the Mittag-Leffler's theorem of meromorphic function. The expansion coefficients of QNMs are analytically expressed with a finite set of elementary scattering coefficients, which avoids the calculation of the mode volume of QNMs that have a spatial divergence at infinity. The model clarifies the physical origin of QNMs and drastically reduces the computational load of QNMs, especially for a large ensemble of grooves for which brute-force numerical tools are not available. The validity of the proposed model is tested against fully vectorial numerical results.

  12. An approach to detect afterslips in giant earthquakes in the normal-mode frequency band

    NASA Astrophysics Data System (ADS)

    Tanimoto, Toshiro; Ji, Chen; Igarashi, Mitsutsugu

    2012-08-01

    An approach to detect afterslips in the source process of giant earthquakes is presented in the normal-mode frequency band (0.3-2.0 mHz). The method is designed to avoid a potential systematic bias problem in the determination of earthquake moment by a typical normal-mode approach. The source of bias is the uncertainties in Q (modal attenuation parameter) which varies by up to about ±10 per cent among published studies. A choice of Q values within this range affects amplitudes in synthetic seismograms significantly if a long time-series of about 5-7 d is used for analysis. We present an alternative time-domain approach that can reduce this problem by focusing on a shorter time span with a length of about 1 d. Application of this technique to four recent giant earthquakes is presented: (1) the Tohoku, Japan, earthquake of 2011 March 11, (2) the 2010 Maule, Chile earthquake, (3) the 2004 Sumatra-Andaman earthquake and (4) the Solomon earthquake of 2007 April 1. The Global Centroid Moment Tensor (GCMT) solution for the Tohoku earthquake explains the normal-mode frequency band quite well. The analysis for the 2010 Chile earthquake indicates that the moment is about 7-10 per cent higher than the moment determined by its GCMT solution but further analysis shows that there is little evidence of afterslip; the deviation in moment can be explained by an increase of the dip angle from 18° in the GCMT solution to 19°. This may be a simple trade-off problem between the moment and dip angle but it may also be due to a deeper centroid in the normal-mode frequency band data, as a deeper source could have steeper dip angle due to changes in geometry of the Benioff zone. For the 2004 Sumatra-Andaman earthquake, the five point-source solution by Tsai et al. explains most of the signals but a sixth point-source with long duration improves the fit to the normal-mode frequency band data. The 2007 Solomon earthquake shows that the high-frequency part of our analysis (above 1 mHz) is

  13. Reduced Cβ statistical potentials can outperform all-atom potentials in decoy identification

    PubMed Central

    Fitzgerald, James E.; Jha, Abhishek K.; Colubri, Andres; Sosnick, Tobin R.; Freed, Karl F.

    2007-01-01

    We developed a series of statistical potentials to recognize the native protein from decoys, particularly when using only a reduced representation in which each side chain is treated as a single Cβ atom. Beginning with a highly successful all-atom statistical potential, the Discrete Optimized Protein Energy function (DOPE), we considered the implications of including additional information in the all-atom statistical potential and subsequently reducing to the Cβ representation. One of the potentials includes interaction energies conditional on backbone geometries. A second potential separates sequence local from sequence nonlocal interactions and introduces a novel reference state for the sequence local interactions. The resultant potentials perform better than the original DOPE statistical potential in decoy identification. Moreover, even upon passing to a reduced Cβ representation, these statistical potentials outscore the original (all-atom) DOPE potential in identifying native states for sets of decoys. Interestingly, the backbone-dependent statistical potential is shown to retain nearly all of the information content of the all-atom representation in the Cβ representation. In addition, these new statistical potentials are combined with existing potentials to model hydrogen bonding, torsion energies, and solvation energies to produce even better performing potentials. The ability of the Cβ statistical potentials to accurately represent protein interactions bodes well for computational efficiency in protein folding calculations using reduced backbone representations, while the extensions to DOPE illustrate general principles for improving knowledge-based potentials. PMID:17893359

  14. Folding of proteins with an all-atom Go-model.

    PubMed

    Wu, L; Zhang, J; Qin, M; Liu, F; Wang, W

    2008-06-21

    The Go-like potential at a residual level has been successfully applied to the folding of proteins in many previous works. However, taking into consideration more detailed structural information in the atomic level, the definition of contacts used in these traditional Go-models may not be suitable for all-atom simulations. Here, in this work, we develop a rational definition of contacts considering the screening effect in the crowded intramolecular environment. In such a scheme, a large amount of screened atom pairs are excluded and the number of contacts is decreased compared to the case of the traditional definition. These contacts defined by such a new definition are compatible with the all-atom representation of protein structures. To verify the rationality of the new definition of contacts, the folding of proteins CI2 and SH3 is simulated by all-atom molecular dynamics simulations. A high folding cooperativity and good correlation of the simulated Phi-values with those obtained experimentally, especially for CI2, are found. This suggests that the all-atom Go-model is improved compared to the traditional Go-model. Based on the comparison of the Phi-values, the roles of side chains in the folding are discussed, and it is concluded that the side-chain structures are more important for local contacts in determining the transition state structures. Moreover, the relations between side chain and backbone orderings are also discussed.

  15. Source models of great earthquakes from ultra low-frequency normal mode data

    NASA Astrophysics Data System (ADS)

    Lentas, Konstantinos; Ferreira, Ana; Clévédé, Eric

    2014-05-01

    We present a new earthquake source inversion technique based on normal mode data for the simultaneous determination of the rupture duration, length and moment tensor of large earthquakes with unilateral rupture. We use ultra low-frequency (f < 1 mHz) normal mode spheroidal multiplets and the phases of split free oscillations, which are modelled using Higher Order Perturbation Theory (HOPT), taking into account the Earth's rotation, ellipticity and lateral heterogeneities. A Monte Carlo exploration of the model space is carried out, enabling the assessment of source parameter tradeoffs and uncertainties. We carry out synthetic tests for four different realistic artificial earthquakes with different faulting mechanisms and magnitudes (Mw 8.1-9.3) to investigate errors in the source inversions due to: (i) unmodelled 3-D Earth structure; (ii) noise in the data; (iii) uncertainties in spatio-temporal earthquake location; and, (iv) neglecting the source finiteness in point source moment tensor inversions. We find that unmodelled 3-D structure is the most serious source of errors for rupture duration and length determinations especially for the lowest magnitude artificial events. The errors in moment magnitude and fault mechanism are generally small, with the rake angle showing systematically larger errors (up to 20 degrees). We then carry out source inversions of five giant thrust earthquakes (Mw ≥ 8.5): (i) the 26 December 2004 Sumatra-Andaman earthquake; (ii) the 28 March 2005 Nias, Sumatra earthquake; (iii) the 12 September 2007 Bengkulu earthquake; (iv) the Tohoku, Japan earthquake of 11 March 2011; (v) the Maule, Chile earthquake of 27 February 2010; and (vi) the recent 24 May 2013 Mw 8.3 Okhotsk Sea, Russia, deep (607 km) earthquake. While finite source inversions for rupture length, duration, magnitude and fault mechanism are possible for the Sumatra-Andaman and Tohoku events, for all the other events their lower magnitudes do not allow stable inversions of mode

  16. Possibility of observation of polaron normal modes at the far-infrared spectrum of acetanilide and related organics

    NASA Astrophysics Data System (ADS)

    Kalosakas, G.; Aubry, S.; Tsironis, G. P.

    1998-10-01

    We use a stationary and normal mode analysis of the semiclassical Holstein model in order to connect the low-frequency linear polaron modes to low-lying far-infrared lines of the acetanilide spectrum and through parameter fitting we comment on the validity of the polaron results in this system.

  17. Normal mode energetics and error analysis of GLA GCM simulations with different horizontal resolutions during a winter month

    NASA Technical Reports Server (NTRS)

    Tanaka, H. L.; Kung, E. C.; Baker, W. E.

    1989-01-01

    Comparative energetics is presented for a series of four general circulation model simulations for January 1979 conducted by the Goddard Laboratory for Atmospheres. The simulations include cases of coarse and fine horizontal model resolutions with two slightly different initial conditions. Using a three-dimensional normal mode expansion, it is found that the gravity-mode energy levels are significantly reduced in the higher wavenumbers and in the higher-order internal vertical modes by the increase of horizontal model resolution.

  18. Source models of great earthquakes from ultra low-frequency normal mode data

    NASA Astrophysics Data System (ADS)

    Lentas, K.; Ferreira, A. M. G.; Clévédé, E.; Roch, J.

    2014-08-01

    We present a new earthquake source inversion technique based on normal mode data for the simultaneous determination of the rupture duration, length and moment tensor of large earthquakes with unilateral rupture. We use ultra low-frequency (f <1 mHz) mode singlets and multiplets which are modelled using Higher Order Perturbation Theory (HOPT), taking into account the Earth’s rotation, ellipticity and lateral heterogeneities. A Monte Carlo exploration of the model space is carried out, enabling the assessment of source parameter tradeoffs and uncertainties. We carry out synthetic tests to investigate errors in the source inversions due to: (i) unmodelled 3-D Earth structure; (ii) noise in the data; (iii) uncertainties in spatio-temporal earthquake location; and, (iv) neglecting the source finiteness in point source inversions. We find that unmodelled 3-D structure is the most serious source of errors for rupture duration and length determinations especially for the lowest magnitude events. The errors in moment magnitude and fault mechanism are generally small, with the rake angle showing systematically larger errors (up to 20°). We then investigate five real thrust earthquakes (Mw⩾8.5): (i) Sumatra-Andaman (26th December 2004); (ii) Nias, Sumatra (28th March 2005); (iii) Bengkulu (12th September 2007); (iv) Tohoku, Japan (11th March 2011); (v) Maule, Chile (27th February 2010); and, (vi) the 24 May 2013 Mw 8.3 Okhotsk Sea, Russia, deep (607 km) event. While finite source inversions for rupture length, duration, magnitude and fault mechanism are possible for the Sumatra-Andaman and Tohoku events, for all the other events their lower magnitudes only allow stable point source inversions of mode multiplets. We obtain the first normal mode finite source model for the 2011 Tohoku earthquake, which yields a fault length of 461 km, a rupture duration of 151 s, and hence an average rupture velocity of 3.05 km/s, giving an independent confirmation of the compact nature of

  19. Computational modes and the Machenauer N.L.N.M.I. of the GLAS 4th order model. [NonLinear Normal Mode Initialization in numerical weather forecasting

    NASA Technical Reports Server (NTRS)

    Navon, I. M.; Bloom, S.; Takacs, L. L.

    1985-01-01

    An attempt was made to use the GLAS global 4th order shallow water equations to perform a Machenhauer nonlinear normal mode initialization (NLNMI) for the external vertical mode. A new algorithm was defined for identifying and filtering out computational modes which affect the convergence of the Machenhauer iterative procedure. The computational modes and zonal waves were linearly initialized and gravitational modes were nonlinearly initialized. The Machenhauer NLNMI was insensitive to the absence of high zonal wave numbers. The effects of the Machenhauer scheme were evaluated by performing 24 hr integrations with nondissipative and dissipative explicit time integration models. The NLNMI was found to be inferior to the Rasch (1984) pseudo-secant technique for obtaining convergence when the time scales of nonlinear forcing were much smaller than the time scales expected from the natural frequency of the mode.

  20. Normal vibrational modes of phospholipid bilayers observed by low-frequency Raman scattering

    NASA Astrophysics Data System (ADS)

    Surovtsev, N. V.; Dmitriev, A. A.; Dzuba, S. A.

    2017-03-01

    Low-frequency Raman spectra of multilamellar vesicles made either of 1-palmitoyl-2-oleoyl-s n -glycero-3-phosphocholine (POPC) or 1,2-dipalmitoyl-s n -glycero-3-phosphocholine (DPPC) have been studied in a wide temperature range. Below 0 ∘C two peaks are found at frequencies around 8-9 and 14 -17 c m -1 and attributed to the normal vibrational modes of the phospholipid bilayer, which are determined by the bilayer thickness and stiffness (elastic modulus). The spectral positions of the peaks depend on the temperature and the bilayer composition. It is suggested that the ratio of the intensities of the first and second peaks can serve as a measure of the interleaflet elastic coupling. The addition of cholesterol to the phospholipid bilayer leads to peak shift and broadening, which may be assigned to the composition heterogeneities commonly attributed to the lipid raft formation.

  1. Normal modes of a superconducting transmission-line resonator with embedded lumped element circuit components

    NASA Astrophysics Data System (ADS)

    Mortensen, Henrik Lund; Mølmer, Klaus; Andersen, Christian Kraglund

    2016-11-01

    We present a method to identify the coupled, normal modes of a superconducting transmission line with an embedded lumped element circuit. We evaluate the effective transmission-line nonlinearities in the case of Kerr-like Josephson interactions in the circuit and in the case where the embedded circuit constitutes a qubit degree of freedom, which is Rabi coupled to the field in the transmission line. Our theory quantitatively accounts for the very high and positive Kerr nonlinearities observed in a recent experiment [M. Rehák, P. Neilinger, M. Grajcar, G. Oelsner, U. Hübner, E. Il'ichev, and H.-G. Meyer, Appl. Phys. Lett. 104, 162604 (2014), 10.1063/1.4873719], and we can evaluate the accomplishments of modified versions of the experimental circuit.

  2. Superconducting Gravimeter Data for the IRIS Seismology Database: Application to Normal Modes from the Sumatra Earthquake

    NASA Astrophysics Data System (ADS)

    Crossley, D.; Rivera, L.; Hinderer, J.; Rosat, S.

    2009-04-01

    For several years, it has been the goal of the Global Geodynamics Project (GGP) to convert high rate acceleration data recorded on superconducting gravimeters (SG) to a format compatible with the seismic data archived at IRIS. The problem for the GGP community has been to properly establish the metadata for characterizing the response of the instrument, particularly its phase characteristics. Although SG data exists at IRIS from the Membach GGP station in Belgium, up to now most of the data from the GGP network has been on hold until the response problem was solved. This we have now been able to do, and we hope to show that data from the Strasbourg SG station will be at IRIS and available. We will also upload all the data from the SGs from after the Sumatra earthquake and show some results on normal mode analysis that demonstrates the benefit of the good amplitude calibration feature and high precision of the SG instruments.

  3. Polaritonic normal-mode splitting and light localization in a one-dimensional nanoguide

    NASA Astrophysics Data System (ADS)

    Haakh, Harald R.; Faez, Sanli; Sandoghdar, Vahid

    2016-11-01

    We theoretically investigate the interaction of light and a collection of emitters in a subwavelength one-dimensional medium (nanoguide), where enhanced emitter-photon coupling leads to efficient multiple scattering of photons. We show that the spectrum of the transmitted light undergoes normal-mode splitting even though no external cavity resonance is employed. By considering densities much higher than those encountered in cold atom experiments, we study the influence of the near-field dipole coupling and disorder on the resulting complex super-radiant and subradiant polaritonic states. In particular, we provide evidence for the longitudinal localization of light in a one-dimensional open system and provide a polaritonic phase diagram. Our results motivate a number of experiments, where new coherent superposition states of light and matter can be realized in the solid state.

  4. Rotational normal modes of triaxial two-layered anelastic Earth model

    NASA Astrophysics Data System (ADS)

    Yang, Zhuo; Shen, WenBin

    2016-04-01

    This study focuses on providing rotational normal modes of a triaxial two-layered anelastic Earth model with considering the electromagnetic coupling. We formulate the rotation equation of the triaxial two-layered anelastic Earth model and then provide solution of that equation. We obtain four mathematically possible solutions which might exist in reality. Based on present choice of the conventional reference systems, only two of these four solutions correspond to the real existing prograde Chandler wobble (CW) and the retrograde free core nutation (FCN). We provide the periods of CW and FCN as well as their quality factors based on various experiments and observations. This study is supported by National 973 Project China (grant No. 2013CB733305) and NSFC (grant Nos. 41174011, 41210006, 41429401).

  5. Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data

    PubMed Central

    Gorba, Christian; Tama, Florence

    2010-01-01

    We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures. This method uses a linear combination of low-frequency normal modes from an elastic network description of the molecule in an iterative manner to deform the structure to conform optimally to the target pair distribution function derived from SAXS data. For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained. In this paper, we demonstrate the validity of our coarse-graining approach to study SAXS data. Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented. PMID:20634984

  6. Regional variation of inner core anisotropy from seismic normal mode observations.

    PubMed

    Deuss, Arwen; Irving, Jessica C E; Woodhouse, John H

    2010-05-21

    Earth's solid inner core is surrounded by a convecting liquid outer core, creating the geodynamo driving the planet's magnetic field. Seismic studies using compressional body waves suggest hemispherical variation in the anisotropic structure of the inner core, but are poorly constrained because of limited earthquake and receiver distribution. Here, using normal mode splitting function measurements from large earthquakes, based on extended cross-coupling theory, we observe both regional variations and eastern versus western hemispherical anisotropy in the inner core. The similarity of this pattern with Earth's magnetic field suggests freezing-in of crystal alignment during solidification or texturing by Maxwell stress as origins of the anisotropy. These observations limit the amount of inner core super rotation, but would be consistent with oscillation.

  7. Notch strengthening or weakening governed by transition of shear failure to normal mode fracture

    PubMed Central

    Lei, Xianqi; Li, Congling; Shi, Xinghua; Xu, Xianghong; Wei, Yujie

    2015-01-01

    It is generally observed that the existence of geometrical discontinuity like notches in materials will lead to strength weakening, as a resultant of local stress concentration. By comparing the influence of notches to the strength of three typical materials, aluminum alloys with intermediate tensile ductility, metallic glasses with no tensile ductility, and brittle ceramics, we observed strengthening in aluminum alloys and metallic glasses: Tensile strength of the net section in circumferentially notched cylinders increases with the constraint quantified by the ratio of notch depth over notch root radius; in contrast, the ceramic exhibit notch weakening. The strengthening in the former two is due to resultant deformation transition: Shear failure occurs in intact samples while samples with deep notches break in normal mode fracture. No such deformation transition was observed in the ceramic, and stress concentration leads to its notch weakening. The experimental results are confirmed by theoretical analyses and numerical simulation. The results reported here suggest that the conventional criterion to use brittleness and/or ductility to differentiate notch strengthening or weakening is not physically sound. Notch strengthening or weakening relies on the existence of failure mode transition and materials exhibiting shear failure while subjected to tension will notch strengthen. PMID:26022892

  8. Normal modes from the 2013 Sea of Okhotsk earthquake, the largest deep event ever recorded

    NASA Astrophysics Data System (ADS)

    Okal, E. A.

    2013-12-01

    With a moment of 4.1 10**28 dyn*cm, the Sea of Okhotsk earthquake of 24 May 2013 is the largest deep event ever recorded. This provides a unique opportunity to study the excitation of low-frequency normal modes, including overtone and radial ones. The principal questions addressed will be the possible existence of a slow component to the source, which is not warranted by preliminary results; and the possible presence of an isotropic component to the moment tensor of its source. The latter was strongly debated in the case of the 1970 Colombian event (Gilbert and Dziewonski, 1973; Okal and Geller, 1979), and clearly found absent from the source of the 1994 Bolivian one (Kikuchi and Kanamori, 1994; Okal, 1996). Critical in this respect will be the investigation of the relative excitation of the the radial modes, and in particular, the fundamental 0s0, for which a sufficiently long (90 days) time series was not available by the submission deadline.

  9. Notch strengthening or weakening governed by transition of shear failure to normal mode fracture.

    PubMed

    Lei, Xianqi; Li, Congling; Shi, Xinghua; Xu, Xianghong; Wei, Yujie

    2015-05-29

    It is generally observed that the existence of geometrical discontinuity like notches in materials will lead to strength weakening, as a resultant of local stress concentration. By comparing the influence of notches to the strength of three typical materials, aluminum alloys with intermediate tensile ductility, metallic glasses with no tensile ductility, and brittle ceramics, we observed strengthening in aluminum alloys and metallic glasses: Tensile strength of the net section in circumferentially notched cylinders increases with the constraint quantified by the ratio of notch depth over notch root radius; in contrast, the ceramic exhibit notch weakening. The strengthening in the former two is due to resultant deformation transition: Shear failure occurs in intact samples while samples with deep notches break in normal mode fracture. No such deformation transition was observed in the ceramic, and stress concentration leads to its notch weakening. The experimental results are confirmed by theoretical analyses and numerical simulation. The results reported here suggest that the conventional criterion to use brittleness and/or ductility to differentiate notch strengthening or weakening is not physically sound. Notch strengthening or weakening relies on the existence of failure mode transition and materials exhibiting shear failure while subjected to tension will notch strengthen.

  10. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    PubMed

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  11. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

    PubMed

    Das, Rhiju; Qian, Bin; Raman, Srivatsan; Vernon, Robert; Thompson, James; Bradley, Philip; Khare, Sagar; Tyka, Michael D; Bhat, Divya; Chivian, Dylan; Kim, David E; Sheffler, William H; Malmström, Lars; Wollacott, Andrew M; Wang, Chu; Andre, Ingemar; Baker, David

    2007-01-01

    We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template-based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near-atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions.

  12. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    PubMed

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  13. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals.

    PubMed

    Kaushik, Ananth P; Clancy, Paulette

    2012-03-21

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.

  14. Structure prediction for CASP8 with all-atom refinement using Rosetta.

    PubMed

    Raman, Srivatsan; Vernon, Robert; Thompson, James; Tyka, Michael; Sadreyev, Ruslan; Pei, Jimin; Kim, David; Kellogg, Elizabeth; DiMaio, Frank; Lange, Oliver; Kinch, Lisa; Sheffler, Will; Kim, Bong-Hyun; Das, Rhiju; Grishin, Nick V; Baker, David

    2009-01-01

    We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.

  15. High-energy square pulses and burst-mode pulses in an all-normal dispersion double-clad mode-locked fiber laser

    NASA Astrophysics Data System (ADS)

    Qiao, Zhi; Wang, Xiaochao; Wang, Chao; Jing, Yuanyuan; Fan, Wei; Lin, Zunqi

    2016-05-01

    A double-clad Yb-doped mode-locked fiber laser that can operate in burst-mode and square-pulse states is experimentally investigated. In the burst-mode state, a burst train with 55 pulses of 500 ps duration is obtained. In the square-pulse state, which is similar to noiselike pulses, the maximum pulse energy is 820 nJ and the duration can be tuned from 15.8 to 546 ns. The square pulses have a narrow and multipeak spectrum, which is quite different from that of normal noiselike pulses. The fiber laser promises an alternative formation mechanism for burst-mode and square-pulse mode-locked fiber lasers.

  16. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    SciTech Connect

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-07

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  17. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    NASA Astrophysics Data System (ADS)

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-01

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  18. Observation of self-mode-locked noise-like pulses from a net normal dispersion erbium-doped fiber laser

    NASA Astrophysics Data System (ADS)

    Li, Kexuan; Tian, Jinrong; Guoyu, Heyang; Xu, Runqin; Song, Yanrong

    2017-04-01

    Self-mode-locked noise-like pulses (NLPs) were experimentally investigated from a normal dispersion erbium-doped fiber laser. Different from noise-like pulses with a broadband spectrum, the self-mode-locked NLPs have a narrow optical spectrum of 1–2 nm and hundreds of nanoseconds duration. However, the intra-cavity maximum energy of NLPs is up to 560 nJ without pulse breaking. The higher pulse energy output is promising in the proposed fiber laser. To confirm whether self-mode-locked NLPs are caused by an invisible nonlinear polarization rotation (NPR) mechanism owing to slight residual polarization asymmetry of the fiber and components used, we compared the output characteristics between self-mode-locked NLPs and NPR mode-locked pulses in the same cavity. The experimental results show that the formation mechanism of such self-mode-locked NLPs could be related to a weak NPR effect.

  19. Dynamic elastic moduli in magnetic gels: Normal modes and linear response

    NASA Astrophysics Data System (ADS)

    Pessot, Giorgio; Löwen, Hartmut; Menzel, Andreas M.

    2016-09-01

    In the perspective of developing smart hybrid materials with customized features, ferrogels and magnetorheological elastomers allow a synergy of elasticity and magnetism. The interplay between elastic and magnetic properties gives rise to a unique reversible control of the material behavior by applying an external magnetic field. Albeit few works have been performed on the time-dependent properties so far, understanding the dynamic behavior is the key to model many practical situations, e.g., applications as vibration absorbers. Here we present a way to calculate the frequency-dependent elastic moduli based on the decomposition of the linear response to an external stress in normal modes. We use a minimal three-dimensional dipole-spring model to theoretically describe the magnetic and elastic interactions on the mesoscopic level. Specifically, the magnetic particles carry permanent magnetic dipole moments and are spatially arranged in a prescribed way, before they are linked by elastic springs. An external magnetic field aligns the magnetic moments. On the one hand, we study regular lattice-like particle arrangements to compare with previous results in the literature. On the other hand, we calculate the dynamic elastic moduli for irregular, more realistic particle distributions. Our approach measures the tunability of the linear dynamic response as a function of the particle arrangement, the system orientation with respect to the external magnetic field, as well as the magnitude of the magnetic interaction between the particles. The strength of the present approach is that it explicitly connects the relaxational modes of the system with the rheological properties as well as with the internal rearrangement of the particles in the sample, providing new insight into the dynamics of these remarkable materials.

  20. Wave normal angles of whistler mode chorus rising and falling tones

    NASA Astrophysics Data System (ADS)

    Taubenschuss, Ulrich; Khotyaintsev, Yuri V.; Santolík, Ondrej; Vaivads, Andris; Cully, Christopher M.; Contel, Olivier Le; Angelopoulos, Vassilis

    2014-12-01

    We present a study of wave normal angles (θk) of whistler mode chorus emission as observed by Time History of Events and Macroscale Interactions during Substorms (THEMIS) during the year 2008. The three inner THEMIS satellites THA, THD, and THE usually orbit Earth close to the dipole magnetic equator (±20°), covering a large range of L shells from the plasmasphere out to the magnetopause. Waveform measurements of electric and magnetic fields enable a detailed polarization analysis of chorus below 4 kHz. When displayed in a frequency-θk histogram, four characteristic regions of occurrence are evident. They are separated by gaps at f/fc,e≈0.5 (f is the chorus frequency, fc,e is the local electron cyclotron frequency) and at θk˜40°. Below θk˜40°, the average value for θk is predominantly field aligned, but slightly increasing with frequency toward half of fc,e (θk up to 20°). Above half of fc,e, the average θk is again decreasing with frequency. Above θk˜40°, wave normal angles are usually close to the resonance cone angle. Furthermore, we present a detailed comparison of electric and magnetic fields of chorus rising and falling tones. Falling tones exhibit peaks in occurrence solely for θk>40° and are propagating close to the resonance cone angle. Nevertheless, when comparing rising tones to falling tones at θk>40°, the ratio of magnetic to electric field shows no significant differences. Thus, we conclude that falling tones are generated under similar conditions as rising tones, with common source regions close to the magnetic equatorial plane.

  1. Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

    PubMed Central

    Hsieh, Yin-Chen; Poitevin, Frédéric; Delarue, Marc; Koehl, Patrice

    2016-01-01

    Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis. We describe the elements of DD-NMA that are relevant to the analysis of large systems, such as virus capsids. In particular, we introduce our implementation of simplified elastic networks and justify their parametrization. Using DD-NMA, we illustrate the importance of packing interactions within the virus capsids on the dynamics of the E proteins of DENV and ZIKV. We identify differences between the computed atomic fluctuations of the E proteins in DENV and ZIKV and relate those differences to changes observed in their high resolution structures. We conclude with a discussion on additional analyses that are needed to fully characterize the dynamics of the two viruses. PMID:28083537

  2. Elastic network normal modes provide a basis for protein structure refinement

    NASA Astrophysics Data System (ADS)

    Gniewek, Pawel; Kolinski, Andrzej; Jernigan, Robert L.; Kloczkowski, Andrzej

    2012-05-01

    It is well recognized that thermal motions of atoms in the protein native state, the fluctuations about the minimum of the global free energy, are well reproduced by the simple elastic network models (ENMs) such as the anisotropic network model (ANM). Elastic network models represent protein dynamics as vibrations of a network of nodes (usually represented by positions of the heavy atoms or by the Cα atoms only for coarse-grained representations) in which the spatially close nodes are connected by harmonic springs. These models provide a reliable representation of the fluctuational dynamics of proteins and RNA, and explain various conformational changes in protein structures including those important for ligand binding. In the present paper, we study the problem of protein structure refinement by analyzing thermal motions of proteins in non-native states. We represent the conformational space close to the native state by a set of decoys generated by the I-TASSER protein structure prediction server utilizing template-free modeling. The protein substates are selected by hierarchical structure clustering. The main finding is that thermal motions for some substates, overlap significantly with the deformations necessary to reach the native state. Additionally, more mobile residues yield higher overlaps with the required deformations than do the less mobile ones. These findings suggest that structural refinement of poorly resolved protein models can be significantly enhanced by reduction of the conformational space to the motions imposed by the dominant normal modes.

  3. Spherical harmonic stacking for the singlets of Earth's normal modes of free oscillation

    NASA Astrophysics Data System (ADS)

    Chao, Benjamin F.; Ding, Hao

    2014-08-01

    We extend the spherical harmonic stacking (SHS) method of Buland et al. (1979) for the radial (vertical) component in the seismogram to the transverse (horizontal) components of the displacement field. Taking advantage of the orthogonality of the spherical harmonic functions (scalar and vectorial), SHS isolates and accentuates the signals of individual singlets of the Earth's normal modes of free oscillation. We apply the SHS on the broadband Incorporated Research Institutions for Seismology (IRIS) seismograms from up to 97 IRIS seismic stations for the 2004 Sumatra-Andaman earthquake, in experiments targeted to spheroidal as well as toroidal modes—2S1, 0S3, 2S2, 3S1, 1S3, 0T2, and 0T3. We report the complete resolution of the singlet frequencies of these multiplets, some for the first time, and estimate the singlets' complex frequencies using the frequency domain autoregressive method of Chao and Gilbert (1980). The latter contain useful information to be used in inversions for the 3-D structure of the Earth's interior.

  4. The Theoretical Foundation of 3D Alfvén Resonances: Normal Modes

    NASA Astrophysics Data System (ADS)

    Wright, Andrew N.; Elsden, Thomas

    2016-12-01

    We consider the resonant coupling of fast and Alfvén magnetohydrodynamic (MHD) waves in a 3D equilibrium. Numerical solutions to normal modes (\\propto \\exp (-iω t)) are presented, along with a theoretical framework to interpret them. The solutions we find are fundamentally different from those in 1D and 2D. In 3D there exists an infinite number of possible resonant solutions within a “Resonant Zone,” and we show how boundary conditions and locally 2D regions can favor particular solutions. A unique feature of the resonance in 3D is switching between different permissible solutions when the boundary of the Resonant Zone is encountered. The theoretical foundation that we develop relies upon recognizing that, in 3D, the orientation of the resonant surface will not align in a simple fashion with an equilibrium coordinate. We present a method for generating the Alfvén wave natural frequencies for an arbitrarily oriented Alfvén wave, which requires a careful treatment of scale factors describing the background magnetic field geometry.

  5. A Comparison of the Bounded Derivative and the Normal Mode Initialization Methods Using Real Data

    NASA Technical Reports Server (NTRS)

    Semazzi, F. H. M.; Navon, I. M.

    1985-01-01

    Browning et al. (1980) proposed an initialization method called the bounded derivative method (BDI). They used analytical data to test the new method. Kasahara (1982) theoretically demonstrated the equivalence between BDI and the well known nonlinear normal mode initialization method (NMI). The purposes of this study are the extension of the application of BDI to real data and comparison with NMI. The unbalanced initial state (UBD) is data of January, 1979 OOZ which were interpolated from the adjacent sigma levels of the GLAS GCM to the 300 mb surface. The global barotropic model described by Takacs and Balgovind (1983) is used. Orographic forcing is explicitly included in the model. Many comparisons are performed between various quantities. However, we only present a comparison of the time evolution at two grid points A(50 S, 90 E) and B(10 S, 20 E) which represent low and middle latitude locations. To facilitate a more complete comparison an initialization experiment based on the classical balance equation (CBE) was also included.

  6. Normal Modes for Dynamic Motions of a Topoisomerase II enzyme upon DNA-Binding and Bending

    NASA Astrophysics Data System (ADS)

    Mentes, Ahmet

    We have used Molecular Dynamics (MD) simulation methods and two analytical approaches (the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM)) to investigate the internal dynamic motions of the S. cerevisiae Topoisomerase (TopoII) during the first step of its catalytic cycle. At the initial state of the first step of its catalytic cycle, the protein and a 34 bp straight-DNA structure have no interaction. At the final state of the cycle, we have the bended-DNA/TopoII complex where the protein binds to DNA and, at this stage, the protein binds and bends the DNA, just before the DNA cleavage by TopoII. Normal mode analysis is used to characterize the functional flexibility of the protein, especially the C-gate domain closing/opening during the DNA binding/bending process and before DNA cleavage. Because of its clinical importance, our study might be helpful to better understand the next steps of its catalytic cycle and may provide new insight into the dynamics and structure of other TopoII-DNA complexes.

  7. Nonradiating normal modes in a classical many-body model of matter-radiation interaction

    NASA Astrophysics Data System (ADS)

    Carati, A.; Galgani, L.

    2003-08-01

    We consider a classical model of matter-radiation interaction, in which the matter is represented by a system of infinitely many dipoles on a one-dimensional lattice, and the system is dealt with in the so-called dipole ( linearized) approximation. We prove that there exist normal-mode solutions of the complete system, so that in particular the dipoles, though performing accelerated motions, do not radiate energy. This comes about in virtue of an exact compensation which we prove to occur, for each dipole, between the “radiation reaction force” and a part of the retarded forces due to all the other dipoles. This fact corresponds to a certain identity which we name after Oseen, since it occurs that this researcher did actually propose it, already in the year 1916. We finally make a connection with a paper of Wheeler and Feynman on the foundations of electrodynamics. It turns out indeed that the Oseen identity, which we prove here in a particular model, is in fact a weak form of a general identity that such authors were assuming as an independent postulate.

  8. An all-atom simulation study of the ordering of liquid squalane near a solid surface

    NASA Astrophysics Data System (ADS)

    Tsige, Mesfin; Patnaik, Soumya S.

    2008-05-01

    An all-atom molecular dynamics study using the OPLS force field has been carried out to obtain new insights in to the orientation and ordering of liquid squalane near a solid surface. As observed in previous experiments, the squalane molecules closest to a SiO 2 substrate are found to be tightly bound with their molecular axis preferentially parallel to the interface. Unlike linear alkanes, the squalane molecules are also found to lie preferentially parallel to the liquid/vapor interface. The simulation results predict that the molecular plane orientation of the squalane molecules changes from mainly parallel to perpendicular to the substrate in going further away from the substrate.

  9. Brillouin light scattering study of magnetic-element normal modes in a square artificial spin ice geometry

    NASA Astrophysics Data System (ADS)

    Li, Y.; Gubbiotti, G.; Casoli, F.; Gonçalves, F. J. T.; Morley, S. A.; Rosamond, M. C.; Linfield, E. H.; Marrows, C. H.; McVitie, S.; Stamps, R. L.

    2017-01-01

    We report the results, from experimental and micromagnetic studies, of the magnetic normal modes in artificial square spin ice systems consisting of ferromagnetic-monodomain islands. Spin-wave properties are measured by Brillouin light scattering. The mode spectra contain several branches whose frequencies are sensitive to the magnitude and in-plane orientation of an applied magnetic field. We also identify soft modes that exhibit different behaviours depending on the direction of the applied magnetic field. The obtained results are well described with micromagnetic simulations of independent magnetic elements arranged along two sublattices.

  10. Configuration of three distributed lines for reducing noise due to the coupling of the common and normal modes

    NASA Astrophysics Data System (ADS)

    Jinno, Souma; Toki, Hiroshi; Abe, Masayoshi

    2017-02-01

    In this study, the coupling between the common and normal modes in distributed lines and the resulting electromagnetic noise were considered. The telegraph equations of three distributed lines with the boundary conditions of a lumped circuit reveal the presence of mode-coupling noise. To reduce the coupling noise, the geometrically and electrically symmetric configuration of the three distributed lines is proposed. The simulation results show that the proposed configuration can decrease the mode-coupling noise by a factor of 1 ×10-8 in comparison with that of asymmetric configurations.

  11. All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5

    NASA Astrophysics Data System (ADS)

    Genheden, Samuel; Essex, Jonathan W.

    2016-11-01

    We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.

  12. All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2016-11-01

    We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.

  13. All-atom contact model for understanding protein dynamics from crystallographic B-factors.

    PubMed

    Li, Da-Wei; Brüschweiler, Rafael

    2009-04-22

    An all-atom local contact model is described that can be used to predict protein motions underlying isotropic crystallographic B-factors. It uses a mean-field approximation to represent the motion of an atom in a harmonic potential generated by the surrounding atoms resting at their equilibrium positions. Based on a 400-ns molecular dynamics simulation of ubiquitin in explicit water, it is found that each surrounding atom stiffens the spring constant by a term that on average scales exponentially with the interatomic distance. This model combines features of the local density model by Halle and the local contact model by Zhang and Brüschweiler. When applied to a nonredundant set of 98 ultra-high resolution protein structures, an average correlation coefficient of 0.75 is obtained for all atoms. The systematic inclusion of crystal contact contributions and fraying effects is found to enhance the performance substantially. Because the computational cost of the local contact model scales linearly with the number of protein atoms, it is applicable to proteins of any size for the prediction of B-factors of both backbone and side-chain atoms. The model performs as well as or better than several other models tested, such as rigid-body motional models, the local density model, and various forms of the elastic network model. It is concluded that at the currently achievable level of accuracy, collective intramolecular motions are not essential for the interpretation of B-factors.

  14. An all-atom model of the structure of human copper transporter 1.

    PubMed

    Tsigelny, Igor F; Sharikov, Yuriy; Greenberg, Jerry P; Miller, Mark A; Kouznetsova, Valentina L; Larson, Christopher A; Howell, Stephen B

    2012-07-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin.

  15. An All-Atom Model of the Structure of Human Copper Transporter 1

    PubMed Central

    Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.

    2013-01-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840

  16. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

    PubMed

    Higo, Junichi; Umezawa, Koji

    2014-01-01

    We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

  17. Normal and hyperspherical mode analysis of NO-doped Kr crystals upon Rydberg excitation of the impurity.

    PubMed

    Castro Palacio, J C; Velazquez Abad, L; Lombardi, A; Aquilanti, V; Rubayo Soneíra, J

    2007-05-07

    Molecular dynamics simulations and both normal mode and hyperspherical mode analyses of NO-doped Kr solid are carried out in order to get insights into the structural relaxation of the medium upon electronic excitation of the NO molecule. A combined study is reported on the time evolution of the cage radius and on the density of vibrational states, according to the hyperspherical and normal mode analyses. For the hyperspherical modes, hyper-radial and grand angular contributions are considered. For the normal modes, radial and tangential contributions are examined. Results show that the first shell radius dynamics is driven by modes with frequencies at approximately 47 and approximately 15 cm-1. The first one is related to the ultrafast regime where a large part of the energy is transmitted to the lattice and the second one to relaxation and slow redistribution of the energy. The density of vibrational states gamma(omega) is characterized by a broad distribution of bands peaking around the frequencies of approximately 13, approximately 19, approximately 25, approximately 31, approximately 37, approximately 47, and approximately 103 cm-1 (very small band). The dominant modes in the relaxation process were at 14.89, 23.49, and 53.78 cm-1; they present the largest amplitudes and the greatest energy contributions. The mode at 14.89 cm-1 is present in both the fit of the first shell radius and in the hyper-radial kinetic energy spectrum and resulted the one with the largest amplitude, although could not be revealed by the total kinetic energy power spectrum.

  18. Normal mode analysis of macromolecular systems with the mobile block Hessian method

    SciTech Connect

    Ghysels, An; Van Speybroeck, Veronique; Van Neck, Dimitri; Waroquier, Michel; Brooks, Bernard R.

    2015-01-22

    Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N{sub a}×3N{sub a} matrix with N{sub a} the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

  19. Normal mode analysis of macromolecular systems with the mobile block Hessian method

    NASA Astrophysics Data System (ADS)

    Ghysels, An; Van Speybroeck, Veronique; Van Neck, Dimitri; Brooks, Bernard R.; Waroquier, Michel

    2015-01-01

    Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3Na×3Na matrix with Na the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

  20. Instantaneous normal modes, resonances, and decay channels in the vibrational relaxation of the amide I mode of N-methylacetamide-D in liquid deuterated water.

    PubMed

    Bastida, Adolfo; Soler, Miguel Angel; Zúñiga, José; Requena, Alberto; Kalstein, Adrián; Fernández-Alberti, Sebastián

    2010-06-14

    A nonequilibrium molecular dynamics (MD) study of the vibrational relaxation of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D(2)O) solution is carried out using instantaneous normal modes (INMs). The identification of the INMs as they evolve over time, which is necessary to analyze the energy fluxes, is made by using a novel algorithm which allows us to assign unequivocally each INM to an individual equilibrium normal mode (ENM) or to a group of ENMs during the MD simulations. The time evolution of the energy stored in each INM is monitored and the occurrence of resonances during the relaxation process is then investigated. The decay of the amide I mode, initially excited with one vibrational quantum, is confirmed to fit well to a biexponential function, implying that the relaxation process involves at least two mechanisms with different rate constants. By freezing the internal motions of the solvent, it is shown that the intermolecular vibration-vibration channel to the bending modes of the solvent is closed. The INM analysis reveals then the existence of a major and faster decay channel, which corresponds to an intramolecular vibrational redistribution process and a minor, and slower, decay channel which involves the participation of the librational motions of the solvent. The faster relaxation pathway can be rationalized in turn using a sequential kinetic mechanism of the type P-->M+L-->L, where P (parent) is the initially excited amide I mode, and M (medium) and L (low) are specific midrange and lower-frequency NMAD vibrational modes, respectively.

  1. On the possibility of representing an acoustic field in shallow water as the sum of normal modes and quasimodes

    NASA Astrophysics Data System (ADS)

    Grigor'ev, V. A.; Petnikov, V. G.

    2016-11-01

    Using the example of a shallow-water acoustic waveguide with a homogeneous water layer of constant thickness H lying on a homogeneous fluid absorbing half-space (bottom), we obtain estimates of distance r from a source, for which it is possible to ignore the continuous spectrum for the mode description of the depth dependence of the intensity of a low-frequency sound field in the bottom layer. We have compared two discrete representations of the field using (1) the total set of normal modes and (2) the total set of normal modes and quasimodes. It is shown that in the case when there is at least one normal mode in the channel, additional allowance for quasimodes makes it possible by an order of magnitude to approximate the boundary of applicability of mode theory and on average establish it at a level of r H or less. We explain the functional dependences of the contribution of the continuous spectrum to the total field on the waveguide parameters and find the conditions of its minimization. We present examples of description of the field in the bottom, where the advantage of using quasimodes at short distances is also demonstrated.

  2. Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model.

    PubMed

    Bertaccini, Edward J; Trudell, James R; Lindahl, Erik

    2010-08-18

    We have previously used molecular modeling and normal-mode analyses combined with experimental data to visualize a plausible model of a transmembrane ligand-gated ion channel. We also postulated how the gating motion of the channel may be affected by the presence of various ligands, especially anesthetics. As is typical for normal-mode analyses, those studies were performed in vacuo to reduce the computational complexity of the problem. While such calculations constitute an efficient way to model the large scale structural flexibility of transmembrane proteins, they can be criticized for neglecting the effects of an explicit phospholipid bilayer or hydrated environment. Here, we show the successful calculation of normal-mode motions for our model of a glycine α-1 receptor, now suspended in a fully hydrated lipid bilayer. Despite the almost uniform atomic density, the introduction of water and lipid does not grossly distort the overall gating motion. Normal-mode analysis revealed that even a fully immersed glycine α-1 receptor continues to demonstrate an iris-like channel gating motion as a low-frequency, high-amplitude natural harmonic vibration consistent with channel gating. Furthermore, the introduction of periodic boundary conditions allows the examination of simultaneous harmonic vibrations of lipid in synchrony with the protein gating motions that are compatible with reasonable lipid bilayer perturbations. While these perturbations tend to influence the overall protein motion, this work provides continued support for the iris-like motion model that characterizes gating within the family of ligand-gated ion channels.

  3. Effect of temperature on the mixed-mode impact behavior of a normalized 1050 steel

    SciTech Connect

    Manoharan, M.; Seow, H.P.

    1997-10-01

    A considerable amount of work on mixed mode I/III fracture toughness of materials is available using proportional loading methods and all the work using such a loading method has recently been summarized. The superposition of mode III loading results in drastic reduction in fracture toughness in some materials whereas in other materials it has little effect or even results in an increase in the fracture toughness. Fracture mechanism maps delineating regions of susceptibility to tensile and shear loads have been proposed to explain such differences. In the mixed mode fracture toughness tests outlined above, the use of a modified compact tension specimen has enabled the testing of materials under a variety of combinations of mode I and mode III loadings. By using appropriately defined mixed-mode versions of the stress intensity factor K and the J integral, the susceptibility of these materials to mixed-mode fracture can be quantified. In addition to compact tension specimens, three point bend specimens with an inclined crack can also be used to determine the mixed-mode fracture behavior of materials. The aim of the present study was to study the feasibility of extending the mixed mode fracture concept to impact testing using a charpy type test specimen.

  4. Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields.

    PubMed

    Dahlgren, Markus K; Schyman, Patric; Tirado-Rives, Julian; Jorgensen, William L

    2013-05-24

    The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parametrization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and nonplanar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 °C) are also reported.

  5. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  6. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

    PubMed Central

    2016-01-01

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  7. Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.

    PubMed

    Henry, Eric R; Best, Robert B; Eaton, William A

    2013-10-29

    Advances in computing have enabled microsecond all-atom molecular dynamics trajectories of protein folding that can be used to compare with and test critical assumptions of theoretical models. We show that recent simulations by the Shaw group (10, 11, 14, 15) are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain, with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter, is remarkably similar to the distribution in the molecular dynamics trajectories.

  8. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    PubMed

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  9. All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer

    PubMed Central

    Perlmutter, Jason D.; Drasler, William J.; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N.

    2011-01-01

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native and functional state for longer periods than detergents do. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles, with a mass of ~40 kDa and a Rg of ~2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. While AAMD simulations result in cohesive and stable particles over a 45-ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond timescale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations, and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows higher-resolution characterization of a configuration determined by a long-timescale simulation. An excellent agreement is observed between MD models and experimental, small angle neutron scattering data. The MD data provides new insights into the structure and dynamics of A8-35 particles, possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes. PMID:21806035

  10. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

    PubMed

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-10-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

  11. Re-analysis of the Normal Mode Spectra of the 1960 Chile Earthquake

    NASA Astrophysics Data System (ADS)

    Watada, S.

    2015-12-01

    After the great 1960 Chile earthquake, Press et al. (1961) created a unilateral source rupture model with a length of 1000 km at a speed of 3- 4km/s. Kanamori and Cipar (1974), looked at long-period motion before the main shock in the strain-meter record at ISA and hinted the existence of a slow precursor. Kanamori and Anderson (1975) interpreted that the anomalous decrease of the Fourier spectral amplitude near 1.8 and 3.0mHz of the UCLA gravimeter record and the Press-Ewing seismometer record at PAS are caused by the interference between the main-shock and an un-modeled precursor. Cifuentes and Silver (1989) collected IGY seismographic data and confirmed the existence of the spectral holes at 4 stations all situated in the continental U.S. and modeled the holes with a large precursor or a post-cursor with magnitude comparable to the main shock. CS89 reported no such normal mode spectral holes outside North America. If the spectrum holes are due to destructive interference of a large pre- or post-cursor, the spectrum pattern will be a global feature. Seismograms outside North America are well explained by the unilateral rupture model. KA75 and CS89 synthetic spectra did not consider the spheroidal-toroidal modal coupling effect. We compared the amplitude spectra computed for earthquake models of a line source and a point source, and for the PREM and a rotating elliptic Earth model with laterally heterogeneity inside. The spectra are computed for the same time series presented in CS89 and directly compared with their amplitude pattern. The observed amplitude spectrum patterns are re-produced at 8 globally distributed stations including the amplitude holes at 4 stations in the U.S by a 920km-long line source (same to the CS89 source) for a rotating elliptic earth model with lateral heterogeneity inside. The synthetic spectrum tests indicate that the long-period precursor or post-cursor proposed by Cifuentes and Silver (1989) and Kanamori and Anderson (1975) is

  12. Modeling alkane+perfluoroalkane interactions using all-atom potentials: Failure of the usual combining rules

    NASA Astrophysics Data System (ADS)

    Song, W.; Rossky, P. J.; Maroncelli, M.

    2003-11-01

    We have tested the ability of the OPLS-AA models (optimized potentials for liquid simulations) of alkanes and perfluoroalkanes recently developed by Jorgensen and co-workers to represent the unusual mixing behavior of alkane+perfluoroalkane systems. We find that these all-atom Lennard-Jones (6-12)+Coulomb representations, together with the usual Lorentz-Berthelot combining rules, fail to reproduce the weaker-than-anticipated interactions between these two classes of molecules. Systematic disagreements with experiment are found in the case of second pressure virial coefficients, gas solubilities, and liquid-liquid mixing properties. These discrepancies are not specific to the choice of OPLS-AA potentials, but are rather linked to the failure of the geometric mean combining rule for relating unlike atom interactions. In all cases examined, a reduction in the strength of cross H+F interactions by ˜25% relative to the geometric mean is required in order to achieve reasonable agreement with experiment. Several less commonly used combining rules were also examined. Although some of these rules are able to provide a reasonable description of the interactions among perfluoroalkane and alkane species, they fail to provide a consistent treatment when atoms other than C, H, and F are considered, as is necessary for modeling the interaction of the former molecules with rare-gas atoms.

  13. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    SciTech Connect

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  14. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    NASA Astrophysics Data System (ADS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  15. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

    PubMed

    Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-28

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  16. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.

    PubMed

    Shimada, J; Kussell, E L; Shakhnovich, E I

    2001-04-20

    We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding, all side-chain and backbone torsions, and uses a Go potential. In this study, we focus on the 46 residue alpha/beta protein crambin and two of its structural components, the helix and helix hairpin. For a wide range of temperatures, we recorded multiple folding events of these three structures from random coils to native conformations that differ by less than 1 A C(alpha) dRMS from their crystal structure coordinates. The thermodynamics and kinetic mechanism of the helix-coil transition obtained from our simulation shows excellent agreement with currently available experimental and molecular dynamics data. Based on insights obtained from folding its smaller structural components, a possible folding mechanism for crambin is proposed. We observed that the folding occurs via a cooperative, first order-like process, and that many folding pathways to the native state exist. One particular sequence of events constitutes a "fast-folding" pathway where kinetic traps are avoided. At very low temperatures, a kinetic trap arising from the incorrect packing of side-chains was observed. These results demonstrate that folding to the native state can be observed in a reasonable amount of time on desktop computers even when an all-atom representation is used, provided the energetics sufficiently stabilize the native state.

  17. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

  18. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    PubMed

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  19. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  20. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  1. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

    PubMed Central

    Davis, Ian W.; Leaver-Fay, Andrew; Chen, Vincent B.; Block, Jeremy N.; Kapral, Gary J.; Wang, Xueyi; Murray, Laura W.; Arendall, W. Bryan; Snoeyink, Jack; Richardson, Jane S.; Richardson, David C.

    2007-01-01

    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu. PMID:17452350

  2. A real-time all-atom structural search engine for proteins.

    PubMed

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

    2014-07-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

  3. All-atom molecular dynamics simulation of a photosystem i/detergent complex.

    PubMed

    Harris, Bradley J; Cheng, Xiaolin; Frymier, Paul

    2014-10-09

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  4. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension.

    PubMed

    Sonne, Jacob; Jensen, Morten Ø; Hansen, Flemming Y; Hemmingsen, Lars; Peters, Günther H

    2007-06-15

    Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.

  5. Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model.

    PubMed

    Genheden, Samuel

    2016-01-12

    The solvation free energy is an essential quantity in force field development and in numerous applications. Here, we present the estimation of solvation free energies in polar (water, hexanol, octanol, and nonanol) and in apolar (hexane, octane, and nonane) media. The estimates are produced using molecular dynamics simulations employing a simple all-atom/coarse-grained hybrid model (AA/ELBA) and are therefore very efficient. More than 150 solutes were taken from the Minnesota solvation database and represent small, organic molecules. The mean absolute deviation for the different solvents ranges between 2.0 and 4.1 kJ/mol, and the correlation coefficient ranges between 0.78 and 0.99, indicating that the predictions are accurate. Outliers are identified, and potential avenues for improvements are discussed. Furthermore, partition coefficients between water and the organic solvents were estimated, and the percentage of the predictions that has the correct sign ranges between 74% (for octane) and 92% (for octanol and hexanol). Finally, membrane/water partition coefficients are replaced with hexane/water and octanol/water partition coefficients, and the latter is found to be as accurate as the expensive membrane calculations, indicating a wider application area.

  6. All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples.

    PubMed

    Kutchukian, Peter S; Yang, Jae Shick; Verdine, Gregory L; Shakhnovich, Eugene I

    2009-04-08

    Recent work has shown that the incorporation of an all-hydrocarbon "staple" into peptides can greatly increase their alpha-helix propensity, leading to an improvement in pharmaceutical properties such as proteolytic stability, receptor affinity, and cell permeability. Stapled peptides thus show promise as a new class of drugs capable of accessing intractable targets such as those that engage in intracellular protein-protein interactions. The extent of alpha-helix stabilization provided by stapling has proven to be substantially context dependent, requiring cumbersome screening to identify the optimal site for staple incorporation. In certain cases, a staple encompassing one turn of the helix (attached at residues i and i+4) furnishes greater helix stabilization than one encompassing two turns (i,i+7 staple), which runs counter to expectation based on polymer theory. These findings highlight the need for a more thorough understanding of the forces that underlie helix stabilization by hydrocarbon staples. Here we report all-atom Monte Carlo folding simulations comparing unmodified peptides derived from RNase A and BID BH3 with various i,i+4 and i,i+7 stapled versions thereof. The results of these simulations were found to be in quantitative agreement with experimentally determined helix propensities. We also discovered that staples can stabilize quasi-stable decoy conformations, and that the removal of these states plays a major role in determining the helix stability of stapled peptides. Finally, we critically investigate why our method works, exposing the underlying physical forces that stabilize stapled peptides.

  7. Protein model refinement using an optimized physics-based all-atom force field.

    PubMed

    Jagielska, Anna; Wroblewska, Liliana; Skolnick, Jeffrey

    2008-06-17

    One of the greatest challenges in protein structure prediction is the refinement of low-resolution predicted models to high-resolution structures that are close to the native state. Although contemporary structure prediction methods can assemble the correct topology for a large fraction of protein domains, such approximate models are often not of the resolution required for many important applications, including studies of reaction mechanisms and virtual ligand screening. Thus, the development of a method that could bring those structures closer to the native state is of great importance. We recently optimized the relative weights of the components of the Amber ff03 potential on a large set of decoy structures to create a funnel-shaped energy landscape with the native structure at the global minimum. Such an energy function might be able to drive proteins toward their native structure. In this work, for a test set of 47 proteins, with 100 decoy structures per protein that have a range of structural similarities to the native state, we demonstrate that our optimized potential can drive protein models closer to their native structure. Comparing the lowest-energy structure from each trajectory with the starting decoy, structural improvement is seen for 70% of the models on average. The ability to do such systematic structural refinements by using a physics-based all-atom potential represents a promising approach to high-resolution structure prediction.

  8. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

    PubMed

    Davis, Ian W; Leaver-Fay, Andrew; Chen, Vincent B; Block, Jeremy N; Kapral, Gary J; Wang, Xueyi; Murray, Laura W; Arendall, W Bryan; Snoeyink, Jack; Richardson, Jane S; Richardson, David C

    2007-07-01

    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

  9. High-throughput all-atom molecular dynamics simulations using distributed computing.

    PubMed

    Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G

    2010-03-22

    Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

  10. A hybrid all-atom/coarse grain model for multiscale simulations of DNA.

    PubMed

    Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio

    2011-10-28

    Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulations. Our method allows us to forthrightly link a state-of-the-art force field for AA simulations of DNA with a CG representation developed by our group. We show that no modification is needed for any of the existing residues (neither AA nor CG). Only the bonding parameters at the hybrid interface are enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems, which are studied by molecular dynamics simulations using an implicit solvent. The simplicity of the approach potentially permits us to study the effect of mutations/modifications as well as DNA binding molecules at the atomistic level within a significantly larger DNA scaffold considered at the CG level. Since all the interactions are computed within the same classical Hamiltonian, the extension to a quantum/classical/coarse-grain multilayer approach using QM/MM modules implemented in widely used simulation packages is straightforward.

  11. Drive Train Normal Modes Analysis for the ERDA/NASA 100-Kilowatt Wind Turbine Generator

    NASA Technical Reports Server (NTRS)

    Sullivan, T. L.; Miller, D. R.; Spera, D. A.

    1977-01-01

    Natural frequencies, as a function of power were determined using a finite element model. Operating conditions investigated were operation with a resistive electrical load and operation synchronized to an electrical utility grid. The influence of certain drive train components on frequencies and mode shapes is shown. An approximate method for obtaining drive train natural frequencies is presented.

  12. Normal modes of magnetic domain wall motion in a confined stripe domain lattice

    SciTech Connect

    Spreen, J.H.; Argyle, B.E.

    1982-06-01

    We report the observation of standing wave modes in an array of stripe domains confined by a pair of parallel cracks in a Gd, Ga:YIG film. These modes appear in the response spectrum of the confined lattice as shallow minima or maxima at frequencies lower than that of the usual domain wall resonance peak. A simple model, analogous to the forced response of a membrane clamped at the edges, fits the spatial patterns of wall motion observed at the frequencies of the maxima and minima. Experimental frequency-wave vector values, interpreted with guidance from this analogy, provide the first experimental dispersion curve for a stripe domain lattice. We compare this result with recent theoretical calculations. The experimental value of the uniform mode frequency is 41.5 +- 0.2 MHz, with a long wavelength group velocity of 330 +- 50 m/sec. A surprising conclusion from the observed extrema of the spatial patterns is that the damping of the waves is an order of magnitude less than expected from the damping of the uniform mode. The estimated decay length for a propagating wave is 400 ..mu...

  13. A Pictorial Visualization of Normal Mode Vibrations of the Fullerene (C[subscript 60]) Molecule in Terms of Vibrations of a Hollow Sphere

    ERIC Educational Resources Information Center

    Dunn, Janette L.

    2010-01-01

    Understanding the normal mode vibrations of a molecule is important in the analysis of vibrational spectra. However, the complicated 3D motion of large molecules can be difficult to interpret. We show how images of normal modes of the fullerene molecule C[subscript 60] can be made easier to understand by superimposing them on images of the normal…

  14. Characterization of mode-locking in an all-fiber, all normal dispersion ytterbium based fiber oscillator

    NASA Astrophysics Data System (ADS)

    Cserteg, András.; Sági, Veronika; Drozdy, András.; Varallyay, Zoltán.; Gajdátsy, Gábor

    2015-03-01

    An ytterbium based all fiber, all normal dispersion fiber oscillator with integrated SESAM can have several operation modes like mode-locked, Q-switched and noise-like. To know and to control the quality of the mode-locking is essential for the application of such laser oscillators, otherwise the whole laser setup can be damaged or the expected operation characteristics of the oscillator driven systems cannot be achieved. Usually the two-photon signal generated by the short pulses is used to indicate the mode locked operation, however such detection can be misleading in certain cases and not always able to predict the forthcoming degradation or vanishing of mode locking. The characterization method that we propose uses only the radio frequency spectrum of the oscillator output and can identify the different operation regimes of our laser setup. The optical spectra measured simultaneously with the RF signals proves the reliability of our method. With this kind of characterization stable mode locking can be initiated and maintained during the laser operation. The method combined with the ability to align the polarization states automatically in the laser cavity leads to the possibility to record a polarization map where the stability domains can be identified and classified. With such map the region where the mode locking is self starting and maintainable with minimal polarization alignment can be selected. The developed oscillator reported here with its compact setup and self alignment ability can be a reliable source with long term error free operation without the need of expensive monitoring tools.

  15. Part of evanescent modes in the normally incident gravity surface wave's energy layout around a submerged obstacle

    NASA Astrophysics Data System (ADS)

    Charland, J.; Rey, V.; Touboul, J.

    2012-04-01

    Part of evanescent modes in the normally incident gravity surface wave's energy layout around a submerged obstacle Jenna Charland *1, Vincent Rey *2, Julien Touboul *2 *1 Mediterraneen Institute of Oceanography. Institut des Sciences de l'Ingénieur Toulon-Var. Avenue Georges Pompidou, BP 56, 83162 La Valette du Var Cedex, France. Centre National de la Recherche Scientifique, Délégation Normandie. Projet soutenu financièrement par la Délégation Générale de l'Armement. *2 Mediterraneen Institute of Oceanography. Institut des Sciences de l'Ingénieur Toulon-Var. Avenue Georges Pompidou, BP 56, 83162 La Valette du Var Cedex, France. During the last decades various studies have been performed to understand the wave propagation over varying bathymetries. Few answers related to this non linear problem were given by the Patarapanich's studies which described the reflection coefficient of a submerged plate as a function of the wavelength. Later Le-Thi-Minh [2] demonstrated the necessity of taking into account the evanescent modes to better describe the propagation of waves over a varying bathymetry. However, all these studies stare at pseudo-stationary state that allows neither the comprehension of the transient behaviour of propagative modes nor the role of the evanescent modes in this unstationnary process. Our study deals with the wave establishment over a submerged plate or step and focuses on the evanescent modes establishment. Rey [3] described the propagation of a normally incident surface gravity wave over a varying topography on the behaviour of the fluid using a linearized potential theory solved by a numerical model using an integral method. This model has a large field of application and has been adapted to our case. This code still solves a stationary problem but allows us to calculate the contribution of the evanescent modes in the energy layout around a submerged plate or a submerged step. The results will show the importance of the trapped energy

  16. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  17. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    SciTech Connect

    Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  18. All-atom molecular dynamics studies of the full-length β-amyloid peptides

    NASA Astrophysics Data System (ADS)

    Luttmann, Edgar; Fels, Gregor

    2006-03-01

    β-Amyloid peptides are believed to play an essential role in Alzheimer's disease (AD), due to their sedimentation in the form of β-amyloid aggregates in the brain of AD-patients, and the in vitro neurotoxicity of oligomeric aggregates. The monomeric peptides come in different lengths of 39-43 residues, of which the 42 alloform seems to be most strongly associated with AD-symptoms. Structural information on these peptides to date comes from NMR studies in acidic solutions, organic solvents, or on shorter fragments of the peptide. In addition X-ray and solid-state NMR investigations of amyloid fibrils yield insight into the structure of the final aggregate and therefore define the endpoint of any conformational change of an Aβ-monomer along the aggregation process. The conformational changes necessary to connect the experimentally known conformations are not yet understood and this process is an active field of research. In this paper, we report results from all-atom molecular dynamics simulations based on experimental data from four different peptides of 40 amino acids and two peptides consisting of 42 amino acids. The simulations allow for the analysis of intramolecular interactions and the role of structural features. In particular, they show the appearance of β-turn in the region between amino acid 21 and 33, forming a hook-like shape as it is known to exist in the fibrillar Aβ-structures. This folding does not depend on the formation of a salt bridge between Asp-23 and Lys-28 but requires the Aβ(1-42) as such structure was not observed in the shorter system Aβ(1-40).

  19. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    PubMed

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  20. Effect of Calcium and Magnesium on Phosphatidylserine Membranes: Experiments and All-Atomic Simulations

    PubMed Central

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-01-01

    It is known that phosphatidylserine (PS−) lipids have a very similar affinity for Ca2+ and Mg2+ cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca2+ or Mg2+ induces very different aggregation behavior for PS− liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca2+ or Mg2+ cations. These puzzling results suggest that although these two cations have a similar affinity for PS− lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS− membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca2+ and Mg2+ cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca2+ cations present a peak at a distance ∼2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg2+ cations has two different peaks, located a few angstroms before and after the Ca2+ peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca2+ and Mg2+, respectively. PMID:22824273

  1. Effect of calcium and magnesium on phosphatidylserine membranes: experiments and all-atomic simulations.

    PubMed

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-05-02

    It is known that phosphatidylserine (PS(-)) lipids have a very similar affinity for Ca(2+) and Mg(2+) cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca(2+) or Mg(2+) induces very different aggregation behavior for PS(-) liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca(2+) or Mg(2+) cations. These puzzling results suggest that although these two cations have a similar affinity for PS(-) lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS(-) membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca(2+) and Mg(2+) cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca(2+) cations present a peak at a distance ~2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg(2+) cations has two different peaks, located a few angstroms before and after the Ca(2+) peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca(2+) and Mg(2

  2. MolProbity: all-atom structure validation for macromolecular crystallography.

    PubMed

    Chen, Vincent B; Arendall, W Bryan; Headd, Jeffrey J; Keedy, Daniel A; Immormino, Robert M; Kapral, Gary J; Murray, Laura W; Richardson, Jane S; Richardson, David C

    2010-01-01

    MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

  3. Free-energy function based on an all-atom model for proteins.

    PubMed

    Yoshidome, Takashi; Oda, Koji; Harano, Yuichi; Roth, Roland; Sugita, Yuji; Ikeguchi, Mitsunori; Kinoshita, Masahiro

    2009-12-01

    We have developed a free-energy function based on an all-atom model for proteins. It comprises two components, the hydration entropy (HE) and the total dehydration penalty (TDP). Upon a transition to a more compact structure, the number of accessible configurations arising from the translational displacement of water molecules in the system increases, leading to a water-entropy gain. To fully account for this effect, the HE is calculated using a statistical-mechanical theory applied to a molecular model for water. The TDP corresponds to the sum of the hydration energy and the protein intramolecular energy when a fully extended structure, which possesses the maximum number of hydrogen bonds with water molecules and no intramolecular hydrogen bonds, is chosen as the standard one. When a donor and an acceptor (e.g., N and O, respectively) are buried in the interior after the break of hydrogen bonds with water molecules, if they form an intramolecular hydrogen bond, no penalty is imposed. When a donor or an acceptor is buried with no intramolecular hydrogen bond formed, an energetic penalty is imposed. We examine all the donors and acceptors for backbone-backbone, backbone-side chain, and side chain-side chain intramolecular hydrogen bonds and calculate the TDP. Our free-energy function has been tested for three different decoy sets. It is better than any other physics-based or knowledge-based potential function in terms of the accuracy in discriminating the native fold from misfolded decoys and the achievement of high Z-scores.

  4. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.

    PubMed

    Zhao, Gongpu; Perilla, Juan R; Yufenyuy, Ernest L; Meng, Xin; Chen, Bo; Ning, Jiying; Ahn, Jinwoo; Gronenborn, Angela M; Schulten, Klaus; Aiken, Christopher; Zhang, Peijun

    2013-05-30

    Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.

  5. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

  6. QUANTUM MODE-COUPLING THEORY: Formulation and Applications to Normal and Supercooled Quantum Liquids

    NASA Astrophysics Data System (ADS)

    Rabani, Eran; Reichman, David R.

    2005-05-01

    We review our recent efforts to formulate and study a mode-coupling approach to real-time dynamic fluctuations in quantum liquids. Comparison is made between the theory and recent neutron scattering experiments performed on liquid ortho-deuterium and para-hydrogen. We discuss extensions of the theory to supercooled and glassy states where quantum fluctuations compete with thermal fluctuations. Experimental scenarios for quantum glassy liquids are briefly discussed.

  7. A Simple Reduction Process for the Normal Vibrational Modes Occurring in Linear Molecules

    ERIC Educational Resources Information Center

    McInerny, William

    2005-01-01

    The students in molecular spectroscopy courses are often required to determine the permitted normal vibrations for linear molecules that belong to particular groups. The reducible group representations generated by the use of Cartesian coordinates can be reduced by the use of a simple algebraic process applied to the group representations. The…

  8. Black phosphorus as a saturable absorber for generating mode-locked fiber laser in normal dispersion regime

    NASA Astrophysics Data System (ADS)

    Latiff, A. A.; Rusdi, M. F. M.; Hisyam, M. B.; Ahmad, H.; Harun, S. W.

    2016-11-01

    This paper reports a few-layer black phosphorus (BP) as a saturable absorber (SA) or phase-locker in generating modelocked pulses from a double-clad ytterbium-doped fiber laser (YDFL). We mechanically exfoliated the BP flakes from BP crystal through a scotch tape, and repeatedly press until the flakes thin and spread homogenously. Then, a piece of BP tape was inserted in the cavity between two fiber connectors end facet. Under 810 mW to 1320 mW pump power, stable mode-locked operation at 1085 nm with a repetition rate of 13.4 MHz is successfully achieved in normal dispersion regime. Before mode-locked operation disappears above maximum pump, the output power and pulse energy is about 80 mW and 6 nJ, respectively. This mode-locked laser produces peak power of 0.74 kW. Our work may validates BP SA as a phase-locker related to two-dimensional nanomaterials and pulsed generation in normal dispersion regime.

  9. Automatic protein design with all atom force-fields by exact and heuristic optimization.

    PubMed

    Wernisch, L; Hery, S; Wodak, S J

    2000-08-18

    A fully automatic procedure for predicting the amino acid sequences compatible with a given target structure is described. It is based on the CHARMM package, and uses an all atom force-field and rotamer libraries to describe and evaluate side-chain types and conformations. Sequences are ranked by a quantity akin to the free energy of folding, which incorporates hydration effects. Exact (Branch and Bound) and heuristic optimisation procedures are used to identifying highly scoring sequences from an astronomical number of possibilities. These sequences include the minimum free energy sequence, as well as all amino acid sequences whose free energy lies within a specified window from the minimum. Several applications of our procedure are illustrated. Prediction of side-chain conformations for a set of ten proteins yields results comparable to those of established side-chain placement programs. Applications to sequence optimisation comprise the re-design of the protein cores of c-Crk SH3 domain, the B1 domain of protein G and Ubiquitin, and of surface residues of the SH3 domain. In all calculations, no restrictions are imposed on the amino acid composition and identical parameter settings are used for core and surface residues. The best scoring sequences for the protein cores are virtually identical to wild-type. They feature no more than one to three mutations in a total of 11-16 variable positions. Tests suggest that this is due to the balance between various contributions in the force-field rather than to overwhelming influence from packing constraints. The effectiveness of our force-field is further supported by the sequence predictions for surface residues of the SH3 domain. More mutations are predicted than in the core, seemingly in order to optimise the network of complementary interactions between polar and charged groups. This appears to be an important energetic requirement in absence of the partner molecules with which the SH3 domain interacts, which were not

  10. An analysis of nearfield normal mode amplitude anomalies of the Landers earthquake

    NASA Technical Reports Server (NTRS)

    Watada, Shingo; Kanamori, Hiroo; Anderson, Don L.

    1993-01-01

    The 1992 Landers earthquake (M(sub w) = 7.3) occurred in the middle of the TERRAscope network. Long-period Rayleigh waves recorded at the TERRAscope stations (delta less than or = 3 deg) after traveling around the Earth show large amplitude anomalies, one order of magnitude larger than spherical Earth predictions up to a period of about 600 s. The ground motions over the epicentral region at and after the arrival of R4-5 are in phase at all stations. These observations are inconsistent with the nearly vertical strike slip mechanism of the Landers earthquake. Synthetic seismograms for a rotating, elliptic, and laterally heterogeneous Earth model calculated by the variational method agree well with the observed waveforms. Calculations for various 3D Earth models demonstrate that the amplitudes are very sensitive to the large scale aspherical structure in the crust and the mantle. The anomalies for modes shorter than 300 s period can be explained by lateral heterogeneity shallower than the upper mantle. Rotation of the Earth and lower mantle heterogeneity are required to explain mode amplitudes at longer periods. Current whole mantle seismic tomographic models can fully explain the observed amplitudes longer than 300 s. To assess the effect of the high order lateral heterogeneity in the mantle more precise estimate of the crustal correction is required.

  11. A comparison of the bounded derivative and the normal mode initialization methods using real data. [in numerical weather forecasting

    NASA Technical Reports Server (NTRS)

    Semazzi, F. H. M.; Navon, I. M.

    1985-01-01

    A bounded derivative initialization method (BDI) formerly used only in theoretical studies to balance gravitational wave influences is extended to a real world data set and the results are compared with those from a normal mode initialization (NMI). BDI proceeds by defining the characteristic scales of motion of interest and then constraining the time derivatives to match motions on a slow scale. A global barotropic model which considers orographic forcing is initialized by the scaled balance equations of the BDI scheme, which uses vorticity alone to achieve an initial balanced state. An external mode projector is employed to realize the NMI scheme, and five Machenhauer iterations reduce the total balance by four orders of magnitude. The initial states generated with both schemes are essentially equivalent, including the time evolution of a height field and divergence behavior being centered around regions of high orographic elevation.

  12. Phase transitions in normal mode spectra of two-dimensional clusters in an anisotropic power-law confining potential

    NASA Astrophysics Data System (ADS)

    Bessaa, Assia; Djebli, Mourad

    2017-02-01

    We present a numerical analysis of several phase transitions which take place in the eigenmode spectrum of a two-dimensional (2D) logarithmic cluster subjected to an anisotropic power law confinement. Varying the anisotropy in a non-parabolic soft confinement drives the system to undergo structural phase transitions of first order, while for a hard wall confinement this variation affects strongly the eigenmode spectrum and breaks the symmetry of the system due to the removal of degeneracy and the coupling between some normal modes.

  13. Mode-locked femtosecond all-normal all-PM Yb-doped fiber laser at 1060 nm

    NASA Astrophysics Data System (ADS)

    Bowen, Patrick; Singh, Harman; Runge, Antoine; Provo, Richard; Broderick, Neil G. R.

    2016-04-01

    We report an all-normal-dispersion, all-fibre, all-PM, laser operating at a central wavelength of 1060 nm. The laser is mode-locked using a nonlinear amplifying loop mirror and generates linearly polarised pulses that can be compressed to 360 fs. The laser is based on our earlier scheme operating at 1030 nm [1] and we discuss the similarities and differences between the two configurations. We also present amplification up to an output power of 1 W using a commercially built amplifier and show through numerical methods that this pulse may be recompressible to 1.65 ps.

  14. Motions in the interiors and atmospheres of Jupiter and Saturn. II - Barotropic instabilities and normal modes of an adiabatic planet

    NASA Technical Reports Server (NTRS)

    Ingersoll, A. P.; Miller, R. L.

    1986-01-01

    A rotating and adiabatic inviscid fluid planet possesses low frequency motions that are barotropic, quasi-geostrophic and quasi-columnar. The limiting curvature at which flow becomes unstable upon projection onto the planetary surface is negative, with an amplitude that is 3-4 times that for thin atmospheres, in planets in which density linearly decreases to zero at the surface. This result is shown to hold for all quasi-columnar perturbations. Both the phase speed of the normal mode oscillations and the barotropic stability criterion have features in common with Saturn and Jupiter oscillations.

  15. A Finite Element Method for Computation of Structural Intensity by the Normal Mode Approach

    NASA Astrophysics Data System (ADS)

    Gavrić, L.; Pavić, G.

    1993-06-01

    A method for numerical computation of structural intensity in thin-walled structures is presented. The method is based on structural finite elements (beam, plate and shell type) enabling computation of real eigenvalues and eigenvectors of the undamped structure which then serve in evaluation of complex response. The distributed structural damping is taken into account by using the modal damping concept, while any localized damping is treated as an external loading, determined by use of impedance matching conditions and eigenproperties of the structure. Emphasis is given to aspects of accuracy of the results and efficiency of the numerical procedures used. High requirements on accuracy of the structural response (displacements and stresses) needed in intensity applications are satisfied by employing the "swept static solution", which effectively takes into account the influence of higher modes otherwise inaccessible to numerical computation. A comparison is made between the results obtained by using analytical methods and the proposed numerical procedure to demonstrate the validity of the method presented.

  16. Folding peptides and proteins with all-atom physics: methods and applications

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2008-03-01

    Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re

  17. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

    PubMed

    Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

    2015-05-12

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the

  18. Fourier transform infrared spectra and normal mode analysis of drug molecules: Zidovudine

    NASA Astrophysics Data System (ADS)

    Jain, Nivedita; Prabhakar, Santosh; Singh, R. A.

    2013-03-01

    The FTIR spectra of zidovudine molecule have been recorded in the range 4000-400 cm-1. The title compound is used as a drug against AIDS or HIV. The molecular structure, fundamental vibrational frequencies and intensities of vibrational bands are evaluated using density functional theory (DFT) using BLYP, B3LYP, B3PW91 and MPW1PW91 methods with 6-31+G(d,p) standard basis set. Comparison of simulated spectra with the experimental spectrum provides important informations and the ability of the computational method to describe the vibrational modes. These calculations have allowed finding most stable conformational structure of AZT. Calculated results of the title compound indicate that the drug molecule has syn orientation. The glycosidic bond in AZT and a minimum-energy structure in which the glycosy torsion angle χ and torsion angle γ values are consistent with those in the conformation of AZT in the AZT5-triphosphate bound to HIV RT is determined.

  19. Multiple-Component Crystal Fabric Measurements from Acoustically-Generated Normal Modes in Borehole

    NASA Astrophysics Data System (ADS)

    Kluskiewicz, D. J.; Waddington, E. D.; McCarthy, M.; Anandakrishnan, S.; Voigt, D.; Matsuoka, K.

    2014-12-01

    Sound wave velocities in ice are a proxy of crystal orientation fabric. Because p- and s-waves respectively travel faster and slower in the direction of an ice crystal c-axis, the velocities of these waves in a fabric are related to the clustering of ice crystal c-axes in the direction of wave propagation. Previous sonic logs at Dome C, NGRIP, WAIS, and NEEM have inferred a single component fabric description from the velocities of vertically-propagating p-waves around each ice core borehole. These records supplement thin-section measurements of crystal fabric by sampling larger numbers of crystals in a depth-continuous log. Observations of azimuthally anisotropic vertical-girdle fabrics at ice-core sites such as WAIS, NGRIP, and EDML underly a benefit for logging methods that are sensitive to such fabrics. We present a theoretical framework for using borehole flexural modes to measure azimuthal crystal-fabric anisotropy, and describe ongoing efforts to develop a sonic logging tool for this purpose. We also present data from p-wave logs and thin section measurements at the WAIS Divide, and describe how a flexural wave log could supplement the existing measurements.

  20. Normal-mode function representation of global 3-D data sets: open-access software for the atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2015-04-01

    This article presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulations across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass and wind fields while considering the whole model depth in contrast to the majority of studies. The paper includes the theory of normal-mode function (NMF) expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the ERA Interim reanalysis data set. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim data set reveals several aspects of the large-scale circulation after it has been partitioned into the linearly balanced and IG components. The global energy distribution is dominated by the balanced energy while the IG modes contribute around 10% of the total wave energy. However, on sub-synoptic scales, IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally averaged and equatorial circulation provide a reference for the validation of climate models.

  1. Changes in structural style of normal faults due to failure mode transition: First results from excavated scale models

    NASA Astrophysics Data System (ADS)

    Kettermann, Michael; Urai, Janos L.

    2015-05-01

    The effects of failure mode transition from tensile to shear on structural style and fault zone architecture have long been recognized but are not well studied in 3D, although the two modes are both common in the upper crust of Earth and terrestrial planets, and are associated with large differences in transport properties. We present a simple method to study this in physical scale models of normal faults, using a cohesive powder embedded in cohesionless sand. By varying the overburden thickness, the failure mode changes from tensile to hybrid and finally to shear. Hardening and excavating the cohesive layer allows post mortem investigation of 3D structures at high resolution. We recognize two end member structural domains that differ strongly in their attributes. In the tensile domain faults are strongly dilatant with steep open fissures and sharp changes in strike at segment boundaries and branch points. In the shear domain fault dips are shallower and fault planes develop striations; map-view fault traces undulate with smaller changes in strike at branches. These attributes may be recognized in subsurface fault maps and could provide a way to better predict fault zone structure in the subsurface.

  2. Nonlinear normal mode interactions in the SF6 molecule studied with the aid of density functional theory

    NASA Astrophysics Data System (ADS)

    Chechin, G.; Ryabov, D.; Shcherbinin, S.

    2015-07-01

    Some exact interactions between vibrational modes in systems with discrete symmetry can be described by the theory of the bushes of nonlinear normal modes (NNMs) [G. M. Chechin and V. P. Sakhnenko, Phys. D (Amsterdam, Neth.) 117, 43 (1998), 10.1016/S0167-2789(98)80012-2]. Each bush represents a dynamical object conserving the energy of the initial excitation. The existence of bushes of NNMs is ensured by some group-theoretical selection rules. In G. M. Chechin et al. [Int. J. Nonlinear Mech. 38, 1451 (2003), 10.1016/S0020-7462(02)00081-1], existence and stability of the bushes of vibrational modes in the simple octahedral model of mass points interacting via Lennard-Jones potential were investigated. In the present paper, we study these dynamical objects by the density functional theory in the SF6 molecule, which possesses the same symmetry and structure. We have fully confirmed the results previously obtained in the framework of the group-theoretical approach and have found some properties of the bushes of NNMs.

  3. Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance raman spectroscopy.

    PubMed

    Xiao, Yuming; Wang, Hongxin; George, Simon J; Smith, Matt C; Adams, Michael W W; Jenney, Francis E; Sturhahn, Wolfgang; Alp, Ercan E; Zhao, Jiyong; Yoda, Y; Dey, Abishek; Solomon, Edward I; Cramer, Stephen P

    2005-10-26

    We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S(cys))(4) site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm(-1); upon reduction these modes shift to 300-320 cm(-1). This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at approximately 150 cm(-1) for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm(-1) for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The (57)Fe partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D(2)(d) Fe(SC)(4) model. A C(1) Fe(SCC)(4) model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant K(Fe-S) for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/A. K(Fe-S) is clearly diminished in reduced Rd; values from approximately 0.89 to 1.00 mdyn/A were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, H(S-Fe-S), were 0.18 mdyn/A for oxidized Rd and 0.15 mdyn/A for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.

  4. NI-23BRAIN BREAST METASTASES RESPOND TO ANTI-ANGIOGENIC THERAPY BY MODES OF VASCULAR NORMALIZATION

    PubMed Central

    Emblem, Kyrre; Pinho, Marco; Chandra, Vyshak; Gerstner, Elizabeth; Stufflebeam, Steve; Sorenson, Greg; Harris, Gordon; Freedman, Rachel; Sohl, Jessica; Younger, Jerry; Krop, Ian; Winer, Eric; Lin, Nancy

    2014-01-01

    INTRODUCTION: As systemic therapy improves, brain metastases are increasingly common in patients with breast cancer. Unfortunately, effective therapy with durable control has remained elusive [1]. Combining bevacizumab and cyototoxic chemotherapy is an appealing approach as the anti-angiogenic effect of bevicizumab may improve delivery of cytotoxic drugs to brain tumors. METHODS: We conducted a Phase II study of patients with parenchymal brain metastasis treated with bevacizumab and carboplatin [2]. Patients could have any hormone receptor status or any number of prior therapies. Patients with HER2+ breast cancer also received trastuzamab. Correlative perfusion MRI scans to look at tumor perfusion, blood volume, vessel calibers and relative oxygen saturation (ΔSO2) levels were performed at baseline, day 1, and after 2 months of therapy [3, 4]. For consistency, the largest contrast-enhancing lesion in each patient visible on all three MR visits was selected for analysis. RESULTS: Thirty-eight patients were enrolled in the study of which 32 had, paired evaluable imaging datasets. Compared to baseline, 12/32 patients were identified as responders by a durable increase in ΔSO2 levels at day 1 and at 2 months above a 5% measurement error threshold. The remaining patients were identified by stable (15/32) or reduced (5/32) ΔSO2 levels. Patients responding to therapy showed increased tumor perfusion (Mann-Whitney; P<0.01) and prolonged survival (625 versus 400 days, Cox regression; P<0.05) Fig. 1B). A collective and selective pruning of macroscopic tumor vessels (>10 µm) were seen across all patients. CONCLUSIONS: Similar to primary brain tumors [2, 3], perfusion MRI demonstrates that anti-angiogenic therapy can induce vascular normalization in a subset of patients with metastatic breast cancer to the brain. Our data indicate that the vascular response may also be associated with improved survival. [1] Lin NU, Lancet Oncol 2013 [2] Sorensen AG, Cancer Res 2012 [3

  5. Frequencies and Normal Modes of Vibration of Benz[a]anthracene Radical Ions

    NASA Astrophysics Data System (ADS)

    Kubba, Rehab M.; Al-ani, Raghida I.; Shanshal, Muthana

    2005-03-01

    MINDO/3-FORCES calculations were carried out for the radical ions of benz[a]anthracene. Both ions exhibit Cs symmetry with C-C bond alternation in all four rings. The obtained equilibrium geometry was applied for the calculation of all 3N - 6 vibration frequencies of each ion, and for the analysis of their normal coordinates. The so calculated frequencies of the radical cation were close to the experimental frequencies and those of the ab initio calculations. They fall in the ranges νCHstr. (3034 - 3087 cm-1), νCCstr. (1237 - 1609 cm-1), δCH (1142 - 1216 cm-1). Interesting correlations could be obtained for the frequencies of similar vibrations, e. g. νsymCHstr. >νasymCHstr. Exception is the frequency of vibration of CHα in ring A for the radical cation and the same bond in ring D for the radical anion. The vibration frequencies for the CH bonds depend on the σ -electron densities of the corresponding carbon atoms, i. e. νCH.+str. >νCHstr. >νCH.-str., where σ -ρĊ+ >σ -ρC >σ -ρĊ- . For the C-C stretching vibrations the relation ν(C-C)str. >ν(C-C).-str. >ν(C-C).+str. holds, with the exception of the Cβ -Cβ bond, for which the relation ν(C-C)str. >ν(C-C).+str. >ν(C-C).-str. is found. As for the in-plane and out of-plane deformations, the following general correlations δ (CH) >δ (CH).- >δ (CH).+ and γ (CC) >γ (CC).- >γ (CC).+.

  6. All-atomic simulations on human telomeric G-quadruplex DNA binding with thioflavin T.

    PubMed

    Luo, Di; Mu, Yuguang

    2015-04-16

    Ligand-stabilized human telomeric G-quadruplex DNA is believed to be an anticancer agent, as it can impede the continuous elongation of telomeres by telomerase in cancer cells. In this study, five well-established human telomeric G-quadruplex DNA models were probed on their binding behaviors with thioflavin T (ThT) via both conventional molecular dynamics (MD) and well-tempered metadynamics (WT-MetaD) simulations. Novel dynamics and characteristic binding patterns were disclosed by the MD simulations. It was observed that the K(+) promoted parallel and hybridized human telomeric G-quadruplex conformations pose higher binding affinities to ThT than the Na(+) and K(+) promoted basket conformations. It is the end, sandwich, and base stacking driven by π-π interactions that are identified as the major binding mechanisms. As the most energy favorable binding mode, the sandwich stacking observed in (3 + 1) hybridized form 1 G-quadruplex conformation is triggered by reversible conformational change of the G-quadruplex. To further examine the free energy landscapes, WT-MetaD simulations were utilized on G-quadruplex-ThT systems. It is found that all of the major binding modes predicted by the MD simulations are confirmed by the WT-MetaD simulations. The results in this work not only accord with existing experimental findings, but also reinforce our understanding on the dynamics of G-quadruplexes and aid future drug developments for G-quadruplex stabilization ligands.

  7. Semianalytical quasi-normal mode theory for the local density of states in coupled photonic crystal cavity-waveguide structures.

    PubMed

    de Lasson, Jakob Rosenkrantz; Kristensen, Philip Trøst; Mørk, Jesper; Gregersen, Niels

    2015-12-15

    We present and validate a semianalytical quasi-normal mode (QNM) theory for the local density of states (LDOS) in coupled photonic crystal (PhC) cavity-waveguide structures. By means of an expansion of the Green's function on one or a few QNMs, a closed-form expression for the LDOS is obtained, and for two types of two-dimensional PhCs, with one and two cavities side-coupled to an extended waveguide, the theory is validated against numerically exact computations. For the single cavity, a slightly asymmetric spectrum is found, which the QNM theory reproduces, and for two cavities, a nontrivial spectrum with a peak and a dip is found, which is reproduced only when including both the two relevant QNMs in the theory. In both cases, we find relative errors below 1% in the bandwidth of interest.

  8. Ultra-broadband dissipative soliton and noise-like pulse generation from a normal dispersion mode-locked Tm-doped all-fiber laser.

    PubMed

    Sobon, Grzegorz; Sotor, Jaroslaw; Martynkien, Tadeusz; Abramski, Krzysztof M

    2016-03-21

    We report generation of ultra-broadband dissipative solitons and noise-like pulses from a simple, fully fiberized mode-locked Tm-doped fiber laser. The oscillator operates in the normal net dispersion regime and is mode-locked via nonlinear polarization evolution. Depending on the cavity dispersion, the laser was capable of generating 60 nm or 100 nm broad dissipative solitons. These are the broadest spectra generated from a normal dispersion mode-locked Tm-doped fiber laser so far. The same oscillator might also operate in the noise-like pulse regime with extremely broad emission spectra (over 300 nm), which also significantly outperforms the previous reports.

  9. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    NASA Astrophysics Data System (ADS)

    Kim, Seung-Yeon; Kwak, Wooseop

    2014-12-01

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z( T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z( T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T 1 and the lower transition temperature T 2 of PTH(1-34) can be interpreted as the collapse temperature T θ and the folding temperature T f , respectively.

  10. Refined OPLS all-atom force field parameters for n-pentadecane, methyl acetate, and dimethyl phosphate.

    PubMed

    Murzyn, Krzysztof; Bratek, Maciej; Pasenkiewicz-Gierula, Marta

    2013-12-27

    OPLS All-Atom (OPLS/AA) is a generic all-atom force field which was fine-tuned to accurately reproduce condensed phase properties of organic liquids. Its application in modeling of lipid membranes is, however, limited mainly due to the inability to correctly describe phase behavior and organization of the hydrophobic core of the model lipid bilayers. Here we report new OPLS/AA parameters for n-pentadecane, methyl acetate, and dimethyl phosphate anion. For the new force field parameters, we show very good agreement between calculated and numerous reference data, including liquid density, enthalpy of vaporization, free energy of hydration, and selected transport properties. The new OPLS/AA parameters have been used in successful submicrosecond MD simulations of bilayers made of bacterial glycolipids whose results will be published elsewhere shortly.

  11. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

  12. An Evolutionary Strategy for All-Atom Folding of the 60-Amino-Acid Bacterial Ribosomal Protein L20

    PubMed Central

    Schug, A.; Wenzel, W.

    2006-01-01

    We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of “native content” in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence. PMID:16565067

  13. Elastic parabolic equation and normal mode solutions for seismo-acoustic propagation in underwater environments with ice covers.

    PubMed

    Collis, Jon M; Frank, Scott D; Metzler, Adam M; Preston, Kimberly S

    2016-05-01

    Sound propagation predictions for ice-covered ocean acoustic environments do not match observational data: received levels in nature are less than expected, suggesting that the effects of the ice are substantial. Effects due to elasticity in overlying ice can be significant enough that low-shear approximations, such as effective complex density treatments, may not be appropriate. Building on recent elastic seafloor modeling developments, a range-dependent parabolic equation solution that treats the ice as an elastic medium is presented. The solution is benchmarked against a derived elastic normal mode solution for range-independent underwater acoustic propagation. Results from both solutions accurately predict plate flexural modes that propagate in the ice layer, as well as Scholte interface waves that propagate at the boundary between the water and the seafloor. The parabolic equation solution is used to model a scenario with range-dependent ice thickness and a water sound speed profile similar to those observed during the 2009 Ice Exercise (ICEX) in the Beaufort Sea.

  14. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations.

    PubMed

    Cota, Junio; Oliveira, Leandro C; Damásio, André R L; Citadini, Ana P; Hoffmam, Zaira B; Alvarez, Thabata M; Codima, Carla A; Leite, Vitor B P; Pastore, Glaucia; de Oliveira-Neto, Mario; Murakami, Mario T; Ruller, Roberto; Squina, Fabio M

    2013-08-01

    Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes.

  15. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    PubMed

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-24

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.

  16. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

    PubMed

    Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing

    2017-03-20

    The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

  17. High-latitude filtering in a global grid-point model using model normal modes. [Fourier filters for synoptic weather forecasting

    NASA Technical Reports Server (NTRS)

    Takacs, L. L.; Kalnay, E.; Navon, I. M.

    1985-01-01

    A normal modes expansion technique is applied to perform high latitude filtering in the GLAS fourth order global shallow water model with orography. The maximum permissible time step in the solution code is controlled by the frequency of the fastest propagating mode, which can be a gravity wave. Numerical methods are defined for filtering the data to identify the number of gravity modes to be included in the computations in order to obtain the appropriate zonal wavenumbers. The performances of the model with and without the filter, and with a time tendency and a prognostic field filter are tested with simulations of the Northern Hemisphere winter. The normal modes expansion technique is shown to leave the Rossby modes intact and permit 3-5 day predictions, a range not possible with the other high-latitude filters.

  18. Automatic Differentiation of Normal and Continuous Adventitious Respiratory Sounds Using Ensemble Empirical Mode Decomposition and Instantaneous Frequency.

    PubMed

    Lozano, Manuel; Fiz, José Antonio; Jané, Raimon

    2016-03-01

    Differentiating normal from adventitious respiratory sounds (RS) is a major challenge in the diagnosis of pulmonary diseases. Particularly, continuous adventitious sounds (CAS) are of clinical interest because they reflect the severity of certain diseases. This study presents a new classifier that automatically distinguishes normal sounds from CAS. It is based on the multiscale analysis of instantaneous frequency (IF) and envelope (IE) calculated after ensemble empirical mode decomposition (EEMD). These techniques have two major advantages over previous techniques: high temporal resolution is achieved by calculating IF-IE and a priori knowledge of signal characteristics is not required for EEMD. The classifier is based on the fact that the IF dispersion of RS signals markedly decreases when CAS appear in respiratory cycles. Therefore, CAS were detected by using a moving window to calculate the dispersion of IF sequences. The study dataset contained 1494 RS segments extracted from 870 inspiratory cycles recorded from 30 patients with asthma. All cycles and their RS segments were previously classified as containing normal sounds or CAS by a highly experienced physician to obtain a gold standard classification. A support vector machine classifier was trained and tested using an iterative procedure in which the dataset was randomly divided into training (65%) and testing (35%) sets inside a loop. The SVM classifier was also tested on 4592 simulated CAS cycles. High total accuracy was obtained with both recorded (94.6% ± 0.3%) and simulated (92.8% ± 3.6%) signals. We conclude that the proposed method is promising for RS analysis and classification.

  19. cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions

    PubMed Central

    Oliwa, Tomasz; Shen, Yang

    2015-01-01

    Motivation: It remains both a fundamental and practical challenge to understand and anticipate motions and conformational changes of proteins during their associations. Conventional normal mode analysis (NMA) based on anisotropic network model (ANM) addresses the challenge by generating normal modes reflecting intrinsic flexibility of proteins, which follows a conformational selection model for protein–protein interactions. But earlier studies have also found cases where conformational selection alone could not adequately explain conformational changes and other models have been proposed. Moreover, there is a pressing demand of constructing a much reduced but still relevant subset of protein conformational space to improve computational efficiency and accuracy in protein docking, especially for the difficult cases with significant conformational changes. Method and results: With both conformational selection and induced fit models considered, we extend ANM to include concurrent but differentiated intra- and inter-molecular interactions and develop an encounter complex-based NMA (cNMA) framework. Theoretical analysis and empirical results over a large data set of significant conformational changes indicate that cNMA is capable of generating conformational vectors considerably better at approximating conformational changes with contributions from both intrinsic flexibility and inter-molecular interactions than conventional NMA only considering intrinsic flexibility does. The empirical results also indicate that a straightforward application of conventional NMA to an encounter complex often does not improve upon NMA for an individual protein under study and intra- and inter-molecular interactions need to be differentiated properly. Moreover, in addition to induced motions of a protein under study, the induced motions of its binding partner and the coupling between the two sets of protein motions present in a near-native encounter complex lead to the improved

  20. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

    PubMed

    Zheng, Wenjun

    2014-07-01

    The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins.

  1. Acoustic normal modes using the propagator matrix technique for a stratified ocean overlaying an inhomogeneous anisotropic porous bed

    NASA Astrophysics Data System (ADS)

    Badiey, M.; Yamamoto, T.

    1986-01-01

    Propogation of acoustic normal modes at excitation frequencies of 50 to 50000 Hz in a shallow stratified ocean overlaying a transverse isotropic poro-elastic sediment bed is modeled. The Biot-Willis stiffness matrix of the poro-elastic anisotropy is defined in terms of physical properties of sediments to model the bed. Propagator matrix method is used to solve the differential equations for the motion stress vectors in both layered sediment and water. The effects of sediment properties on the dispersion and attenuation of acoustic waves are examined numerically. Using the relaxation principle it is observed that the energy loss is maximum at frequency referred to as relaxation frequency of the porous media given by f sub ri = (beta)(nu)/3 pi k (sub si), where beta is the porosity, nu is the kinematic viscosity of the pore fluid and k (sub si) is the anisotropic permeability coefficient. The phase speed of compressional and shear waves in the sediment becomes highly dispersive around this frequency. The sandy bottom's relaxation frequency is the range of several hundred hertz to several kilo hertz. This report presents the derivation of the mathematical expressions used in the model and a complete description of the computer program. Four examples of numerical calculations are provided.

  2. Aligning Experimental and Theoretical Anisotropic B-Factors: Water Models, Normal-Mode Analysis Methods, and Metrics

    PubMed Central

    2014-01-01

    The strength of X-ray crystallography in providing the information for protein dynamics has been under appreciated. The anisotropic B-factors (ADPs) from high-resolution structures are invaluable in studying the relationship among structure, dynamics, and function. Here, starting from an in-depth evaluation of the metrics used for comparing the overlap between two ellipsoids, we applied normal-mode analysis (NMA) to predict the theoretical ADPs and then align them with experimental results. Adding an extra layer of explicitly treated water on protein surface significantly improved the energy minimization results and better reproduced the anisotropy of experimental ADPs. In comparing experimental and theoretical ADPs, we focused on the overlap in shape, the alignment of dominant directions, and the similarity in magnitude. The choices of water molecules, NMA methods, and the metrics for evaluating the overlap of ADPs determined final results. This study provides useful information for exploring the physical basis and the application potential of experimental ADPs. PMID:24673391

  3. All-Atom Molecular-Level Analysis of the Ballistic-Impact-Induced Densification and Devitrification of Fused Silica

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Snipes, J. S.; Ramaswami, S.; Yavari, R.; Barsoum, R. S.

    2015-08-01

    All-atom molecular-level computations are carried out to infer the dynamic response and material microstructure/topology changes of fused silica subjected to ballistic impact by a hard projectile. The analysis was focused on the investigation of specific aspects of the dynamic response and of the microstructural changes such as the deformation of highly sheared and densified regions and the conversion of amorphous fused silica to SiO2 crystalline allotropic modifications (in particular, α-quartz and stishovite). The microstructural changes in question were determined by carrying out a post-processing atom-coordination procedure. This procedure suggested the formation of stishovite (and perhaps α-quartz) within fused silica during ballistic impact. To rationalize the findings obtained, the all-atom molecular-level computational analysis is complemented by a series of quantum-mechanics density functional theory (DFT) computations. The latter computations enable determination of the relative potential energies of the fused silica, α-quartz, and stishovite under ambient pressure (i.e., under their natural densities) as well as under imposed (as high as 50 GPa) pressures (i.e., under higher densities) and shear strains. In addition, the transition states associated with various fused-silica devitrification processes were identified. The results obtained are found to be in good agreement with their respective experimental counterparts.

  4. Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression.

    PubMed

    Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

    2009-10-01

    An accurate scoring function is required for protein structure prediction. The scoring function should distinguish the native structure among model structures (decoys) and it also should have correlation with the quality of the decoys. However, we had observed the trade-off between the two requirements for seven all-atom distance dependent potentials in the previous study, where the native structure could be discriminated by examining the fine atomic details, whereas the correlation could be improved by examining coarse-grained interactions, To overcome this problem, in this study, we tried to make an improved scoring function by combining the seven potentials. First, the seven potentials were normalized by the expected energy values of the native and reference states of the target protein. Second, the relationship between the seven normalized energies and the quality (GDT_TS) of the structure were learned using support vector regression with the decoy sets of CASP6 as the training set. Then the meta-score was obtained as the predicted GDT_TS and it was tested with the decoys of the CASP7 experiment. The meta-score showed improvement in correlations with the GDT_TS and in the Z-score of the native structure. It also showed comparable performances in the GDT and enrichment criteria, with the best component potentials. The meta-score could be also used as the absolute quality of the structures. Our study suggests the benefit of combining several different scoring functions for model evaluation.

  5. Acoustic waves generated from seismic surface waves: propagation properties determined from Doppler sounding observations and normal-mode modelling

    NASA Astrophysics Data System (ADS)

    Artru, Juliette; Farges, Thomas; Lognonné, Philippe

    2004-09-01

    Since 1960, experiments have shown that perturbations of the ionosphere can occur after earthquakes, by way of dynamic coupling between seismic surface waves and the atmosphere. The atmospheric wave is amplified exponentially while propagating upwards due to the decrease of density, and interaction with the ionospheric plasma leads to clearly identified signals on both ground-based or satellite ionospheric measurements. In 1999 and 2000, after an upgrade of the HF Doppler sounder, the Commisariat à l'Énergie Atomique systematically recorded these effects in the ionosphere with the Francourville (France) network, by measuring vertical oscillations of ionospheric layers with the Doppler technique. Normal-mode theory extended to a solid Earth with an atmosphere allows successful modelling of such signals, even if this 1-D approach is probably too crude, especially in the solid Earth, where 20 s surface waves see large lateral variations in the crust. The combination of observations and simulations provides a new tool to determine acoustic gravity wave propagation characteristics from the ground to ionospheric height. Observed velocity and amplification of the atmospheric waves show good agreement from the ground up to moderate sounding altitudes (140-150 km); however, at higher altitudes the propagation speed is found to be much smaller than predicted and attenuation is underestimated. This shows that the standard formalism of acoustic gravity waves in the atmosphere cannot efficiently describe propagation in the ionized atmosphere. Further work is needed to characterize the propagation of acoustic waves in this altitude range: we believe that seismic waves can provide a well-constrained source for such study.

  6. The mass normalization of the displacement and strain mode shapes in a strain experimental modal analysis using the mass-change strategy

    NASA Astrophysics Data System (ADS)

    Kranjc, Tadej; Slavič, Janko; Boltežar, Miha

    2013-12-01

    The classic experimental modal analysis (EMA) is a well-known procedure for determining the modal parameters. The less frequently used strain EMA is based on a response measurement using strain sensors. The results of a strain EMA are the modal parameters, where in addition to the displacement mode shapes the strain mode shapes are also identified. The strain EMA can be used for an experimental investigation of a stress-strain distribution without the need to build a dynamical model. It can also be used to determine the modal parameters when, during modal testing, a motion sensor cannot be used and so a strain sensor is used instead. The displacement and strain mode shapes that are determined with the strain EMA are not mass normalized (scaled with respect to the orthogonality properties of the mass-normalized modal matrix), and therefore some dynamical properties of the system cannot be obtained. The mass normalization can be made with the classic EMA, which requires the use of a motion sensor. In this research a new approach to the mass normalization in the strain EMA, without using a motion sensor, is presented. It is based on the recently introduced mass-change structural modification method, which is used for the mass normalization in an operational modal analysis. This method was modified in such a way that it can be used for the mass normalization in the strain EMA. The mass-normalized displacement and strain mode shapes were obtained using a combination of the proposed approach and the strain EMA. The proposed approach was validated on real structures (beam and plate).

  7. Transform-limited pulse generation in normal cavity dispersion erbium doped single-walled carbon nanotubes mode-locked fiber ring laser.

    PubMed

    Chernysheva, M A; Krylov, A A; Ogleznev, A A; Arutyunyan, N R; Pozharov, A S; Obraztsova, E D; Dianov, E M

    2012-10-08

    We demonstrate an erbium doped fiber ring laser mode-locked with a carboxymetylcellulose high-optical quality film with dispersed single-walled carbon nanotubes (SWCNT). The laser with large normal net cavity dispersion generates near bandwidth-limited picosecond inverse modified soliton pulses at 1.56 µm.

  8. Low-frequency broadband sound source localization using an adaptive normal mode back-propagation approach in a shallow-water ocean.

    PubMed

    Lin, Ying-Tsong; Newhall, Arthur E; Lynch, James F

    2012-02-01

    A variety of localization methods with normal mode theory have been established for localizing low frequency (below a few hundred Hz), broadband signals in a shallow water environment. Gauss-Markov inverse theory is employed in this paper to derive an adaptive normal mode back-propagation approach. Joining with the maximum a posteriori mode filter, this approach is capable of separating signals from noisy data so that the back-propagation will not have significant influence from the noise. Numerical simulations are presented to demonstrate the robustness and accuracy of the approach, along with comparisons to other methods. Applications to real data collected at the edge of the continental shelf off New Jersey, USA are presented, and the effects of water column fluctuations caused by nonlinear internal waves and shelfbreak front variability are discussed.

  9. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  10. Mechanism of Nucleation and Growth of Aβ40 Fibrils from All-Atom and Coarse-Grained Simulations.

    PubMed

    Sasmal, Sukanya; Schwierz, Nadine; Head-Gordon, Teresa

    2016-12-01

    In this work, we characterize the nucleation and elongation mechanisms of the "diseased" polymorph of the amyloid-β 40 (Aβ40) fibril using an off-lattice coarse-grained (CG) protein model. After determining the nucleation size and subsequent stable protofibrillar structure from the CG model, validated with all-atom simulations, we consider the "lock and dock" and "activated monomer" fibril elongation mechanisms for the protofibril by statistical additions of a monomer drawn from four different ensembles of the free Aβ40 peptide to grow the fibril. Our CG model shows that the dominant mechanism for fibril elongation is the lock and dock mechanism across all monomer ensembles, even when the monomer is in the activated form. Although our CG model finds no thermodynamic difference between the two fibril elongation mechanisms, the activated monomer is found to be kinetically faster by a factor of 2 for the "locking" step compared with all other structured or unstructured monomer ensembles.

  11. Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models.

    PubMed

    Genheden, Samuel; Eriksson, Leif A

    2016-09-13

    Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.

  12. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors.

    PubMed

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane-solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane-solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor.

  13. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    PubMed

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  14. Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: effect of changes in bond-stretching force-field terms.

    PubMed

    Pereverzev, Andrey; Sewell, Thomas D

    2011-06-28

    Terahertz (THz) active normal-mode relaxation in crystalline pentaerythritol tetranitrate (PETN) was studied using classical molecular dynamics simulations for energy and density conditions corresponding to room temperature and atmospheric pressure. Two modifications to the fully flexible non-reactive force field due to Borodin et al. [J. Phys. Chem. B 112, 734 (2008)] used in a previous study of THz-active normal-mode relaxation in PETN [J. Chem. Phys. 134, 014513 (2011)] were considered to assess the sensitivity of the earlier predictions to details of the covalent bond-stretching terms in the force field. In the first modification the harmonic bond-stretching potential was replaced with the Morse potential to study the effect of bond anharmonicity on the THz-region mode relaxation. In the second modification the C-H and nitro-group N-O bond lengths were constrained to constant values to mimic lower quantum occupation numbers for those high-frequency modes. The results for relaxation times of the initially excited modes were found to be insensitive to either force-field modification. Overall time scales for energy transfer to other modes in the system were essentially unaffected by the force-field modifications, whereas the detailed pathways by which the energy transfer occurs are more complicated for the Morse potential than for the harmonic-bond and fixed-bond cases. Terahertz infrared absorption spectra constructed using calculated normal-mode frequencies, transition dipoles, and relaxation times for THz-active modes were compared to the spectra obtained from the Fourier transform of the dipole-dipole time autocorrelation function (DDACF). Results from the two approaches are in near agreement with each other and with experimental results in terms of main peak positions. Both theoretical methods yield narrower peaks than observed experimentally and in addition predict a weaker peak at ω ∼ 50 cm(-1) that is weak or absent experimentally. Peaks obtained using

  15. Structural features of small benzene clusters (C6H6)n (n ≤ 30) as investigated with the all-atom OPLS potential.

    PubMed

    Takeuchi, Hiroshi

    2012-10-18

    The structures of the simplest aromatic clusters, benzene clusters (C(6)H(6))(n), are not well elucidated. In the present study, benzene clusters (C(6)H(6))(n) (n ≤ 30) were investigated with the all-atom optimized parameters for liquid simulation (OPLS) potential. The global minima and low-lying minima of the benzene clusters were searched with the heuristic method combined with geometrical perturbations. The structural features and growth sequence of the clusters were examined by carrying out local structure analyses and structural similarity evaluation with rotational constants. Because of the anisotropic interaction between the benzene molecules, the local structures consisting of 13 molecules are considerably deviated from regular icosahedron, and the geometries of some of the clusters are inconsistent with the shapes constructed by the interior molecules. The distribution of the angle between the lines normal to two neighboring benzene rings is anisotropic in the clusters, whereas that in the liquid benzene is nearly isotropic. The geometries and energies of the low-lying configurations and the saddle points between them suggest that most of the configurations previously detected in supersonic expansions take different orientations for one to four neighboring molecules.

  16. High frequency normal mode statistics in a shallow water waveguide: the effect of random linear internal waves.

    PubMed

    Raghukumar, Kaustubha; Colosi, John A

    2014-07-01

    Using transport theory and Monte Carlo numerical simulation, the statistical properties of mode propagation at a frequency of 1 kHz are studied in a shallow water environment with random sound-speed perturbations from linear internal waves. The environment is typical of summer conditions in the mid-Atlantic bight during the Shallow Water 2006 experiment. Observables of interest include the second and fourth moments of the mode amplitudes, which are relevant to full-field mean intensity and scintillation index. It is found that mode phase randomization has a strong adiabatic component while at the same time mode coupling rates are significant. As a consequence, a computationally efficient transport theory is presented, which models cross-mode correlation adiabatically, but accounts for mode coupling using the mode energy equations of Creamer [(1996). J. Acoust. Soc. Am. 99, 2825-2838]. The theory also has closed-form expressions for the internal wave scattering matrix and a correction for an edge effect. The hybrid transport theory is shown to accurately reproduce many statistical quantities from the Monte Carlo simulations.

  17. Steady-state entanglement and normal-mode splitting in an atom-assisted optomechanical system with intensity-dependent coupling

    SciTech Connect

    Barzanjeh, Sh.; Naderi, M. H.; Soltanolkotabi, M.

    2011-12-15

    In this paper, we study theoretically bipartite and tripartite continuous variable entanglement as well as normal-mode splitting in a single-atom cavity optomechanical system with intensity-dependent coupling. The system under consideration is formed by a Fabry-Perot cavity with a thin vibrating end mirror and a two-level atom in the Gaussian standing wave of the cavity mode. We first derive the general form of the Hamiltonian describing the tripartite intensity-dependent atom-field-mirror coupling due to the presence of the cavity mode structure. We then restrict our treatment to the first vibrational sideband of the mechanical resonator and derive a tripartite atom-field-mirror Hamiltonian. We show that when the optical cavity is intensely driven, one can generate bipartite entanglement between any pair in the tripartite system and that, due to entanglement sharing, atom-mirror entanglement is efficiently generated at the expense of optical-mechanical and optical-atom entanglement. We also find that in such a system, when the Lamb-Dicke parameter is large enough, one can simultaneously observe the normal mode splitting into three modes.

  18. Effect of damping on excitability of high-order normal modes. [for a large space telescope spacecraft

    NASA Technical Reports Server (NTRS)

    Merchant, D. H.; Gates, R. M.; Straayer, J. W.

    1975-01-01

    The effect of localized structural damping on the excitability of higher-order large space telescope spacecraft modes is investigated. A preprocessor computer program is developed to incorporate Voigt structural joint damping models in a finite-element dynamic model. A postprocessor computer program is developed to select critical modes for low-frequency attitude control problems and for higher-frequency fine-stabilization problems. The selection is accomplished by ranking the flexible modes based on coefficients for rate gyro, position gyro, and optical sensor, and on image-plane motions due to sinusoidal or random PSD force and torque inputs.

  19. Differential Lipid Profiles of Normal Human Brain Matter and Gliomas by Positive and Negative Mode Desorption Electrospray Ionization – Mass Spectrometry Imaging

    PubMed Central

    Pirro, Valentina; Hattab, Eyas M.; Cohen-Gadol, Aaron A.; Cooks, R. Graham

    2016-01-01

    Desorption electrospray ionization—mass spectrometry (DESI-MS) imaging was used to analyze unmodified human brain tissue sections from 39 subjects sequentially in the positive and negative ionization modes. Acquisition of both MS polarities allowed more complete analysis of the human brain tumor lipidome as some phospholipids ionize preferentially in the positive and others in the negative ion mode. Normal brain parenchyma, comprised of grey matter and white matter, was differentiated from glioma using positive and negative ion mode DESI-MS lipid profiles with the aid of principal component analysis along with linear discriminant analysis. Principal component–linear discriminant analyses of the positive mode lipid profiles was able to distinguish grey matter, white matter, and glioma with an average sensitivity of 93.2% and specificity of 96.6%, while the negative mode lipid profiles had an average sensitivity of 94.1% and specificity of 97.4%. The positive and negative mode lipid profiles provided complementary information. Principal component–linear discriminant analysis of the combined positive and negative mode lipid profiles, via data fusion, resulted in approximately the same average sensitivity (94.7%) and specificity (97.6%) of the positive and negative modes when used individually. However, they complemented each other by improving the sensitivity and specificity of all classes (grey matter, white matter, and glioma) beyond 90% when used in combination. Further principal component analysis using the fused data resulted in the subgrouping of glioma into two groups associated with grey and white matter, respectively, a separation not apparent in the principal component analysis scores plots of the separate positive and negative mode data. The interrelationship of tumor cell percentage and the lipid profiles is discussed, and how such a measure could be used to measure residual tumor at surgical margins. PMID:27658243

  20. High-frequency normal-mode statistics in shallow water: the combined effect of random surface and internal waves.

    PubMed

    Raghukumar, Kaustubha; Colosi, John A

    2015-05-01

    In an earlier article, the statistical properties of mode propagation were studied at a frequency of 1 kHz in a shallow water environment with random sound-speed perturbations from linear internal waves, using a hybrid transport theory and Monte Carlo numerical simulations. Here, the analysis is extended to include the effects of random linear surface waves, in isolation and in combination with internal waves. Mode coupling rates for both surface and internal waves are found to be significant, but strongly dependent on mode number. Mode phase randomization by surface waves is found to be dominated by coupling effects, and therefore a full transport theory treatment of the range evolution of the cross mode coherence matrix is needed. The second-moment of mode amplitudes is calculated using transport theory, thereby providing the mean intensity while the fourth-moment is calculated using Monte Carlo simulations, which provides the scintillation index. The transport theory results for second-moment statistics are shown to closely reproduce Monte Carlo simulations. Both surface waves and internal waves strongly influence the acoustic field fluctuations.

  1. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations*

    PubMed Central

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-01-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  2. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    PubMed

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma.

  3. Multi-step formation of a hemifusion diaphragm for vesicle fusion revealed by all-atom molecular dynamics simulations.

    PubMed

    Tsai, Hui-Hsu Gavin; Chang, Che-Ming; Lee, Jian-Bin

    2014-06-01

    Membrane fusion is essential for intracellular trafficking and virus infection, but the molecular mechanisms underlying the fusion process remain poorly understood. In this study, we employed all-atom molecular dynamics simulations to investigate the membrane fusion mechanism using vesicle models which were pre-bound by inter-vesicle Ca(2+)-lipid clusters to approximate Ca(2+)-catalyzed fusion. Our results show that the formation of the hemifusion diaphragm for vesicle fusion is a multi-step event. This result contrasts with the assumptions made in most continuum models. The neighboring hemifused states are separated by an energy barrier on the energy landscape. The hemifusion diaphragm is much thinner than the planar lipid bilayers. The thinning of the hemifusion diaphragm during its formation results in the opening of a fusion pore for vesicle fusion. This work provides new insights into the formation of the hemifusion diaphragm and thus increases understanding of the molecular mechanism of membrane fusion. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.

  4. All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics.

    PubMed

    Gangupomu, Vamshi K; Abrams, Cameron F

    2010-11-17

    The 27-residue membrane-spanning domain (MSD) of the HIV-1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus, in particular a conserved GXXXG motif and a midspan arginine. However, structure-based explanations for the roles of these and other MSD features remain unclear. Using molecular dynamics and metadynamics calculations of an all-atom, explicit solvent, and membrane-anchored model, we study the conformational variability of the HIV-1 gp41 MSD. We find that the MSD peptide assumes a stable tilted α-helical conformation in the membrane. However, when the side chain of the midspan Arg (694) "snorkels" to the outer leaflet of the viral membrane, the MSD assumes a metastable conformation where the highly-conserved N-terminal core (between Lys(681) and Arg(694) and containing the GXXXG motif) unfolds. In contrast, when the Arg(694) side chain snorkels to the inner leaflet, the MSD peptide assumes a metastable conformation consistent with experimental observations where the peptide kinks at Phe(697) to facilitate Arg(694) snorkeling. Both of these models suggest specific ways that gp41 may destabilize viral membrane, priming the virus for fusion with a target cell.

  5. Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

    DOE PAGES

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2015-12-15

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigatingmore » protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

  6. Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

    SciTech Connect

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2015-12-15

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.

  7. Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study

    PubMed Central

    Thøgersen, Lea; Schiøtt, Birgit; Vosegaard, Thomas; Nielsen, Niels Chr.; Tajkhorshid, Emad

    2008-01-01

    We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-μs CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 μs is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the α-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer. PMID:18676652

  8. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils

    NASA Astrophysics Data System (ADS)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2016-11-01

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

  9. Two-dimensional NMR and All-atom Molecular Dynamics of Cytochrome P450 CYP119 Reveal Hidden Conformational Substates*

    PubMed Central

    Lampe, Jed N.; Brandman, Relly; Sivaramakrishnan, Santhosh; de Montellano, Paul R. Ortiz

    2010-01-01

    Cytochrome P450 enzymes are versatile catalysts involved in a wide variety of biological processes from hormonal regulation and antibiotic synthesis to drug metabolism. A hallmark of their versatility is their promiscuous nature, allowing them to recognize a wide variety of chemically diverse substrates. However, the molecular details of this promiscuity have remained elusive. Here, we have utilized two-dimensional heteronuclear single quantum coherence NMR spectroscopy to examine a series of mutants site-specific labeled with the unnatural amino acid, [13C]p-methoxyphenylalanine, in conjunction with all-atom molecular dynamics simulations to examine substrate and inhibitor binding to CYP119, a P450 from Sulfolobus acidocaldarius. The results suggest that tight binding hydrophobic ligands tend to lock the enzyme into a single conformational substate, whereas weak binding low affinity ligands bind loosely in the active site, resulting in a distribution of localized conformers. Furthermore, the molecular dynamics simulations suggest that the ligand-free enzyme samples ligand-bound conformations of the enzyme and, therefore, that ligand binding may proceed largely through a process of conformational selection rather than induced fit. PMID:20097757

  10. A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions.

    PubMed

    Sutto, Ludovico; Mereu, Ilaria; Gervasio, Francesco Luigi

    2011-12-13

    Structure-based models are successful at conjugating the essence of the energy landscape theory of protein folding with an easy and efficient implementation. Recently, their realm expanded beyond a single protein structure, and structure-based potentials have been used profitably to widely study complex conformational transitions. Still, when dealing with structural rearrangements between two, or more, well-defined structures, an unbiased and transferable description of the local backbone and side chain interactions could be advantageous. Here, we propose an all-atom model that merges a classical force field description of these local interactions with a structure-based long-range potential that takes into account the different conformations. We first validate the model simulating and characterizing the folding reaction and the transition state of two well-known proteins: the villin headpiece and the SH3 domain. Then, we characterize the activation mechanism of the catalytic domain of c-Src kinase. Such a process involves the conformational rearrangement of a large loop and the swing of an α helix. The appearance of a stable intermediate state in the free energy landscape between the two conformational end points suggests the mechanism of the loop opening. The low computational cost of the model together with the satisfactory accuracy of the results make it a promising approach to studying conformational transitions in large protein systems.

  11. Template-free protein structure prediction and quality assessment with an all-atom free-energy model.

    PubMed

    Gopal, Srinivasa Murthy; Klenin, Konstantin; Wenzel, Wolfgang

    2009-11-01

    Biophysical forcefields have contributed less than originally anticipated to recent progress in protein structure prediction. Here, we have investigated the selectivity of a recently developed all-atom free-energy forcefield for protein structure prediction and quality assessment (QA). Using a heuristic method, but excluding homology, we generated decoy-sets for all targets of the CASP7 protein structure prediction assessment with <150 amino acids. The decoys in each set were then ranked by energy in short relaxation simulations and the best low-energy cluster was submitted as a prediction. For four of nine template-free targets, this approach generated high-ranking predictions within the top 10 models submitted in CASP7 for the respective targets. For these targets, our de-novo predictions had an average GDT_S score of 42.81, significantly above the average of all groups. The refinement protocol has difficulty for oligomeric targets and when no near-native decoys are generated in the decoy library. For targets with high-quality decoy sets the refinement approach was highly selective. Motivated by this observation, we rescored all server submissions up to 200 amino acids using a similar refinement protocol, but using no clustering, in a QA exercise. We found an excellent correlation between the best server models and those with the lowest energy in the forcefield. The free-energy refinement protocol may thus be an efficient tool for relative QA and protein structure prediction.

  12. Dynamic performance of duolayers at the air/water interface. 2. Mechanistic insights from all-atom simulations.

    PubMed

    Christofferson, Andrew J; Yiapanis, George; Leung, Andy H M; Prime, Emma L; Tran, Diana N H; Qiao, Greg G; Solomon, David H; Yarovsky, Irene

    2014-09-18

    The novel duolayer system, comprising a monolayer of ethylene glycol monooctadecyl ether (C18E1) and the water-soluble polymer poly(vinylpyrrolidone) (PVP), has been shown to resist forces such as wind stress to a greater degree than the C18E1 monolayer alone. This paper reports all-atom molecular dynamics simulations comparing the monolayer (C18E1 alone) and duolayer systems under an applied force parallel to the air/water interface. The simulations show that, due to the presence of PVP at the interface, the duolayer film exhibits an increase in chain tilt, ordering, and density, as well as a lower lateral velocity compared to the monolayer. These results provide a molecular rationale for the improved performance of the duolayer system under wind conditions, as well as an atomic-level explanation for the observed efficacy of the duolayer system as an evaporation suppressant, which may serve as a useful guide for future development for thin films where resistance to external perturbation is desirable.

  13. Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution.

    PubMed

    Roussel, Guillaume; Michaux, Catherine; Perpète, Eric A

    2014-10-01

    Sodium dodecyl sulfate (SDS) is a well-known anionic detergent widely used in both experimental and theoretical investigations. Many molecular dynamics (MD) simulation have been performed on the SDS molecule at coarse-grained (CG), united-atom (UA), and all-atom (AA) resolutions. However, these simulations are usually based on general parameters determined from large sets of molecules, and as a result, peculiar molecular specificities are often poorly represented. In addition, the parameters (ideal bond lengths, angles, dihedrals and charge distribution) differ according to the resolution, highlighting a lack of coherence. We therefore propose a new set of parameters for CG, UA, and AA resolutions based on a high quantum mechanics (QM) level optimization of the detergent structure and the charge distribution. For the first time, QM-optimized parameters were directly applied to build the AA, UA, and CG model of the SDS molecule, leading to a more coherent description. As a test case, MD simulations were then performed on SDS preformed micelles as previous experimental and theoretical investigations allow direct comparison with our new sets of parameters. While all three models yield similar macromolecular properties (size, shape, and accessible surface) perfectly matching previous results, the attribution of more coherent parameters to SDS enables the description of the specific interactions inside and outside the micelle. These more consistent parameters can now be used to accurately describe new multi-scale systems involving the SDS molecule.

  14. High energy pulses generation with giant spectrum bandwidth and submegahertz repetition rate from a passively mode-locked Yb-doped fiber laser in all normal dispersion cavity

    NASA Astrophysics Data System (ADS)

    Lin, J.-H.; Wang, D.; Lin, K.-H.

    2011-01-01

    Robust passively mode-locked pulse generation with low pulse repetition rate and giant spectrum bandwidth in an all-fiber, all-normal-dispersion ytterbium-doped fiber laser has been experimentally demonstrated using nonlinear polarization evolution technique. The highest pulse energy over 20 nJ with spectrum bandwidth over 50 nm can be experimentally obtained at 175 mW pump power. The mode-locked pulses reveal broadened 3-dB pulsewidth about several nanosecond and widened pedestal in time trace that is resulted from enormous dispersion in laser cavity and gain dynamics. At certain mode-locking state, a spectrum gap around 1056 nm are observed between the three and four energy levels of Yb-doped fiber laser. By properly rotating the polarization controller, the gap can be eliminated due to four-wave mixing to produce more flattened spectrum output.

  15. Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C-H Region of DMSO as a Case Study

    SciTech Connect

    Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; Mifflin, Amanda L.; Hess, Wayne P.; Wang, Hongfei; Cramer, Christopher J.; Govind, Niranjan

    2016-03-03

    Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical iden- tication of hydrocarbons and in vibrational sum-frequency generation (SFG) spec- *troscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a chal- lenge from a theoretical viewpoint. In this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes chal- lenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show signicant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.

  16. Surface enhanced Raman scattering, natural bond orbitals and Mulliken atomic charge distribution in the normal modes of diethyldithiocarbamate cadmium (II) complex, [Cd(DDTC)2

    NASA Astrophysics Data System (ADS)

    Téllez Soto, C. A.; Costa, A. C.; Versiane, O.; Lemma, T.; Machado, N. C. F.; Mondragón, M. A.; Martin, A. A.

    2015-07-01

    Theoretical and experimental bands have been assigned to the Fourier Transform Infrared (FT-IR) and FT-Raman spectra of the bis(diethyldithiocarbamate)Cd(II) complex, abbreviated as ([Cd(DDTC)2]). The calculations and spectral interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra, and band deconvolution analysis to assist in the assignment of observed fundamentals. This study validated the unusual pseudo tetrahedral molecular structure formed around the Cd(II) cation. Surface-enhanced Raman scattering (SERS) was used to determine the interactions of the normal-modes of the diethyldithiocarbamate cadmium (II) complex on nano-structured silver surfaces. Natural bond orbital (NBO) analysis was also carried out to study the Cd(II) hybridization causing the pseudo tetrahedral geometry of the framework of the [Cd(DDTC)2] complex, and to confirm the charge transfer mechanisms through second order perturbation theory analysis of the Fox Matrix. In order to find out the electronic dispersion of the Mulliken atomic charges (MAC) in the normal modes, we calculated the MAC for each normal mode and correlated these values with the SERS effect. Experimental UV-Vis spectra were obtained and charge transfer bands were assigned. Good agreement between the calculated and experimental values for the vibrational and UV-Vis spectra was obtained.

  17. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

    PubMed

    Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

    2016-11-08

    Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

  18. From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations.

    PubMed

    Schwierz, Nadine; Frost, Christina V; Geissler, Phillip L; Zacharias, Martin

    2017-02-02

    Secondary nucleation pathways in which existing amyloid fibrils catalyze the formation of new aggregates and neurotoxic oligomers are of immediate importance for the onset and progression of Alzheimer's disease. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to study surface-activated secondary nucleation pathways at the extended lateral β-sheet surface of a preformed Aβ9-40 filament. Calculation of free-energy profiles allows us to determine binding free energies and conformational intermediates for nucleation complexes consisting of 1-4 Aβ peptides. In addition, we combine the free-energy profiles with position-dependent diffusion profiles to extract complementary kinetic information and macroscopic growth rates. Single monomers bind to the β-sheet surface in a disordered, hydrophobically collapsed conformation, whereas dimers and larger oligomers can retain a cross-β conformation resembling a more ordered fibril structure. The association processes during secondary nucleation follow a dock/lock mechanism consisting of a fast initial encounter phase (docking) and a slow structural rearrangement phase (locking). The major driving forces for surface-activated secondary nucleation are the release of a large number of hydration water molecules and the formation of hydrophobic interface contacts, the latter being in contrast to the elongation process at filament tips, which is dominated by the formation of stable and highly specific interface hydrogen bonds. The calculated binding free energies and the association rates for the attachment of Aβ monomers and oligomers to the extended lateral β-sheet surface of the filament seed are higher compared to those for elongation at the filament tips, indicating that secondary nucleation pathways can become important once a critical concentration of filaments has formed.

  19. Probing the Huntingtin 1-17 membrane anchor on a phospholipid bilayer by using all-atom simulations.

    PubMed

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S; Bechinger, Burkhard; Mousseau, Normand

    2015-03-10

    Mislocalization and aggregation of the huntingtin protein are related to Huntington's disease. Its first exon-more specifically the first 17 amino acids (Htt17)-is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin's activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties-order parameter, thickness, and area per lipid-of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions.

  20. Membrane binding and insertion of a pHLIP peptide studied by all-atom molecular dynamics simulations.

    PubMed

    Deng, Yonghua; Qian, Zhenyu; Luo, Yin; Zhang, Yun; Mu, Yuguang; Wei, Guanghong

    2013-07-12

    Recent experiments in function mechanism study reported that a pH low-insertion peptide (pHLIP) can insert into a zwitterionic palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer at acidic pH while binding to the bilayer surface at basic pH. However, the atomic details of the pH-dependent interaction of pHLIP with a POPC bilayer are not well understood. In this study, we investigate the detailed interactions of pHLIP with a POPC bilayer at acidic and basic pH conditions as those used in function mechanism study, using all-atom molecular dynamics (MD) simulations. Simulations have been performed by employing the initial configurations, where pHLIP is placed in aqueous solution, parallel to bilayer surface (system S), partially-inserted (system P), or fully-inserted (system F) in POPC bilayers. On the basis of multiple 200-ns MD simulations, we found (1) pHLIP in system S can spontaneously insert into a POPC bilayer at acidic pH, while binding to the membrane surface at basic pH; (2) pHLIP in system P can insert deep into a POPC bilayer at acidic pH, while it has a tendency to exit, and stays at bilayer surface at basic pH; (3) pHLIP in system F keeps in an α-helical structure at acidic pH while partially unfolding at basic pH. This study provides at atomic-level the pH-induced insertion of pHLIP into POPC bilayer.

  1. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    NASA Astrophysics Data System (ADS)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  2. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  3. Wilsonville SRC-I pilot plant: I. Fractionation area corrosion studies; II. Hot vs. normal separation mode of operation

    SciTech Connect

    Lee, J.M.

    1981-04-01

    Extensive corrosion studies in solvent recovery columns have been done with different coals (mainly Kentucky number 9 Lafayette, Dotiki and Fies). Sodium carbonate (0.1 to 1.1% of coal) was added as neutralizer to control corrosion rate. Chloride balance runs were made for isolation of corrosive streams with high chlorine content. A caustic wash program of inlet streams has been developed for selective treatment of corrosive streams as an alternative means for possible replacement of sodium carbonate addition. High chlorine content coals such as Kentucky number 9 Lafayette and Dotiki (0.2 to 0.3%) were very corrosive, compared to low chlorine content coal, Kentucky number 9 Fies (< 0.1%). Sodium carbonate addition (0.6 to 0.7% of coal) reduced corrosion rate from 500 MPY to an insignificant level of less than 5 MPY. Caustic wash of solvents could reduce corrosion rate by 50%, removing most corrosive compounds present in the 440 to 480/sup 0/F boiling fraction. Extensive studies for the hot separator mode of operation have been done as a means of saving substantial energy by elimination of dissolver slurry cooling (0.3 MM Btu/hr) and reheating for solvent recovery (1 MM Btu/h). Impacts of the hot separator mode on plant operability, product quality and Kerr-McGee CSD Unit recovery have been studied. The hot separator mode of operation was carried out by controlling the V103 temperature to 740/sup 0/F. It was observed that preasphaltene contents increased in the SRC products such as V110 L/F SRC and CSD feed; CSD unit recovery was not affected significantly; solvent quality was not affected significantly.

  4. Reduction of timing jitter and intensity noise in normal-dispersion passively mode-locked fiber lasers by narrow band-pass filtering.

    PubMed

    Qin, Peng; Song, Youjian; Kim, Hyoji; Shin, Junho; Kwon, Dohyeon; Hu, Minglie; Wang, Chingyue; Kim, Jungwon

    2014-11-17

    Fiber lasers mode-locked with normal cavity dispersion have recently attracted great attention due to large output pulse energy and femtosecond pulse duration. Here we accurately characterized the timing jitter of normal-dispersion fiber lasers using a balanced cross-correlation method. The timing jitter characterization experiments show that the timing jitter of normal-dispersion mode-locked fiber lasers can be significantly reduced by using narrow band-pass filtering (e.g., 7-nm bandwidth filtering in this work). We further identify that the timing jitter of the fiber laser is confined in a limited range, which is almost independent of cavity dispersion map due to the amplifier-similariton formation by insertion of the narrow bandpass filter. The lowest observed timing jitter reaches 0.57 fs (rms) integrated from 10 kHz to 10 MHz Fourier frequency. The rms relative intensity noise (RIN) is also reduced from 0.37% to 0.02% (integrated from 1 kHz to 5 MHz Fourier frequency) by the insertion of narrow band-pass filter.

  5. Passively Q-switched mode-locking Erbium-doped fiber laser with net-normal dispersion using nonlinear polarization rotation technique

    NASA Astrophysics Data System (ADS)

    Wang, L. Y.; Xu, W. C.; Luo, Z. C.; Cao, W. J.; Luo, A. P.; Dong, J. L.; Wang, H. Y.

    2011-10-01

    We experimentally demonstrate a passively Q-switched mode-locking (QML) operation in an Erbium-doped fiber ring laser with net normal dispersion by using nonlinear polarization rotation technique. A 2 m long section of dispersion compensating fiber (DCF) with extra large positive dispersion was inserted into the cavity to ensure the fiber laser working in the region of net positive dispersion. By carefully adjusting the polarization controller, both uniform dissipative mode-locking pulses with fundamental repetition rate and QML pulse trains with tunable repetition rate from 71.58 to 98.83 kHz are achieved. It is found that the QML operation is caused by the interaction between the polarization state of the pulse and the intracavity polarizer.

  6. Application of normal mode theory to seismic source and structure problems: Seismic investigations of upper mantle lateral heterogeneity. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Okal, E. A.

    1978-01-01

    The theory of the normal modes of the earth is investigated and used to build synthetic seismograms in order to solve source and structural problems. A study is made of the physical properties of spheroidal modes leading to a rational classification. Two problems addressed are the observability of deep isotropic seismic sources and the investigation of the physical properties of the earth in the neighborhood of the Core-Mantle boundary, using SH waves diffracted at the core's surface. Data sets of seismic body and surface waves are used in a search for possible deep lateral heterogeneities in the mantle. In both cases, it is found that seismic data do not require structural differences between oceans and continents to extend deeper than 250 km. In general, differences between oceans and continents are found to be on the same order of magnitude as the intrinsic lateral heterogeneity in the oceanic plate brought about by the aging of the oceanic lithosphere.

  7. Global normal mode planetary wave activity: a study using TIMED/SABER observations from the stratosphere to the mesosphere-lower thermosphere

    NASA Astrophysics Data System (ADS)

    John, Sherine Rachel; Kumar, Karanam Kishore

    2016-12-01

    A comprehensive study of three normal mode travelling planetary waves, namely the quasi-16, -10 and -5 day waves, is carried out globally using 5 years (2003-2007) of TIMED/SABER temperature measurements from the stratosphere to the mesosphere-lower thermosphere (MLT) by employing the two dimensional Fourier decomposition technique. From preliminary analysis, it is found that significant amplitudes of normal modes are confined to wave numbers-2 (westward propagating modes) to 2 (eastward propagating modes). The westward propagating quasi 16-day waves with zonal wave number 1 (W1; W1 refers to westward propagating wave with zonal wave number 1) peaks over winter-hemispheric high latitudes with northern hemisphere (NH) having higher amplitudes as compared to their southern hemispheric (SH) counterpart. The W1 quasi 16-day waves exhibit a double peak structure in altitude over winter hemispheric high latitudes. The eastward propagating quasi 16-day waves with wave number 1 (E1; E1 refers to eastward propagating wave with zonal wave number 1) exhibits similar features as that of W1 waves in the NH. In contrast, the E1 quasi 16-day waves in the SH show larger amplitudes as compared to the W1 waves and they do not exhibit double peak structure in altitude. Similar to the quasi 16-day waves, the quasi 10- and 5-day wave amplitudes with respect to their wavenumbers are delineated. Unlike quasi-16 and -10 day waves, quasi-5 day waves peak during vernal equinox both in the SH and NH. The peak activity of the W1 quasi-5 day wave is centered around 40°N and 40°S exhibiting symmetry with respect to the equator. A detailed discussion on the height-latitude structure, interannual variability and inter-hemispheric propagation of quasi 16-, 10- and 5-day waves are discussed. The significance of the present study lies in establishing the 5-year climatology of normal mode planetary waves from the stratosphere to the MLT region including their spatial-temporal evolution, which are

  8. Normal mode analysis of a rotating group of lashed turbine blades by substructures. [calculations for blades at rest and at operating speed

    NASA Technical Reports Server (NTRS)

    Filstrup, A. W.

    1973-01-01

    A group of 5 lashed identical stream turbine blades is studied through the use of single level substructuring using NASTRAN level 15.1. An altered version, similar to DMAP Program Number 3 of the NASTRAN Newsletter, of Rigid Format 13.0 was used. Steady-state displacements and stresses due to centrifugal loads are obtained both without and with consideration of differential stiffness. The normal mode calculations were performed for blades at rest and at operating speed. Substructuring lowered the computation costs of the analysis by a factor of four.

  9. Intramolecular vibrations in low-frequency normal modes of amino acids: L-alanine in the neat solid state.

    PubMed

    Zhang, Feng; Wang, Houng-Wei; Tominaga, Keisuke; Hayashi, Michitoshi

    2015-03-26

    This paper presents a theoretical analysis of the low-frequency phonons of L-alanine by using the solid-state density functional theory at the Γ point. We are particularly interested in the intramolecular vibrations accessing low-frequency phonons via harmonic coupling with intermolecular vibrations. A new mode-analysis method is introduced to quantify the vibrational characteristics of such intramolecular vibrations. We find that the torsional motions of COO(-) are involved in low-frequency phonons, although COO(-) is conventionally assumed to undergo localized torsion. We also find the broad distributions of intramolecular vibrations relevant to important functional groups of amino acids, e.g., the COO(-) and NH3(+) torsions, in the low-frequency phonons. The latter finding is illustrated by the concept of frequency distribution of vibrations. These findings may lead to immediate implications in other amino acid systems.

  10. Simple all-PM-fiber laser system seeded by an all-normal-dispersion oscillator mode-locked with a nonlinear optical loop mirror

    NASA Astrophysics Data System (ADS)

    Szczepanek, Jan; Kardaś, Tomasz; Nejbauer, Michał; Radzewicz, Czesław; Stepanenko, Yuriy

    2016-03-01

    In this paper we report an all-PM-fiber laser amplifier system seeded by an all-normal-dispersion oscillator mode-locked with a Nonlinear Optical Loop Mirror (NOLM). The presented all-normal-dispersion cavity works in a dissipative soliton regime and delivers highly-chirped, high energy pulses above 2.5 nJ with full width at half maximum below 200 fs. The ultrafast oscillator followed by the all-PM-fiber amplifying stage delivered pulses with the energy of 42.5 nJ and time duration below 190 fs. The electrical field of optical pulses from the system was reconstructed using the SPIDER technique. The influence of nonlinear processes on the pulse temporal envelope was investigated.

  11. All-atom Molecular-level Computational Simulations of Planar Longitudinal Shockwave Interactions with Polyurea, Soda-lime Glass and Polyurea/Glass Interfaces

    DTIC Science & Technology

    2014-01-01

    All-atom molecular-level computational simulations of planar longitudinal shockwave interactions with polyurea, soda-lime glass and polyurea/glass...sandwich structures under dynamic-loading conditions involving propagation of planar longitudinal shockwaves . Design/methodology/approach – The problem...of shockwave generation, propagation and interaction with material boundaries is investigated using non-equilibrium molecular dynamics. The results

  12. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  13. Characteristic fault zone architectures as result of different failure modes: first results from scale models of normal faulting

    NASA Astrophysics Data System (ADS)

    Kettermann, Michael; Urai, Janos L.

    2014-05-01

    It is known that fault zone architecture and structural style vary distinctly between tensile and shear failure modes, with strong effects on the associated fluid flow properties. A systematically comparative study in 3D has not been done so far, though. Inferring transport properties in sub-seismic scale from fault network geometries would have important applications in brittle lithologies such as carbonates or basalts. We present a method to investigate the structural properties of fault networks in 3D using cohesive hemihydrate powder (CaSO4 * 1/2H2O) embedded in two layers of dry fine grained sand. The material properties of the sand and powder are well known from previous studies. By increasing the overburden stress the failure mode of the powder can be changed from tensile to shear failure. Using hemihydrate powder allows us to harden and excavate the layer after the deformation by wetting the model slowly and brushing off the overburden sand. Visual investigation of the 3D structures is then possible in very high resolution. Analyses using photographs and 3D models from photogrammetry include qualitative observations as well as measurements of e.g. strike of fault segments, fault dip or graben width. We show a total of eight experiments that produce graben faults at four different overburden stresses (0, 1.5, 3, 6 cm overburden thickness) and at two increasing stages of strain (3 and 5 mm). In this set of models we describe two structural domains that show characteristic differences in their defining attributes. The tensile domain at small overburden stress (0 and 1.5 cm overburden) shows strongly dilatant faults with open fissures, vertical faults and large changes in strike at segment boundaries. The shear domain, formed by larger overburden stress (6 cm overburden), shows shallower fault dips around 65° with striations, numerous undulating fault branches and splays with low-angle fault intersections. Models with 3 cm overburden show a hybrid failure type

  14. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  15. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  16. Using the normal-mode method of probing the infrasonic propagation for purposes of the comprehensive nuclear-test-ban treaty

    NASA Astrophysics Data System (ADS)

    Ponomarev, E. A.; Rudenko, G. V.; Sorokin, A. G.; Dmitrienko, I. S.; Lobycheva, I. Yu.; Baryshnikov, A. K.

    2006-03-01

    We examine the problem of assessing the state of Atmospheric Acoustic Channels, that is, of the possible propagation paths of acoustic signals, based on using a priori information about atmospheric conditions. It is concluded that this can only be best accomplished through the use of global atmospheric models. Based on the normal-mode method, an analysis is made of the generalized characteristics of atmospheric waveguide such as the location of the waveguide boundaries, the mode composition, and the transmissivity of the waveguide upper and lower boundaries. The method can be used to analyze the particular paths as well as the overall situation around a given point. Furthermore, all the surrounding space (extending as far as the whole of the geosphere) is divided into regions that are accessible and inaccessible for a given mode. To determine the particular height distributions of physical characteristics over the entire path, the NRLMSISE-2000 atmosphere model and the HWM-93 wind model are used. Some of the calculated paths are compared with the known source and receiver positions and with observational results. It is concluded that the method can be used in a general assessment of the accessibility of a given region for acoustic monitoring; however, it is not sufficiently reliable to permit real-time predictions.

  17. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes

    NASA Astrophysics Data System (ADS)

    Comandi, G. L.; Chiofalo, M. L.; Toncelli, R.; Bramanti, D.; Polacco, E.; Nobili, A. M.

    2006-03-01

    Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration η between two test bodies—of different compositions, falling in the gravitational field of a source mass—if the measurement is made to the level of η ≃10-13 or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the "Galileo Galilei on the ground" (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation—in particular, its normal modes (Part I) and rejection of common mode effects (Part II)—can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.

  18. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes

    SciTech Connect

    Comandi, G.L.; Chiofalo, M.L.; Toncelli, R.; Bramanti, D.; Polacco, E.; Nobili, A.M.

    2006-03-15

    Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration {eta} between two test bodies-of different compositions, falling in the gravitational field of a source mass--if the measurement is made to the level of {eta}{approx_equal}10{sup -13} or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the 'Galileo Galilei on the ground' (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation-in particular, its normal modes (Part I) and rejection of common mode effects (Part II)-can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.

  19. Normal mode sensitivity to Earth's D″ layer and topography on the core-mantle boundary: what we can and cannot see

    NASA Astrophysics Data System (ADS)

    Koelemeijer, P. J.; Deuss, A.; Trampert, J.

    2012-07-01

    The core-mantle boundary (CMB) is Earth's most profound internal boundary separating the liquid iron outer core and the solid silicate mantle. The detailed structure near the CMB has a major influence on mantle convection and the evolution of the core. Seismic observations, such as topography on the CMB, thin ultra-low velocity zones (ULVZs), seismic anisotropy and the anticorrelation between shear wave and bulk sound velocity heterogeneities have mainly been made using body waves and are still poorly constrained. We investigate the sensitivity of Earth's free oscillations to these features and specifically show how large individual anomalies must be for them to be observable. In addition, we discuss the possible trade-offs between these different lowermost mantle structures. Although modes have strong sensitivity to all the structures inserted, the results illustrate the limits of what normal modes can resolve. Our tests show that: (i) Even small scale features, such as ULVZs, with a thickness larger than 19 km can be observed as long as their distribution contains a long wavelength component. (ii) The peak-to-peak amplitude of CMB topography has a larger influence than its pattern and has to be smaller than 5 km to fit the data. (iii) The effect of scaling between shear wave velocity and density anomalies is less constrained, but a laterally varying pattern is implied by a simple test, suggesting the presence of chemical variations. (iv) A strong trade-off exists between anisotropy in compressional wave velocity and incidence angle whereas shear wave anisotropy is less observable. These findings provide valuable information for future normal mode studies on structures in Earth's lowermost mantle and their trade-offs.

  20. An anisotropic shear velocity model of the Earth's mantle using normal modes, body waves, surface waves and long-period waveforms

    NASA Astrophysics Data System (ADS)

    Moulik, P.; Ekström, G.

    2014-12-01

    We use normal-mode splitting functions in addition to surface wave phase anomalies, body wave traveltimes and long-period waveforms to construct a 3-D model of anisotropic shear wave velocity in the Earth's mantle. Our modelling approach inverts for mantle velocity and anisotropy as well as transition-zone discontinuity topographies, and incorporates new crustal corrections for the splitting functions that are consistent with the non-linear corrections we employ for the waveforms. Our preferred anisotropic model, S362ANI+M, is an update to the earlier model S362ANI, which did not include normal-mode splitting functions in its derivation. The new model has stronger isotropic velocity anomalies in the transition zone and slightly smaller anomalies in the lowermost mantle, as compared with S362ANI. The differences in the mid- to lowermost mantle are primarily restricted to features in the Southern Hemisphere. We compare the isotropic part of S362ANI+M with other recent global tomographic models and show that the level of agreement is higher now than in the earlier generation of models, especially in the transition zone and the lower mantle. The anisotropic part of S362ANI+M is restricted to the upper 300 km in the mantle and is similar to S362ANI. When radial anisotropy is allowed throughout the mantle, large-scale anisotropic patterns are observed in the lowermost mantle with vSV > vSH beneath Africa and South Pacific and vSH > vSV beneath several circum-Pacific regions. The transition zone exhibits localized anisotropic anomalies of ˜3 per cent vSH > vSV beneath North America and the Northwest Pacific and ˜2 per cent vSV > vSH beneath South America. However, small improvements in fits to the data on adding anisotropy at depth leave the question open on whether large-scale radial anisotropy is required in the transition zone and in the lower mantle. We demonstrate the potential of mode-splitting data in reducing the trade-offs between isotropic velocity and

  1. State distributions in two-dimensional parameter spaces of a nonlinear optical loop mirror-based, mode-locked, all-normal-dispersion fiber laser.

    PubMed

    Cai, Jun-Hao; Chen, He; Chen, Sheng-Ping; Hou, Jing

    2017-02-20

    We present the results of numerical simulations of dissipative soliton generation using nonlinear Schrödinger equations in an all-normal-dispersion (ANDi) mode-locked fiber laser based on a nonlinear optical loop mirror (NOLM). Firstly, systematic and computationally intensive analysis of the pulse state distributions in two-dimensional parameter spaces of an ANDi fiber laser was conducted. In addition, we determined that unstable non-vanishing regions including pulsation and noise-like pulses are directly related to the saturable absorptions of NOLMs and that two critical filter bandwidths separate those regions from stable ones. Finally, we found that the multi-pulsing power threshold can be maximized by using an optimal optical filter bandwidth.

  2. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.

    PubMed

    Clementi, Cecilia; García, Angel E; Onuchic, José N

    2003-02-21

    Experimental and theoretical results suggest that, since proteins are energetically minimally frustrated, the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble and on-pathway intermediate states in protein folding. Although the central role of native state topology in determining the folding mechanism is thought to be a quite general result-at least for small two-state folding proteins-there are remarkable exceptions. Recent experimental findings have shown that topology alone cannot always determine the folding mechanism, and demonstrated that the balance between topology and energetics is very delicate. This balance seems to be particularly critical in proteins with a highly symmetrical native structure, such as proteins L and G, which have similar native structure topology but fold by different mechanisms. Simplified, C(alpha)-atom only protein models have shown not be sufficient to differentiate these mechanisms. An all-atom Gō model provides a valuable intermediate model between structurally simplified protein representations and all-atom protein simulations with explicit/implicit solvent descriptions. We present here a detailed study of an all-atom Gō-like representation of protein L, in close comparison with the experimental results and with the results obtained from a simple C(alpha)-atom representation of the same protein. We also perform simulations for protein G, where we obtain a folding mechanism in which the protein symmetry is broken exactly in the opposite way to protein L as has been observed experimentally. A detailed analysis for protein L also shows that the role of specific residues is correctly and quantitatively reproduced by the all-atom Gō model over almost the entire protein.

  3. All-atom effective models for first-principles simulations of the temperature-dependent behavior of complex ferroelectric oxides

    NASA Astrophysics Data System (ADS)

    Iniguez, Jorge; Wojdel, Jacek C.; Hermet, Patrick; Ghosez, Philippe; Zanolli, Zeila

    2011-03-01

    Since its introduction in the 90's, the first-principles effective-Hamiltonian method has been successfully used to simulate temperature-driven phenomena in increasingly complex ferroelectrics, from classic compound BaTi O3 to multiferroic BiFe O3 . Currently, the emergence of nano-structured materials -- e.g., in the form of ultra-thin films or short-period superlattices -- poses new challenges to the simulations, and the development of predictive models seems to require a reconsideration of the traditional approach. Of particular interest are cases in which novel interfacial effects determine the behavior, as in the PbTi O3 - SrTi O3 superlattices of Bousquet et al. [Nature 452, 7188 (2008)]. In such situations a large number of structural distortions may become active, and it may be difficult to decide which ones need to be included in the model. In order to tackle these difficulties, we are extending the first-principles effective-Hamiltonian method so as to retain a full atomistic description of the material, thus removing the so-called local mode approximation. I will describe our new approach and show preliminary results for PbTi O3 . Work funded by the Spanish DGI and the FP7 program of the EU.

  4. Putative model for heat shock protein 70 complexation with receptor of advanced glycation end products through fluorescence proximity assays and normal mode analyses.

    PubMed

    Grunwald, Marcelo Sartori; Ligabue-Braun, Rodrigo; Souza, Cristiane Santos; Heimfarth, Luana; Verli, Hugo; Gelain, Daniel Pens; Moreira, José Cláudio Fonseca

    2017-01-01

    Extracellular heat shock protein 70 (HSP70) is recognized by receptors on the plasma membrane, such as Toll-like receptor 4 (TLR4), TLR2, CD14, and CD40. This leads to activation of nuclear factor-kappa B (NF-κB), release of pro-inflammatory cytokines, enhancement of the phagocytic activity of innate immune cells, and stimulation of antigen-specific responses. However, the specific characteristics of HSP70 binding are still unknown, and all HSP70 receptors have not yet been described. Putative models for HSP70 complexation to the receptor for advanced glycation endproducts (RAGEs), considering both ADP- and ATP-bound states of HSP70, were obtained through molecular docking and interaction energy calculations. This interaction was detected and visualized by a proximity fluorescence-based assay in A549 cells and further analyzed by normal mode analyses of the docking complexes. The interacting energy of the complexes showed that the most favored docking situation occurs between HSP70 ATP-bound and RAGE in its monomeric state. The fluorescence proximity assay presented a higher number of detected spots in the HSP70 ATP treatment, corroborating with the computational result. Normal-mode analyses showed no conformational deformability in the interacting interface of the complexes. Results were compared with previous findings in which oxidized HSP70 was shown to be responsible for the differential modulation of macrophage activation, which could result from a signaling pathway triggered by RAGE binding. Our data provide important insights into the characteristics of HSP70 binding and receptor interactions, as well as putative models with conserved residues on the interface area, which could be useful for future site-directed mutagenesis studies.

  5. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders

    PubMed Central

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-01-01

    It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments. PMID:24187527

  6. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

    PubMed

    Bell, Jeffrey A; Ho, Kenneth L; Farid, Ramy

    2012-08-01

    All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.

  7. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-10-01

    It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments.

  8. Experimental Investigation of Wavelength-Tunable All-Normal-Dispersion Yb-Doped Mode-Locked Fiber Lasers: Compression and Amplification

    NASA Astrophysics Data System (ADS)

    Xiao, Xiao-Sheng; Hua, Yi

    2015-02-01

    Wavelength-tunable ultrashort pulse source with high energy is highly desired for a lot of applications. The wavelength-tunable all-normal-dispersion (ANDi) mode-locked fiber laser, which can be compressed easily and amplified by an all-fiber structure, is a promising seed of such a source with compact structures. The pulse compression and amplification at different center wavelengths (from 1026 to 1058 nm) of the tunable ANDi Ybdoped mode-locked fiber lasers that we previously proposed are experimentally investigated in this work. It is found that, for different wavelengths, the duration and chirp of the direct output pulse from the oscillator vary considerably, however, the duration of compressed pulse fluctuates less. For the amplification process, due to the unflat gain spectrum of Yb-doped fiber, the gain at a short wavelength is larger than that at a long wavelength. Consequently, the trends of spectrum distortions induced by the amplification process are different for different wavelengths. These results and analyses will be helpful for the design of a high-energy and wavelength-tunable ultrashort pulse source based on an ANDi seed.

  9. Supercontinuum generation based on all-normal-dispersion Yb-doped fiber laser mode-locked by nonlinear polarization rotation: Influence of seed's output port

    NASA Astrophysics Data System (ADS)

    Xiao, Xiaosheng; Hua, Yi

    2016-10-01

    All-normal-dispersion (ANDi) mode-locked Yb-doped fiber laser is a promising seed source for supercontinuum (SC) generation, due to its compact structure and broadband output. The influences of output ports of the ANDi laser mode-locked by nonlinear polarization rotation (NPR), on the generated SC are investigated. Two output ports of ANDi laser are considered, one of which is the conventional nonlinear polarization rotation (NPR) port and the other is extracted from a coupler after the NPR port. It is found that, the SC originated from the coupler port is much broader than that from the NPR port, which is validated by lots of experiments with different output parameters. Furthermore, the conclusion is verified and generalized to general ANDi lasers by numerical simulations, because the output pulse from coupler port could be cleaner than that from NPR port. Besides, there are no significant differences in the phase coherence and temporal stability between the SCs generated from both ports. Hence for the SC generation based on ANDi laser, it is preferred to use the pulse of coupler port (i.e. pulse after NPR port) serving as the seed source.

  10. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

    PubMed Central

    2015-01-01

    We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically

  11. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation.

    PubMed

    Zheng, Wenjun; Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant--while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  12. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  13. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  14. Molecular Structures, Vibrational Spectroscopy, and Normal-Mode Analysis of M(2)(C&tbd1;CR)(4)(PMe(3))(4) Dimetallatetraynes. Observation of Strongly Mixed Metal-Metal and Metal-Ligand Vibrational Modes.

    PubMed

    John, Kevin D.; Miskowski, Vincent M.; Vance, Michael A.; Dallinger, Richard F.; Wang, Louis C.; Geib, Steven J.; Hopkins, Michael D.

    1998-12-28

    The nature of the skeletal vibrational modes of complexes of the type M(2)(C&tbd1;CR)(4)(PMe(3))(4) (M = Mo, W; R = H, Me, Bu(t)(), SiMe(3)) has been deduced. Metrical data from X-ray crystallographic studies of Mo(2)(C&tbd1;CR)(4)(PMe(3))(4) (R = Me, Bu(t)(), SiMe(3)) and W(2)(C&tbd1;CMe)(4)(PMe(3))(4) reveal that the core bond distances and angles are within normal ranges and do not differ in a statistically significant way as a function of the alkynyl substituent, indicating that their associated force constants should be similarly invariant among these compounds. The crystal structures of Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) and Mo(2)(C&tbd1;CBu(t)())(4)(PMe(3))(4) are complicated by 3-fold disorder of the Mo(2) unit within apparently ordered ligand arrays. Resonance-Raman spectra ((1)(delta-->delta) excitation, THF solution) of Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) and its isotopomers (PMe(3)-d(9), C&tbd1;CSiMe(3)-d(9), (13)C&tbd1;(13)CSiMe(3)) exhibit resonance-enhanced bands due to a(1)-symmetry fundamentals (nu(a) = 362, nu(b) = 397, nu(c) = 254 cm(-)(1) for the natural-abundance complex) and their overtones and combinations. The frequencies and relative intensities of the fundamentals are highly sensitive to isotopic substitution of the C&tbd1;CSiMe(3) ligands, but are insensitive to deuteration of the PMe(3) ligands. Nonresonance-Raman spectra (FT-Raman, 1064 nm excitation, crystalline samples) for the Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) compounds and for Mo(2)(C&tbd1;CR)(4)(PMe(3))(4) (R = H, D, Me, Bu(t)(), SiMe(3)) and W(2)(C&tbd1;CMe)(4)(PMe(3))(4) exhibit nu(a), nu(b), and nu(c) and numerous bands due to alkynyl- and phosphine-localized modes, the latter of which are assigned by comparisons to FT-Raman spectra of Mo(2)X(4)L(4) (X = Cl, Br, I; L = PMe(3), PMe(3)-d(9))(4) and Mo(2)Cl(4)(AsMe(3))(4). Valence force-field normal-coordinate calculations on the model compound Mo(2)(C&tbd1;CH)(4)P(4), using core force constants transferred from a calculation

  15. Vibrational normal modes calculation in the crystalline state of methylated monosaccharides: Anomers of the methyl-D-glucopyranoside and methyl-D-xylopyranoside molecules.

    PubMed

    Taleb-Mokhtari, Ilham Naoual; Lazreg, Abbassia; Sekkal-Rahal, Majda; Bestaoui, Noreya

    2016-01-15

    A structural investigation of the organic molecules is being carried out using vibrational spectroscopy. In this study, normal co-ordinate calculations of anomers of the methyl-D-glucopyranoside and methyl-β-D-xylopyranoside in the crystalline state have been performed using the modified Urey-Bradley-Shimanouchi force field (mUBSFF) combined with an intermolecular potential energy function. The latter includes Van der Waals interactions, electrostatic terms, and explicit hydrogen bond functions. The vibrational spectra of the compounds recorded in the crystalline state, in the 4000-500 cm(-1) spectral region for the IR spectra, and in the 4000-20 cm(-1) spectral range for the Raman spectra are presented. After their careful examination, several differences in the intensities and frequency shifts have been observed. The theoretical spectra have been obtained after a tedious refinement of the force constants. Thus, on the basis of the obtained potential distribution, each observed band in IR and in Raman has been assigned to a vibrational mode. The obtained results are indeed in agreement with those observed experimentally and thus confirm the previous assignments made for the methyl-α and β-D-glucopyranoside, as well as for the methyl-β-D-xylopyranoside.

  16. Mode-locking pulse generation with MoS2-PVA saturable absorber in both anomalous and ultra-long normal dispersion regimes.

    PubMed

    Ahmed, M H M; Latiff, A A; Arof, H; Harun, S W

    2016-05-20

    We experimentally demonstrate a stable and simple mode locked erbium doped fiber laser (EDFL) utilizing passive few-layer molybdenum disulfide (MoS2) as a saturable absorber. The MoS2 is obtained by liquid phase exfoliation before it is embedded in a polymer composite film and then inserted in the laser cavity. A stable soliton pulse train started at a low threshold pump power of 20 mW in the anomalous dispersion regime after fine-tuning the rotation of the polarization controller. The central wavelength, 3 dB bandwidth, pulse width, and repetition rate of the soliton pulses are 1574.6 nm, 9.5 nm, 790 fs, and 29.5 MHz, respectively. By inserting a 850 m long dispersion shifted fiber (DSF) in the cavity, a dissipative soliton with square pulse train is obtained in the normal dispersion regime where the operating wavelength is centered at 1567.44 nm with a 3 dB bandwidth of 19.68 nm. The dissipative soliton pulse has a pulse width of 90 ns at a low repetition rate of 231.5 kHz due to the long DSF used. These results are a contribution to the pool of knowledge in nonlinear optical properties of two-dimensional nanomaterials especially for ultrafast photonic applications.

  17. Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: a molecular dynamics and normal mode analysis study.

    PubMed

    Vemparala, Satyavani; Mehrotra, Sonali; Balaram, Hemalatha

    2011-05-01

    Enzymes from thermophiles are poorly active at temperatures at which their mesophilic homologs exhibit high activity and attain corresponding active states at high temperatures. In this study, comparative molecular dynamics (MD) simulations, supplemented by normal mode analysis, have been performed on an enzyme Adenylosuccinate synthetase (AdSS) from E. coli (mesophilic) and P. horikoshii (thermophilic) systems to understand the effects of loop dynamics on thermal stability of AdSS. In mesophilic AdSS, both ligand binding and catalysis are facilitated through the coordinated movement of five loops on the protein. The simulation results suggest that thermophilic P. horikoshii preserves structure and catalytic function at high temperatures by using the movement of only a subset of loops (two out of five) for ligand binding and catalysis unlike its mesophilic counterpart in E. coli. The pre-arrangement of the catalytic residues in P. horikoshii is well-preserved and salt bridges remain stable at high temperature (363K). The simulations suggest a general mechanism (including pre-arrangement of catalytic residues, increased polar residue content, stable salt bridges, increased rigidity, and fewer loop movements) used by thermophilic enzymes to preserve structure and be catalytically active at elevated temperatures.

  18. A normal-mode formula for the derivative of a waveguide pressure field with respect to an arbitrary three-dimensional sound speed perturbation

    NASA Astrophysics Data System (ADS)

    Thode, Aaron

    2003-10-01

    Semi-analytic expressions are derived for the first order derivative of a pressure field in a laterally homogeneous depth waveguide, with respect to an arbitrary three-dimensional refractive index perturbation in either the water column or ocean bottom. These expressions for the environmental derivative, derived using an adjoint method, require a three-dimensional spatial correlation between two Greens functions, weighted by an environmental parameter basis function, with the Greens functions expressed in terms of normal modes. When a particular set of orthogonal spatial basis functions is chosen, the three-dimensional spatial integral can be converted into a set of one-dimensional integrations over depth and azimuth. The use of the orthogonal basis permits environmental derivatives to be computed for any arbitrary sound-speed perturbation. To illustrate the formulas, a sensitivity study is presented that explores the impact of three-dimensional plane wave and cylindrical perturbations on the environmental derivative. Under certain circumstances it is found that perturbation components outside the vertical plane connecting the source and receiver have non-negligible effects on the pressure derivative. Potential applications of these formulas include benchmarking three-dimensional propagation codes, computing Cramer-Rao bounds for three-dimensional environmental parameter estimates, and potentially inverting for small three-dimensional refractive index distributions.

  19. Computational modeling of the Fc αRI receptor binding in the Fc α domain of the human antibody IgA: Normal Modes Analysis (NMA) study

    NASA Astrophysics Data System (ADS)

    Jayasinghe, Manori; Posgai, Monica; Tonddast-Navaei, Sam; Ibrahim, George; Stan, George; Herr, Andrew; George Stan Group Collaboration; Herr's Group Team

    2014-03-01

    Fc αRI receptor binding in the Fc α domain of the antibody IgA triggers immune effector responses such as phagocytosis and antibody-dependent cell-mediated cytotoxicity in eukaryotic cells. Fc α is a dimer of heavy chains of the IgA antibody and each Fc α heavy chain which consisted of two immunoglobulin constant domains, CH2 and CH3, can bind one Fc αRI molecule at the CH2-CH3 interface forming a 2:1 stoichiometry. Experimental evidences confirmed that Fc αRI binding to the Fc α CH2-CH3 junction altered the kinetics of HAA lectin binding at the distant IgA1 hinge. Our focus in this research was to understand the conformational changes and the network of residues which co-ordinate the receptor binding dynamics of the Fc α dimer complex. Structure-based elastic network modeling was used to compute normal modes of distinct Fc α configurations. Asymmetric and un-liganded Fc α configurations were obtained from the high resolution crystal structure of Fc α-Fc αRI 2:1 symmetric complex of PDB ID 1OW0. Our findings confirmed that Fc αRI binding, either in asymmetric or symmetric complex with Fc α, propagated long-range conformational changes across the Fc domains, potentially also impacting the distant IgA1 hinge.

  20. Vibrational normal modes calculation in the crystalline state of methylated monosaccharides: Anomers of the methyl-D-glucopyranoside and methyl-D-xylopyranoside molecules

    NASA Astrophysics Data System (ADS)

    Taleb-Mokhtari, Ilham Naoual; Lazreg, Abbassia; Sekkal-Rahal, Majda; Bestaoui, Noreya

    2016-01-01

    A structural investigation of the organic molecules is being carried out using vibrational spectroscopy. In this study, normal co-ordinate calculations of anomers of the methyl-D-glucopyranoside and methyl-β-D-xylopyranoside in the crystalline state have been performed using the modified Urey-Bradley-Shimanouchi force field (mUBSFF) combined with an intermolecular potential energy function. The latter includes Van der Waals interactions, electrostatic terms, and explicit hydrogen bond functions. The vibrational spectra of the compounds recorded in the crystalline state, in the 4000-500 cm- 1 spectral region for the IR spectra, and in the 4000-20 cm- 1 spectral range for the Raman spectra are presented. After their careful examination, several differences in the intensities and frequency shifts have been observed. The theoretical spectra have been obtained after a tedious refinement of the force constants. Thus, on the basis of the obtained potential distribution, each observed band in IR and in Raman has been assigned to a vibrational mode. The obtained results are indeed in agreement with those observed experimentally and thus confirm the previous assignments made for the methyl-α and β-D-glucopyranoside, as well as for the methyl-β-D-xylopyranoside.

  1. Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.

    PubMed

    Wambo, Thierry O; Chen, Liao Y; McHardy, Stanton F; Tsin, Andrew T

    2016-01-01

    Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases.

  2. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-08

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups.

  3. Coulombic free energy and salt ion association per phosphate of all-atom models of DNA oligomer: dependence on oligomer size.

    PubMed

    Shkel, Irina A; Record, M Thomas

    2012-08-23

    We investigate how the coulombic Gibbs free energy and salt ion association per phosphate charge of DNA oligomers vary with oligomer size (i.e. number of charged residues ∣ZD∣) at 0.15 M univalent salt by non-linear Poisson Boltzmann (NLPB) analysis of all-atom DNA models. Calculations of these quantities ([Formula: see text], [Formula: see text]) are performed for short and long double-stranded (ds) and single-stranded (ss) DNA oligomers, ranging from 4 to 118 phosphates (ds) and from 2 to 59 phosphates (ss). Behaviors of [Formula: see text] and [Formula: see text] as functions of ∣ZD∣ provide a measure of the range of the coulombic end effect and determine the size of an oligomer at which an interior region with the properties (per charge) of the infinite-length polyelectrolyte first appears. This size (10-11 phosphates at each end for ds DNA and 6-9 for ss DNA at 0.15 M salt) is in close agreement with values obtained previously by Monte Carlo and NLPB calculations for cylindrical models of polyions, and by analysis of binding of oligocations to DNA oligomers. Differences in [Formula: see text] and in [Formula: see text] between ss and ds DNA are used to predict effects of oligomeric size and salt concentration on duplex stability in the vicinity of 0.15 M salt. Results of all-atom calculations are compared with results of less structurally detailed models and with experimental data.

  4. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

    NASA Astrophysics Data System (ADS)

    Wallace, Jason A.; Shen, Jana K.

    2012-11-01

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  5. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

    PubMed

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-07

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  6. All-atom ab initio native structure prediction of a mixed fold (1FME): a comparison of structural and folding characteristics of various beta beta alpha miniproteins.

    PubMed

    Kim, Eunae; Jang, Soonmin; Pak, Youngshang

    2009-11-21

    We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold beta beta alpha miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other beta beta alpha miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue beta beta alpha miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1-->Glu1 and Ile7-->Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I(') turn (1FME) was well reproduced with the present simulation.

  7. Normal-mode frequency band view of the Off-the-West-Coast of Northern Sumatra Earthquake of April 11, 2012

    NASA Astrophysics Data System (ADS)

    Igarashi, M.; Tanimoto, T.

    2012-12-01

    Many studies with body-wave and long-period surface wave analyses on the Off-the-West-coast of Northern Sumatra Earthquake of April 11, 2012, have already pointed out complexities of this event (e.g., Meng et al., 2012). A sequence of events with fairly wide spatial and temporal extent are clearly needed to explain many facets of seismic data. In this study, we attempt to summarize a few distinct features from the normal-mode frequency band (0.3-2.0 mHz) which are obviously much simpler by their long wavelength and long periods. We analyzed long-period seismic data from STS1 and KS54000 sensors for the first 12 hours of the main event using the time-domain waveform fitting technique (Tanimoto, et al., 2012). Adoption of this short time series is partly to avoid uncertain Q parameters on amplitudes but also to avoid the effects from two earthquakes in Oregon (Mw6.0) and Mexico (Mw6.7) that occurred about 23rd hour on the same day. These events are much smaller but their effects cannot be ignored in seismic stations in North America. Two major events reported by the Global CMT project, the Mw8.6 main shock and the Mw8.2 aftershock that occurred two hours later, are clearly not sufficient to explain the amplitude data at about 1 mHz (0.6-1.5 mHz). Synthetic seismograms for the two events under-predicts data by about 30 percent. Amplitudes also show two-theta azimuthal variation that indicates a necessity of at least one hidden event (if not rupture propagation). This necessity has already been pointed out by various groups (e.g., Duputel et al., 2012, Shao et al., 2012). Duputel et al. (2012), for example, reports that the Mw8.6 main event by GCMT should be split up by two large events, the Mw8.5 main event and Mw8.3 event that occurred 70 seconds later. Our analysis shows that their three-source solution, including the Mw8.2 event two hours later, satisfies overall amplitude data in the normal-mode frequency band. However, their solution still shows two

  8. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

    PubMed

    Wang, Jinan; Shao, Qiang; Xu, Zhijian; Liu, Yingtao; Yang, Zhuo; Cossins, Benjamin P; Jiang, Hualiang; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang

    2014-01-09

    Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.

  9. Shape-dependent global deformation modes of large protein structures

    NASA Astrophysics Data System (ADS)

    Miloshevsky, Gennady V.; Hassanein, Ahmed; Jordan, Peter C.

    2010-05-01

    Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT Aa proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT Aa biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following and its simplification using a rotation-translation of protein blocks (RTB), are described and applied to gain insight into the nature of gating transitions in gA and KcsA. These studies demonstrate the severe limitations of standard NMA in characterizing the structural rearrangements associated with gating transitions. Comparison of all-atom and RTB transition pathways in gA clearly illustrates the impact of the rigid protein block approximation and the need to include all degrees of freedom and their relaxation in computational studies of protein gating. The effects of atomic level structure, pH, hydrogen bonding and charged residues on the large-scale conformational changes associated with gating transitions are discussed.

  10. All-atom molecular dynamics study of EAK16 peptide: the effect of pH on single-chain conformation, dimerization and self-assembly behavior.

    PubMed

    Emamyari, Soheila; Fazli, Hossein

    2014-05-01

    Single-chain equilibrium conformation and dimerization of the three types of ionic EAK16 peptide are studied under three pH conditions using all-atom molecular dynamics simulations. It is found that both the single-chain conformation and the dimerization process of EAK16-IV are considerably different from those of the two other types, EAK16-I and EAK16-II. The value of pH is found to have a stronger effect on the single-chain conformation and dimerization of EAK16-IV. It is shown that in addition to the charge pattern on the peptide chains, the size of the side chains of the charged amino acids plays role in the conformation of the peptide chains and their dimerization. The results shed light on the pH-dependent self-assembly behavior of EAK16 peptide in the bulk solution, which has been reported in the literature.

  11. Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field.

    PubMed

    MacCallum, Justin L; Tieleman, D Peter

    2003-11-30

    We calculated the free energy of solvation of the neutral analogs of 18 amino acid side-chains (not including glycine and proline) using the OPLS all-atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid.

  12. Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: insights from all-atom simulations.

    PubMed

    Nam, Hoang Bao; Kouza, Maksim; Zung, Hoang; Li, Mai Suan

    2010-04-28

    Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

  13. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length.

    PubMed

    Wong, Hua; Victor, Jean-Marc; Mozziconacci, Julien

    2007-09-12

    In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.

  14. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  15. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  16. Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model.

    PubMed

    Mitomo, Daisuke; Nakamura, Hironori K; Ikeda, Kazuyoshi; Yamagishi, Akihiko; Higo, Junichi

    2006-09-01

    The src SH3 domain has been known to be a two-state folder near room temperature. However, in a previous study with an all-atom model simulation near room temperature, the transition state of this protein was not successfully detected on a free-energy profile using two axes: the radius of gyration (R(g)) and native contact reproduction ratio (Q value). In this study, we focused on an atom packing effect to characterize the transition state and tried another analysis to detect it. To explore the atom packing effect more efficiently, we introduced a charge-neutralized all-atom model, where all of the atoms in the protein and water molecules were treated explicitly, but their partial atomic charges were set to zero. Ten molecular dynamics simulations were performed starting from the native structure at 300 K, where the simulation length of each run was 90 ns, and the protein unfolded in all runs. The integrated trajectories (10 x 90 = 900 ns) were analyzed by a principal component analysis (PCA) and showed a clear free-energy barrier between folded- and unfolded-state conformational clusters in a conformational space generated by PCA. There were segments that largely deformed when the conformation passed through the free-energy barrier. These segments correlated well with the structural core regions characterized by large phi-values, and the atom-packing changes correlated with the conformational deformations. Interestingly, using the same simulation data, no significant barrier was found in a free-energy profile using the R(g) and Q values for the coordinate axes. These results suggest that the atom packing effect may be one of the most important determinants of the transition state.

  17. Observations of the azimuthal dependence of normal mode coupling below 4 mHz at the South Pole and its nearby stations: Insights into the anisotropy beneath the Transantarctic Mountains

    NASA Astrophysics Data System (ADS)

    Hu, Xiao Gang

    2016-08-01

    Normal mode coupling pair 0S26-0T26 and 0S27-0T27 are significantly present at the South Pole station QSPA after the 2011/03/11 Mw9.1 Tohoku earthquake. In an attempt to determine the mechanisms responsible for the coupling pairs, I first investigate mode observations at 43 stations distributed along the polar great-circle path for the earthquake and observations at 32 Antarctic stations. I rule out the effect of Earth's rotation as well as the effect of global large-scale lateral heterogeneity, but argue instead for the effect of small-scale local azimuthal anisotropy in a depth extent about 300 km. The presence of quasi-Love waveform in 2-5 mHz at QSPA and its nearby stations confirms the predication. Secondly, I analyze normal mode observations at the South Pole location after 28 large earthquakes from 1998 to 2015. The result indicates that the presence of the mode coupling is azimuthal dependent, which is related to event azimuths in -46° to -18°. I also make a comparison between the shear-wave splitting measurements of previous studies and the mode coupling observations of this study, suggesting that their difference can be explained by a case that the anisotropy responsible for the mode coupling is not just below the South Pole location but located below region close to the Transantarctic Mountains (TAM). Furthermore, more signals of local azimuthal anisotropy in normal-mode observations at QSPA and SBA, such as coupling of 0S12-0T11 and vertical polarization anomaly for 0T10, confirms the existence of deep anisotropy close to TAM, which may be caused by asthenospheric mantle flow and edge convection around cratonic keel of TAM.

  18. Comparative HPLC methods for β-blockers separation using different types of chiral stationary phases in normal phase and polar organic phase elution modes. Analysis of propranolol enantiomers in natural waters.

    PubMed

    Morante-Zarcero, Sonia; Sierra, Isabel

    2012-03-25

    The enantioselectivities of β-blockers (propranolol, metoprolol, atenolol and pindolol) on four different types of chiral stationary phases (CSPs): Chiralpak AD-H, Lux Cellulose-1, Chirobiotic T and Sumichiral OA-4900 were compared using polar organic (PO) elution mode and normal phase (NP) elution mode. Method optimizations were demonstrated by modifying parameters such as organic modifier composition (ethanol, 2-propanol and acetonitrile) and basic mobile phase additives (triethylamine, diethylamine, ethanolamine, and buthylamine). In normal phase elution mode with Lux Cellulose-1, the four pairs of enantiomers can be separated in the same run in gradient elution mode. Additionally, a simple chiral HPLC-DAD method using a newly commercialized polysaccharide-based CSP by Phenomenex (Lux Cellulose-1) in NP elution mode for enantioselective determination of propranolol in water samples by highly selective molecularly imprinted polymers extraction was validated. The optimized conditions were a mobile phase composed by n-hexane/ethanol/DEA (70/30/0.3, v/v/v) at a flow rate of 1.0 mL min(-1) and 25 °C. The method is selective, precise and accurate and was found to be linear in the range of 0.125-50 μg mL(-1) (R(2)>0.999) with a method detection limit (MLD) of 0.4 μg mL(-1) for both enantiomers. Recoveries achieved with both enantiomers ranged from 97 to 109%.

  19. Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates.

    PubMed

    Ghoufi, A; Morineau, D; Lefort, R; Malfreyt, P

    2010-10-12

    Many interesting physical phenomena occur on length and time scales that are not accessible by atomistic molecular simulations. By introducing a coarse graining of the degrees of freedom, coarse-grained (CG) models allow ther study of larger scale systems for longer times. Coarse-grained force fields have been mostly derived for large molecules, including polymeric materials and proteins. By contrast, there exist no satisfactory CG potentials for mesostructured porous solid materials in the literature. This issue has become critical among a growing number of studies on confinement effects on fluid properties, which require both long time and large scale simulations and the conservation of a sufficient level of atomistic description to account for interfacial phenomena. In this paper, we present a general multiscale procedure to derive a hybrid coarse grained/all atoms force field CG/AA model for mesoporous systems. The method is applied to mesostructured MCM-41 molecular sieves, while the parameters of the mesoscopic interaction potentials are obtained and validated from the computation of the adsorption isotherm of methanol by grand canonical molecular dynamic simulation.

  20. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    PubMed

    Gould, Tim; Bučko, Tomáš

    2016-08-09

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (<5% errors) in ∼80% of the cases, but can break down badly (>30% errors) in a small fraction of cases.

  1. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

    2017-03-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to  ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning’s theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1{{k}\\text{B}}T . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  2. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  3. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

    PubMed

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  4. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    NASA Astrophysics Data System (ADS)

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  5. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

    PubMed Central

    Nguyen, Trang Truc; Viet, Man Hoang

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM. PMID:24672329

  6. Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase.

    PubMed

    Nguyen, Trang Truc; Viet, Man Hoang; Li, Mai Suan

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔG(bind) decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.

  7. An all-atom model of the pore-like structure of hexameric VP40 from Ebola: structural insights into the monomer-hexamer transition.

    PubMed

    Nguyen, Tam Luong; Schoehn, Guy; Weissenhorn, Winfried; Hermone, Ann R; Burnett, James C; Panchal, Rekha G; McGrath, Connor; Zaharevitz, Dan W; Aman, M Javad; Gussio, Rick; Bavari, Sina

    2005-07-01

    The matrix protein VP40 is an indispensable component of viral assembly and budding by the Ebola virus. VP40 is a monomer in solution, but can fold into hexameric and octameric states, two oligomeric conformations that play central roles in the Ebola viral life cycle. While the X-ray structures of monomeric and octameric VP40 have been determined, the structure of hexameric VP40 has only been solved by three-dimensional electron microscopy (EM) to a resolution of approximately 30 A. In this paper, we present the refinement of the EM reconstruction of truncated hexameric VP40 to approximately 20 A and the construction of an all-atom model (residues 44-212) using the EM model at approximately 20 A and the X-ray structure of monomeric VP40 as templates. The hexamer model suggests that the monomer-hexamer transition involves a conformational change in the N-terminal domain that is not evident during octamerization and therefore, may provide the basis for elucidating the biological function of VP40.

  8. Uncovering the microscopic mechanism of strand exchange during RecA mediated homologous recombination using all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shankla, Manish; Yoo, Jejoong; Aksimentiev, Aleksei

    2012-02-01

    Homologous recombination (HR) is a key step during the repair process of double-stranded DNA (dsDNA) breakage. RecA is a protein that mediates HR in bacteria. RecA monomers polymerize on a single-stranded DNA (ssDNA) separated from the broken dsDNA to form a helical filament, thus allowing strand exchange to occur. Recent crystal structures depict each RecA monomer in contact with three contiguous nucleotides called DNA triplets. Surprisingly, the conformation of each triplet is similar to that of a triplet in B-form DNA. However, in the filament the neighboring triplets are separated by loops of the RecA proteins. Single molecule experiments demonstrated that strand exchange propagation occurs in 3 base-pair increments. However, the temporal resolution of the experiments was insufficient to determine the exact molecular mechanism of the triplet propagation. Using all-atom molecular dynamics simulations, we investigated the effect of both the RecA protein and the conformation of the bound ssDNA fragment on the stability of the duplex DNA intermediate formed during the strand-exchange process. Specifically, we report simulations of force-induced unzipping of duplex DNA in the presence and absence of the RecA filament that explored the effect of the triplet ladder conformation.

  9. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid protein interactions, side chain transfer free energies and model proteins

    NASA Astrophysics Data System (ADS)

    Tieleman, D. Peter; MacCallum, Justin L.; Ash, Walter L.; Kandt, Christian; Xu, Zhitao; Monticelli, Luca

    2006-07-01

    We have reparameterized the dihedral parameters in a commonly used united-atom lipid force field so that they can be used with the all-atom OPLS force field for proteins implemented in the molecular dynamics simulation software GROMACS. Simulations with this new combination give stable trajectories and sensible behaviour of both lipids and protein. We have calculated the free energy of transfer of amino acid side chains between water and 'lipid-cyclohexane', made of lipid force field methylene groups, as a hydrophobic mimic of the membrane interior, for both the OPLS-AA and a modified OPLS-AA force field which gives better hydration free energies under simulation conditions close to those preferred for the lipid force field. The average error is 4.3 kJ mol-1 for water-'lipid-cyclohexane' compared to 3.2 kJ mol-1 for OPLS-AA cyclohexane and 2.4 kJ mol-1 for the modified OPLS-AA water-'lipid-cyclohexane'. We have also investigated the effect of different methods to combine parameters between the united-atom lipid force field and the united-atom protein force field ffgmx. In a widely used combination, the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering. Using straight combination rules improves the results. Combined, we suggest that using OPLS-AA together with the united-atom lipid force field implemented in GROMACS is a reasonable approach to membrane protein simulations. We also suggest that using partial volume information and free energies of transfer may help to improve the parameterization of lipid-protein interactions and point out the need for accurate experimental data to validate and improve force field descriptions of such interactions.

  10. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations

    PubMed Central

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-01-01

    In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of

  11. All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.

    PubMed

    Vashisth, Harish; Abrams, Cameron F

    2013-06-01

    Insulin regulates blood glucose levels in higher organisms by binding to and activating insulin receptor (IR), a constitutively homodimeric glycoprotein of the receptor tyrosine kinase (RTK) superfamily. Therapeutic efforts in treating diabetes have been significantly impeded by the absence of structural information on the activated form of the insulin/IR complex. Mutagenesis and photo-crosslinking experiments and structural information on insulin and apo-IR strongly suggest that the dual-chain insulin molecule, unlike the related single-chain insulin-like growth factors, binds to IR in a very different conformation than what is displayed in storage forms of the hormone. In particular, hydrophobic residues buried in the core of the folded insulin molecule engage the receptor. There is also the possibility of plasticity in the receptor structure based on these data, which may in part be due to rearrangement of the so-called CT-peptide, a tandem hormone-binding element of IR. These possibilities provide opportunity for large-scale molecular modeling to contribute to our understanding of this system. Using various atomistic simulation approaches, we have constructed all-atom structural models of hormone/receptor complexes in the presence of CT in its crystallographic position and a thermodynamically favorable displaced position. In the "displaced-CT" complex, many more insulin-receptor contacts suggested by experiments are satisfied, and our simulations also suggest that R-insulin potentially represents the receptor-bound form of hormone. The results presented in this work have further implications for the design of receptor-specific agonists/antagonists.

  12. All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.

    PubMed

    Vashisth, Harish; Abrams, Cameron F

    2010-07-16

    Type 1 insulin-like growth factor receptor (IGF1R) is a membrane-spanning glycoprotein of the insulin receptor family that has been implicated in a variety of cancers. The key questions related to molecular mechanisms governing ligand recognition by IGF1R remain unanswered, partly due to the lack of testable structural models of apo or ligand-bound receptor complexes. Using a homology model of the IGF1R ectodomain IGF1RDeltabeta, we present the first experimentally consistent all-atom structural models of IGF1/IGF1RDeltabeta and IGF2/IGF1RDeltabeta complexes. Our explicit-solvent molecular dynamics (MD) simulation of apo-IGF1RDeltabeta shows that it displays asymmetric flexibility mechanisms that result in one of two binding pockets accessible to growth factors IGF1 and IGF2, as demonstrated via an MD-assisted Monte Carlo docking procedure. Our MD-generated ensemble of structures of apo and IGF1-bound IGF1RDeltabeta agrees reasonably well with published small-angle X-ray scattering data. We observe simultaneous contacts of each growth factor with sites 1 and 2 of IGF1R, suggesting cross-linking of receptor subunits. Our models provide direct evidence in favor of suggested electrostatic complementarity between the C-domain (IGF1) and the cysteine-rich domain (IGF1R). Our IGF1/IGF1RDeltabeta model provides structural bases for the observation that a single IGF1 molecule binds to IGF1RDeltabeta at low concentrations in small-angle X-ray scattering studies. We also suggest new possible structural bases for differences in the affinities of insulin, IGF1, and IGF2 for their noncognate receptors.

  13. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins.

    PubMed

    Tieleman, D Peter; Maccallum, Justin L; Ash, Walter L; Kandt, Christian; Xu, Zhitao; Monticelli, Luca

    2006-07-19

    We have reparameterized the dihedral parameters in a commonly used united-atom lipid force field so that they can be used with the all-atom OPLS force field for proteins implemented in the molecular dynamics simulation software GROMACS. Simulations with this new combination give stable trajectories and sensible behaviour of both lipids and protein. We have calculated the free energy of transfer of amino acid side chains between water and 'lipid-cyclohexane', made of lipid force field methylene groups, as a hydrophobic mimic of the membrane interior, for both the OPLS-AA and a modified OPLS-AA force field which gives better hydration free energies under simulation conditions close to those preferred for the lipid force field. The average error is 4.3 kJ mol(-1) for water-'lipid-cyclohexane' compared to 3.2 kJ mol(-1) for OPLS-AA cyclohexane and 2.4 kJ mol(-1) for the modified OPLS-AA water-'lipid-cyclohexane'. We have also investigated the effect of different methods to combine parameters between the united-atom lipid force field and the united-atom protein force field ffgmx. In a widely used combination, the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering. Using straight combination rules improves the results. Combined, we suggest that using OPLS-AA together with the united-atom lipid force field implemented in GROMACS is a reasonable approach to membrane protein simulations. We also suggest that using partial volume information and free energies of transfer may help to improve the parameterization of lipid-protein interactions and point out the need for accurate experimental data to validate and improve force field descriptions of such interactions.

  14. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

    2008-06-01

    Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation

  15. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.

    PubMed

    Arnautova, Yelena A; Vorobjev, Yury N; Vila, Jorge A; Scheraga, Harold A

    2009-10-01

    Availability of energy functions which can discriminate native-like from non-native protein conformations is crucial for theoretical protein structure prediction and refinement of low-resolution protein models. This article reports the results of benchmark tests for scoring functions based on two all-atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent-accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent-accessible surface area model of Ooi et al. (Proc Natl Acad Sci USA 1987;84:3086-3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/FAMBEpH). Short Monte Carlo-with-Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native-like and non-native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native-like structures with C(alpha) root-mean-square-deviations below 3.5 A as lowest-energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein-solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native-like structures cannot be discriminated as those with low

  16. FTIR spectra and normal-mode analysis of a tetranuclear Manganese adamantane-like complex in two electrochemically prepared oxidation states: Relevance to the oxygen-evolving complex of Photosystem II

    SciTech Connect

    Visser, Hendrik; Dube, Christopher E.; Armstrong, William H.; Sauer, Kenneth; Yachandra, Vittal K.

    2002-03-19

    The IR spectra and normal-mode analysis of the adamantane-like compound [Mn4O6(bpea)4]n+ in two oxidation states, MnIV4 and MnIIIMnIV3, that are relevant to the oxygen-evolving complex of photosystem II are presented. Mn-O vibrational modes are identified with isotopic exchange, 16O->18O, of the mono-(mu)-oxo bridging atoms in the complex. IR spectra of the MnIIIMnIV3 species are obtained by electrochemical reduction of the MnIV4 species using a spectroelectrochemical cell, based on attenuated total reflection [Visser et al. Anal Chem 2001, 73, 4374-4378]. A novel method of subtraction is used to reduce background contributions from solvent and ligand modes, and the difference and double-difference spectra are used in identifying Mn-O bridging modes that are sensitive to oxidation state change. Two strong IR bands are observed for the MnIV4 species at 745 and 707 cm-1 and a weaker band at 510 cm-1. Upon reduction, the MnIIIMnIV3 species exhibits two strong IR bands at 745 and 680 cm-1, and several weaker bands are observed in the 510 - 425 cm-1 range. A normal mode analysis is performed to assign all the relevant bridging modes in the oxidized MnIV4 and reduced MnIIIMnIV3 species. The calculated force constants for the MnIV4 species are = 3.15 mdynAngstrom, = 0.55 mdyn/Angstrom, and = 0.20 mdyn/Angstrom. The force constants for the MnIIIMnIV3 species are = 3.10 mdyn/Angstrom, = 2.45 mdyn/Angstrom, = 0.40, and = 0.15 mdyn/Angstrom. This study provides insights for the identification of Mn-O modes in the IR spectra of the photosynthetic oxygen-evolving complex during its catalytic cycle.

  17. FTIR Spectra and Normal-Mode Analysis of a Tetranuclear Manganese Adamantane-like Complex in Two Electrochemically Prepared Oxidation States: Relevance to the Oxygen-Evolving Complex of Photosystem II

    PubMed Central

    Visser, Hendrik; Dubé, Christopher E.; Armstrong, William H.; Sauer, Kenneth; Yachandra, Vittal K.

    2014-01-01

    The IR spectra and normal-mode analysis of the adamantane-like compound [Mn4O6(bpea)4]n+ (bpea = N,N-bis(2-pyridylmethyl)ethylamine) in two oxidation states, MnIV4 and MnIIIMnIV3, that are relevant to the oxygen-evolving complex of photosystem II are presented. Mn–O vibrational modes are identified with isotopic exchange, 16O→18O, of the mono-μ-oxo bridging atoms in the complex. IR spectra of the MnIIIMnIV3 species are obtained by electrochemical reduction of the MnIV4 species using a spectroelectrochemical cell, based on attenuated total reflection [Visser, H.; et al. Anal. Chem. 2001, 73, 4374–4378]. A novel method of subtraction is used to reduce background contributions from solvent and ligand modes, and the difference and double-difference spectra are used in identifying Mn–O bridging modes that are sensitive to oxidation state change. Two strong IR bands are observed for the MnIV4 species at 745 and 707 cm−1, and a weaker band is observed at 510 cm−1. Upon reduction, the MnIIIMnIV3 species exhibits two strong IR bands at 745 and 680 cm−1, and several weaker bands are observed in the 510–425 cm−1 range. A normal-mode analysis is performed to assign all the relevant bridging modes in the oxidized MnIV4 and reduced MnIIIMnIV3 species. The calculated force constants for the MnIV4 species are frIV = 3.15 mdyn/Å, frOr = 0.55 mdyn/Å, and frMnr = 0.20 mdyn/Å. The force constants for the MnIIIMnIV3 species are frIV = 3.10 mdyn/Å, frIII = 2.45 mdyn/Å, frOr = 0.40 mdyn/Å, and frMnr = 0.15 mdyn/Å. This study provides insights for the identification of Mn–O modes in the IR spectra of the photosynthetic oxygen-evolving complex during its catalytic cycle. PMID:12224948

  18. FTIR spectra and normal-mode analysis of a tetranuclear manganese adamantane-like complex in two electrochemically prepared oxidation states: relevance to the oxygen-evolving complex of photosystem II.

    PubMed

    Visser, Hendrik; Dubé, Christopher E; Armstrong, William H; Sauer, Kenneth; Yachandra, Vittal K

    2002-09-18

    The IR spectra and normal-mode analysis of the adamantane-like compound [Mn(4)O(6)(bpea)(4)](n+) (bpea = N,N-bis(2-pyridylmethyl)ethylamine) in two oxidation states, Mn(IV)(4) and Mn(III)Mn(IV)(3), that are relevant to the oxygen-evolving complex of photosystem II are presented. Mn-O vibrational modes are identified with isotopic exchange, (16)O-->(18)O, of the mono-micro-oxo bridging atoms in the complex. IR spectra of the Mn(III)Mn(IV)(3) species are obtained by electrochemical reduction of the Mn(IV)(4) species using a spectroelectrochemical cell, based on attenuated total reflection [Visser, H.; et al. Anal. Chem. 2001, 73, 4374-4378]. A novel method of subtraction is used to reduce background contributions from solvent and ligand modes, and the difference and double-difference spectra are used in identifying Mn-O bridging modes that are sensitive to oxidation state change. Two strong IR bands are observed for the Mn(IV)(4) species at 745 and 707 cm(-1), and a weaker band is observed at 510 cm(-1). Upon reduction, the Mn(III)Mn(IV)(3) species exhibits two strong IR bands at 745 and 680 cm(-1), and several weaker bands are observed in the 510-425 cm(-1) range. A normal-mode analysis is performed to assign all the relevant bridging modes in the oxidized Mn(IV)(4) and reduced Mn(III)Mn(IV)(3) species. The calculated force constants for the Mn(IV)(4) species are f(r)(IV)= 3.15 mdyn/A, f(rOr) = 0.55 mdyn/A, and f(rMnr) = 0.20 mdyn/A. The force constants for the Mn(III)Mn(IV)(3) species are f(r)(IV)= 3.10 mdyn/A, f(r)(III)= 2.45 mdyn/A, f(rOr) = 0.40 mdyn/A, and f(rMnr) = 0.15 mdyn/A. This study provides insights for the identification of Mn-O modes in the IR spectra of the photosynthetic oxygen-evolving complex during its catalytic cycle.

  19. Inversion of the moment-tensor Mrr components of the 2012 Sumatra strike-slip double earthquake using radial normal modes

    NASA Astrophysics Data System (ADS)

    Zábranová, Eliška; Matyska, Ctirad

    2017-01-01

    On April 11, 2012, two strike-slip Sumatra earthquakes with moment magnitudes higher than 8 generated strong, preferentially horizontal, motions. If only body and surface waves are inverted, their centroid-moment-tensor (CMT) parameters producing vertical motions, in particular the Mrr components, are poorly resolved. Independent constraints can be obtained from observations of the radial free-oscillation modes. The signal of radial modes is acquired from four unperturbed superconducting gravimeter records with low noise levels in submillihertz frequency range. We show that the observed signal substantially differs from the synthetic calculations for most of the published CMTs except for the Global CMT solution, which agrees better. We perform modal inversions considering uncertainties in centroid times and calculate marginal posterior probability density function of the Mrr components. The amplitude-spectrum inversion is robust enough to estimate the intervals of admissible Mrr values. Finally, we incorporate also a phase information and reduce the trade-off between the Mrr components of the two studied events.

  20. The normal modes of a resonant cavity containing discrete inhomogeneities - The influence of fibril magnetic fields on the solar acoustic oscillations

    NASA Technical Reports Server (NTRS)

    Bogdan, Thomas J.; Cattaneo, Fausto

    1989-01-01

    Motivated by considerations of the interaction between fibril magnetic fields and solar p-modes, the acoustic spectrum of a cylindrical cavity filled with ideal gas in which a number of magnetic flux tubes are embedded is studied. A formalism, based on the T-matrix approach to acoustic scattering, is developed which can be used to determine the eigenfrequencies and eigenfunctions for any arbitrary distribution of flux tubes. For weak scatterers, the frequency shifts and velocity eigenfunctions are calculated using perturbation theory for the cases of a single flux tube and a random distribution of up to 100 flux tubes. The results of this 'exact' approach are used to give a critical appraisal of the predictions of theories based on some form of averaging, such as the one discussed recently by Bogdan and Zweibel (1987).

  1. All-fiber normal-dispersion single-polarization passively mode-locked laser based on a 45°-tilted fiber grating.

    PubMed

    Liu, Xianglian; Wang, Hushan; Yan, Zhijun; Wang, Yishan; Zhao, Wei; Zhang, Wei; Zhang, Lin; Yang, Zhi; Hu, Xiaohong; Li, Xiaohui; Shen, Deyuan; Li, Cheng; Chen, Guangde

    2012-08-13

    An all-fiber normal-dispersion Yb-doped fiber laser with 45°-tilted fiber grating (TFG) is, to the best of our knowledge, experimentally demonstrated for the first time. Stable linearly-chirped pulses with the duration of 4 ps and the bandwidth of 9 nm can be directly generated from the laser cavity. By employing the 45° TFG with the polarization-dependent loss of 33 dB, output pulses with high polarization extinction ratio of 26 dB are implemented in the experiment. Our result shows that the 45° TFG can work effectively as a polarizer, which could be exploited to single-polarization all-fiber lasers.

  2. Micromagnetic simulations of spin-wave normal modes and the spin-transfer-torque driven magnetization dynamics of a ferromagnetic cross

    SciTech Connect

    Pramanik, Tanmoy Roy, Urmimala; Register, Leonard F.; Banerjee, Sanjay K.; Tsoi, Maxim

    2014-05-07

    We studied spin-transfer-torque (STT) switching of a cross-shaped magnetic tunnel junction in a recent report [Roy et al., J. Appl. Phys. 113, 223904 (2013)]. In that structure, the free layer is designed to have four stable energy states using the shape anisotropy of a cross. STT switching showed different regions with increasing current density. Here, we employ the micromagnetic spectral mapping technique in an attempt to understand how the asymmetry of cross dimensions and spin polarization direction of the injected current affect the magnetization dynamics. We compute spatially averaged frequency-domain spectrum of the time-domain magnetization dynamics in the presence of the current-induced STT term. At low currents, the asymmetry of polarization direction and that of the arms are observed to cause a splitting of the excited frequency modes. Higher harmonics are also observed, presumably due to spin-wave wells caused by the regions of spatially non-uniform effective magnetic field. The results could be used towards designing a multi-bit-per-cell STT-based random access memory with an improved storage density.

  3. Dark current studies on a normal-conducting high-brightness very-high-frequency electron gun operating in continuous wave mode

    NASA Astrophysics Data System (ADS)

    Huang, R.; Filippetto, D.; Papadopoulos, C. F.; Qian, H.; Sannibale, F.; Zolotorev, M.

    2015-01-01

    We report on measurements and analysis of a field-emitted electron current in the very-high-frequency (VHF) gun, a room temperature rf gun operating at high field and continuous wave (CW) mode at the Lawrence Berkeley National Laboratory (LBNL). The VHF gun is the core of the Advanced Photo-injector Experiment (APEX) at LBNL, geared toward the development of an injector for driving the next generation of high average power x-ray free electron lasers. High accelerating fields at the cathode are necessary for the high-brightness performance of an electron gun. When coupled with CW operation, such fields can generate a significant amount of field-emitted electrons that can be transported downstream the accelerator forming the so-called "dark current." Elevated levels of a dark current can cause radiation damage, increase the heat load in the downstream cryogenic systems, and ultimately limit the overall performance and reliability of the facility. We performed systematic measurements that allowed us to characterize the field emission from the VHF gun, determine the location of the main emitters, and define an effective strategy to reduce and control the level of dark current at APEX. Furthermore, the energy spectra of isolated sources have been measured. A simple model for energy data analysis was developed that allows one to extract information on the emitter from a single energy distribution measurement.

  4. Technique for the normalization of electro-rheological fluid performance data in cylindrical/shear and pressure/flow modes of steady operation

    NASA Astrophysics Data System (ADS)

    Peel, David J.; Bullough, William A.

    1998-04-01

    A general technique providing effective but approximate characterization of electro-rheological fluids as continua (as against their apparent device specific performance) is extended by relating data from cylindrical, sliding electrode induced shear flow, and fixed, plane electrode, pressure induced linear flow types of test rigs. The motion being laminar, use is made of the well known Buckingham relationships: the yield stress in the fluid is taken to vary at constant excitation whilst the well defined unexcited viscosity remains fixed. On the basis of experimental data, and within an acceptable error band (for engineering design purposes) the two modes of operation are shown to share common fluid characteristics in terms of Hedstrom and Reynolds Numbers at constant excitation, and when these are related to a Friction Coefficient, a technique of using `fluid alone' data is made available. This technique allows small sample, low shear rate fluid test results from Couette-type apparatus to be applied in user friendly fashion to the prediction of performance of parallel plate valves and cylindrical clutches operating in the engineering scale.

  5. Mode-locking of Er-doped fiber laser using a multilayer MoS2 thin film as a saturable absorber in both anomalous and normal dispersion regimes.

    PubMed

    Khazaeizhad, Reza; Kassani, Sahar Hosseinzadeh; Jeong, Hwanseong; Yeom, Dong-Il; Oh, Kyunghwan

    2014-09-22

    Application of a multilayer Molybdenum Disulfide (MoS2) thin film as a saturable absorber was experimentally demonstrated by realizing a stable and robust passive mode-locked fiber laser via the evanescent field interaction between the light and the film. The MoS2 film was grown by chemical vapor deposition, and was then transferred to a side polished fiber by a lift-off method. Intensity-dependent optical transmission through the MoS2 thin film on side polished fiber was experimentally observed showing efficient saturable absorption characteristics. Using erbium doped fiber as an optical gain medium, we built an all-fiber ring cavity, where the MoS2 film on the side polished fiber was inserted as a saturable absorber. Stable dissipative soliton pulse trains were successfully generated in the normal dispersion regime with a spectral bandwidth of 23.2 nm and the pulse width of 4.98 ps. By adjusting the total dispersion in the cavity, we also obtained soliton pulses with a width of 637 fs in the anomalous dispersion regime near the lasing wavelength λ = 1.55 μm. Detailed and systematic experimental comparisons were made for stable mode locking of an all-fiber laser cavity in both the normal and anomalous regimes.

  6. Substorm recurrence during steady and variable solar wind driving: Evidence for a normal mode in the unloading dynamics of the magnetosphere

    NASA Technical Reports Server (NTRS)

    Klimas, A. J.; Baker, D. N.; Vassiliadis, D.; Roberts, D. A.

    1994-01-01

    recurrence rate observed by Farrugia et al. can be interpreted as both being due to the existence of a normal unloading recurrence period in the dynamics of the magnetosphere.

  7. Spectral fitting inversion of low-frequency normal modes with self-coupling and cross-coupling of toroidal and spheroidal multiplets: numerical experiments to estimate the isotropic and anisotropic velocity structures

    NASA Astrophysics Data System (ADS)

    Oda, Hitoshi

    2016-06-01

    The aspherical structure of the Earth is described in terms of lateral heterogeneity and anisotropy of the P- and S-wave velocities, density heterogeneity, ellipticity and rotation of the Earth and undulation of the discontinuity interfaces of the seismic wave velocities. Its structure significantly influences the normal mode spectra of the Earth's free oscillation in the form of cross-coupling between toroidal and spheroidal multiplets and self-coupling between the singlets forming them. Thus, the aspherical structure must be conversely estimated from the free oscillation spectra influenced by the cross-coupling and self-coupling. In the present study, we improve a spectral fitting inversion algorithm which was developed in a previous study to retrieve the global structures of the isotropic and anisotropic velocities of the P and S waves from the free oscillation spectra. The main improvement is that the geographical distribution of the intensity of the S-wave azimuthal anisotropy is represented by a nonlinear combination of structure coefficients for the anisotropic velocity structure, whereas in the previous study it was expanded into a generalized spherical harmonic series. Consequently, the improved inversion algorithm reduces the number of unknown parameters that must be determined compared to the previous inversion algorithm and employs a one-step inversion method by which the structure coefficients for the isotropic and anisotropic velocities are directly estimated from the fee oscillation spectra. The applicability of the improved inversion is examined by several numerical experiments using synthetic spectral data, which are produced by supposing a variety of isotropic and anisotropic velocity structures, earthquake source parameters and station-event pairs. Furthermore, the robustness of the inversion algorithm is investigated with respect to the back-ground noise contaminating the spectral data as well as truncating the series expansions by finite terms

  8. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

    PubMed

    De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

    2014-12-09

    A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

  9. Characteristics of the default mode functional connectivity in normal ageing and Alzheimer's disease using resting state fMRI with a combined approach of entropy-based and graph theoretical measurements.

    PubMed

    Toussaint, Paule-Joanne; Maiz, Sofiane; Coynel, David; Doyon, Julien; Messé, Arnaud; de Souza, Leonardo Cruz; Sarazin, Marie; Perlbarg, Vincent; Habert, Marie-Odile; Benali, Habib

    2014-11-01

    Cognitive decline in normal ageing and Alzheimer's disease (AD) emerges from functional disruption in the coordination of large-scale brain systems sustaining cognition. Integrity of these systems can be examined by correlation methods based on analysis of resting state functional magnetic resonance imaging (fMRI). Here we investigate functional connectivity within the default mode network (DMN) in normal ageing and AD using resting state fMRI. Images from young and elderly controls, and patients with AD were processed using spatial independent component analysis to identify the DMN. Functional connectivity was quantified using integration and indices derived from graph theory. Four DMN sub-systems were identified: Frontal (medial and superior), parietal (precuneus-posterior cingulate, lateral parietal), temporal (medial temporal), and hippocampal (bilateral). There was a decrease in antero-posterior interactions (lower global efficiency), but increased interactions within the frontal and parietal sub-systems (higher local clustering) in elderly compared to young controls. This decreased antero-posterior integration was more pronounced in AD patients compared to elderly controls, particularly in the precuneus-posterior cingulate region. Conjoint knowledge of integration measures and graph indices in the same data helps in the interpretation of functional connectivity results, as comprehension of one measure improves with understanding of the other. The approach allows for complete characterisation of connectivity changes and could be applied to other resting state networks and different pathologies.

  10. Refringence, field theory and normal modes

    NASA Astrophysics Data System (ADS)

    Barceló, Carlos; Liberati, Stefano; Visser, Matt

    2002-06-01

    In a previous paper [Barceló C et al 2001 Class. Quantum Grav. 18 3595-610 (Preprint gr-qc/0104001)] we have shown that the occurrence of curved spacetime 'effective Lorentzian geometries' is a generic result of linearizing an arbitrary classical field theory around some nontrivial background configuration. This observation explains the ubiquitous nature of the 'analogue models' for general relativity that have recently been developed based on condensed matter physics. In the simple (single scalar field) situation analysed in our previous paper, there is a single unique effective metric; more complicated situations can lead to bi-metric and multi-metric theories. In the present paper we will investigate the conditions required to keep the situation under control and compatible with experiment - either by enforcing a unique effective metric (as would be required to be strictly compatible with the Einstein equivalence principle), or at the worst by arranging things so that there are multiple metrics that are all 'close' to each other (in order to be compatible with the Eötvös experiment). The algebraically most general situation leads to a physical model whose mathematical description requires an extension of the usual notion of Finsler geometry to a Lorentzian-signature pseudo-Finsler geometry; while this is possibly of some interest in its own right, this particular case does not seem to be immediately relevant for either particle physics or gravitation. The key result is that wide classes of theories lend themselves to an effective metric description. This observation provides further evidence that the notion of 'analogue gravity' is rather generic.

  11. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model.

    PubMed

    Felts, Anthony K; Gallicchio, Emilio; Wallqvist, Anders; Levy, Ronald M

    2002-08-01

    Protein decoy data sets provide a benchmark for testing scoring functions designed for fold recognition and protein homology modeling problems. It is commonly believed that statistical potentials based on reduced atomic models are better able to discriminate native-like from misfolded decoys than scoring functions based on more detailed molecular mechanics models. Recent benchmark tests on small data sets, however, suggest otherwise. In this work, we report the results of extensive decoy detection tests using an effective free energy function based on the OPLS all-atom (OPLS-AA) force field and the Surface Generalized Born (SGB) model for the solvent electrostatic effects. The OPLS-AA/SGB effective free energy is used as a scoring function to detect native protein folds among a total of 48,832 decoys for 32 different proteins from Park and Levitt's 4-state-reduced, Levitt's local-minima, Baker's ROSETTA all-atom, and Skolnick's decoy sets. Solvent electrostatic effects are included through the Surface Generalized Born (SGB) model. All structures are locally minimized without restraints. From an analysis of the individual energy components of the OPLS-AA/SGB energy function for the native and the best-ranked decoy, it is determined that a balance of the terms of the potential is responsible for the minimized energies that most successfully distinguish the native from the misfolded conformations. Different combinations of individual energy terms provide less discrimination than the total energy. The results are consistent with observations that all-atom molecular potentials coupled with intermediate level solvent dielectric models are competitive with knowledge-based potentials for decoy detection and protein modeling problems such as fold recognition and homology modeling.

  12. Multidimentional Normal Mode Calculations for the OH Vibrational Spectra of (H_2O)_3^+, (H_2O)_3^+Ar, H^+(H_2O)_3, and H^+(H_2O)_3Ar

    NASA Astrophysics Data System (ADS)

    Li, Ying-Cheng; Chuang, Hsiao-Han; Tan, Jake Acedera; Takahashi, Kaito; Kuo, Jer-Lai

    2014-06-01

    Recent experimental observations of (H_2O)_3^+, (H_2O)_3^+Ar, H^+(H_2O)_3, and H^+(H_2O)_3Ar clusters in the region 1400-3800 wn show that the OH stretching vibration has distinct characteristics. Multidimensional normal mode calculations were carried out for OH stretching vibrations in the 1200-4000 wn photon energy range. The potential energy and dipole surfaces were evaluated by using first-principles methods. By comparing the calculated frequencies and intensities of OH stretching vibration with experimental spectra, we found that the assignment of OH strecthing of H_3O^+ moiety and free OH strectching vibration have resonable agreement with experimental data. Jeffrey M. Headrick, Eric G. Diken, Richard S. Walters, Nathan I. Hammer, Richard A. Christie, Jun Cui, Evgeniy M. Myshakin, Michael A. Duncan, Mark A. Johnson, Kenneth D. Jordan, Science, 2005, 17, 1765. Kenta Mizuse, Jer-Lai Kuo and Asuka Fujii, Chem. Sci., 2011, 2, 868 Kenta Mizuse and Asuka Fujii, J. Phys. Chem. A, 2013, 117, 929.

  13. Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

    PubMed

    Araujo, Gabriela C; Silva, Ricardo H T; Scott, Luis P B; Araujo, Alexandre S; Souza, Fatima P; de Oliveira, Ronaldo Junio

    2016-12-01

    The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.

  14. Multivariate normality

    NASA Technical Reports Server (NTRS)

    Crutcher, H. L.; Falls, L. W.

    1976-01-01

    Sets of experimentally determined or routinely observed data provide information about the past, present and, hopefully, future sets of similarly produced data. An infinite set of statistical models exists which may be used to describe the data sets. The normal distribution is one model. If it serves at all, it serves well. If a data set, or a transformation of the set, representative of a larger population can be described by the normal distribution, then valid statistical inferences can be drawn. There are several tests which may be applied to a data set to determine whether the univariate normal model adequately describes the set. The chi-square test based on Pearson's work in the late nineteenth and early twentieth centuries is often used. Like all tests, it has some weaknesses which are discussed in elementary texts. Extension of the chi-square test to the multivariate normal model is provided. Tables and graphs permit easier application of the test in the higher dimensions. Several examples, using recorded data, illustrate the procedures. Tests of maximum absolute differences, mean sum of squares of residuals, runs and changes of sign are included in these tests. Dimensions one through five with selected sample sizes 11 to 101 are used to illustrate the statistical tests developed.

  15. Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: a combined dynamic fluorescence and all-atom molecular dynamics simulation study.

    PubMed

    Guchhait, Biswajit; Biswas, Ranjit; Ghorai, Pradip K

    2013-03-28

    Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements.

  16. A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent.

    PubMed

    Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

    2013-05-14

    We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.

  17. All-atom molecular dynamics study of a spherical micelle composed of N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) block copolymers: a potential carrier of drug delivery systems for cancer.

    PubMed

    Kuramochi, Hiroshi; Andoh, Yoshimichi; Yoshii, Noriyuki; Okazaki, Susumu

    2009-11-19

    An all-atom molecular dynamics simulation of a spherical micelle composed of amphiphilic N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) (PEG-PBLG-Ac) block copolymers was performed in aqueous solution at 298.15 K and 1 atm. Such copolymers have received considerable attention as carriers in drug delivery systems. In this study, we used copolymers consisting of 11 EG units and 9 BLG units as models. Starting from the copolymers arranged spherically, the calculation predicted an equilibrium state consisting of a slightly elliptical micelle structure with a hydrophobic PBLG inner core and a hydrophilic PEG outer shell. The micelle structure was dynamically stable during the simulation, with the PEG blocks showing a compact helical conformation and the PBLG blocks an alpha-helix form. Multiple hydrogen bonds with solvent water molecules stabilized the helical conformation of the PEG blocks, leading to their hydration as shown by longer residence times of water molecules near the PEG ether oxygen atoms compared with that of bulk water. Some water molecules have also been found distributed within the hydrophobic core; they showed continuous exchange with bulk water during the simulation. Those molecules existed mostly as a cluster in spaces between the copolymers, forming hydrogen bonds among themselves as well as with the hydrophobic core through hydrophilic groups such as esters and amides. The water molecules forming hydrogen bonds with the micelle may play an important role in the stabilization of the micelle structure.

  18. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

    PubMed

    Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

    2015-05-12

    Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

  19. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  20. Theory of psychological adaptive modes.

    PubMed

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes.

  1. Generalised Hermite-Gaussian beams and mode transformations

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Chen, Yujie; Zhang, Yanfeng; Chen, Hui; Yu, Siyuan

    2016-05-01

    Generalised Hermite-Gaussian modes (gHG modes), an extended notion of Hermite-Gaussian modes (HG modes), are formed by the summation of normal HG modes with a characteristic function α, which can be used to unite conventional HG modes and Laguerre-Gaussian modes (LG modes). An infinite number of normalised orthogonal modes can thus be obtained by modulation of the function α. The gHG mode notion provides a useful tool in analysis of the deformation and transformation phenomena occurring in propagation of HG and LG modes with astigmatic perturbation.

  2. Whispering-mode waveguide

    NASA Astrophysics Data System (ADS)

    Kurnit, N. A.

    Properties of a relatively new type of waveguide structure of potential use of confining infrared radiation to a small mode volume over long path lengths are reviewed. A single guiding surface with curvature radius rho and band radius R allows propagation of a near-grazing incidence whispering mode of transverse width approximately (lambda square root of rho R/pi) sup 1/2 and radial width approximately 1/2 (sq lambda R)/sup 1/3. For sufficiently large rho, the loss per revolution for TE mode propagation is approximately pi A/sub N/, where A/sub N/ is the normal-incidence reflection loss. Results on a number of prototype structures in general agreement with these considerations are described.

  3. Automatic determination of important mode-mode correlations in many-mode vibrational wave functions.

    PubMed

    König, Carolin; Christiansen, Ove

    2015-04-14

    We introduce new automatic procedures for parameterizing vibrational coupled cluster (VCC) and vibrational configuration interaction wave functions. Importance measures for individual mode combinations in the wave function are derived based on upper bounds to Hamiltonian matrix elements and/or the size of perturbative corrections derived in the framework of VCC. With a threshold, this enables an automatic, system-adapted way of choosing which mode-mode correlations are explicitly parameterized in the many-mode wave function. The effect of different importance measures and thresholds is investigated for zero-point energies and infrared spectra for formaldehyde and furan. Furthermore, the direct link between important mode-mode correlations and coordinates is illustrated employing water clusters as examples: Using optimized coordinates, a larger number of mode combinations can be neglected in the correlated many-mode vibrational wave function than with normal coordinates for the same accuracy. Moreover, the fraction of important mode-mode correlations compared to the total number of correlations decreases with system size. This underlines the potential gain in efficiency when using optimized coordinates in combination with a flexible scheme for choosing the mode-mode correlations included in the parameterization of the correlated many-mode vibrational wave function. All in all, it is found that the introduced schemes for parameterizing correlated many-mode vibrational wave functions lead to at least as systematic and accurate calculations as those using more standard and straightforward excitation level definitions. This new way of defining approximate calculations offers potential for future calculations on larger systems.

  4. Intrinsic Localized Modes in Proteins

    PubMed Central

    Nicolaï, Adrien; Delarue, Patrice; Senet, Patrick

    2015-01-01

    Protein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states). PMID:26658321

  5. Mechanical stratigraphy and normal faulting

    NASA Astrophysics Data System (ADS)

    Ferrill, David A.; Morris, Alan P.; McGinnis, Ronald N.; Smart, Kevin J.; Wigginton, Sarah S.; Hill, Nicola J.

    2017-01-01

    Mechanical stratigraphy encompasses the mechanical properties, thicknesses, and interface properties of rock units. Although mechanical stratigraphy often relates directly to lithostratigraphy, lithologic description alone does not adequately describe mechanical behavior. Analyses of normal faults with displacements of millimeters to 10's of kilometers in mechanically layered rocks reveal that mechanical stratigraphy influences nucleation, failure mode, fault geometry, displacement gradient, displacement distribution, fault core and damage zone characteristics, and fault zone deformation processes. The relationship between normal faulting and mechanical stratigraphy can be used either to predict structural style using knowledge of mechanical stratigraphy, or conversely to interpret mechanical stratigraphy based on characterization of the structural style. This review paper explores a range of mechanical stratigraphic controls on normal faulting illustrated by natural and modeled examples.

  6. The mode switching of PSR B2020+28

    NASA Astrophysics Data System (ADS)

    Wen, Z. G.; Wang, N.; Yan, W. M.; Yuan, J. P.; Liu, Z. Y.; Chen, M. Z.; Chen, J. L.

    2016-08-01

    This paper reports on polarimetric radiation properties based on the switching modes of normal PSR B2020+28 by analyzing the data acquired from the Nanshan 25-m radio telescope at 1556 MHz. With nearly 8 hours quasi-continuous observation, the data presented some striking and updated phenomena. The change of relative intensity between the leading and trailing components is the predominant feature of mode switching. The intensity ratio between the leading and trailing components are measured for the individual profiles averaged over 30 seconds. It is found that there is an excess of high ratios over the normal distribution, which indicates that two modes exist in the pulsar. The distribution of abnormal mode has a narrower width indicating that the abnormal mode is more stable than the normal mode. A total of 76 mode switching events are detected in our data. It spends 89 % in the normal mode and 11 % in the abnormal mode. The intrinsic distributions of mode timescales are constrained with power-law distributions. The significant difference in the index of the duration distribution between normal and abnormal modes possibly indicates that the timescale for the abnormal mode to get stable is shorter than that for the normal mode. The frequent switching between both modes may indicate that the oscillations between different magnetospheric states are rapid.

  7. Intrinsic modes of radiation in ferrite patch antennas

    NASA Astrophysics Data System (ADS)

    How, Hoton; Fang, Ta-Ming; Vittoria, Carmine

    1994-06-01

    We have found two types of radiation modes for patch antennas loaded with ferrite materials. Each mode of radiation is a linear combination of normal modes of propagation in parallel plate waveguide separated by a slab of ferrite material. We have introduced new boundary conditions in which only TE modes of oscillation in the patch antenna cavity result.

  8. Homogeneous modes of cosmological instantons

    SciTech Connect

    Gratton, Steven; Turok, Neil

    2001-06-15

    We discuss the O(4) invariant perturbation modes of cosmological instantons. These modes are spatially homogeneous in Lorentzian spacetime and thus not relevant to density perturbations. But their properties are important in establishing the meaning of the Euclidean path integral. If negative modes are present, the Euclidean path integral is not well defined, but may nevertheless be useful in an approximate description of the decay of an unstable state. When gravitational dynamics is included, counting negative modes requires a careful treatment of the conformal factor problem. We demonstrate that for an appropriate choice of coordinate on phase space, the second order Euclidean action is bounded below for normalized perturbations and has a finite number of negative modes. We prove that there is a negative mode for many gravitational instantons of the Hawking-Moss or Coleman{endash}De Luccia type, and discuss the associated spectral flow. We also investigate Hawking-Turok constrained instantons, which occur in a generic inflationary model. Implementing the regularization and constraint proposed by Kirklin, Turok and Wiseman, we find that those instantons leading to substantial inflation do not possess negative modes. Using an alternate regularization and constraint motivated by reduction from five dimensions, we find a negative mode is present. These investigations shed new light on the suitability of Euclidean quantum gravity as a potential description of our universe.

  9. Exact mode volume and Purcell factor of open optical systems

    NASA Astrophysics Data System (ADS)

    Muljarov, E. A.; Langbein, W.

    2016-12-01

    The Purcell factor quantifies the change of the radiative decay of a dipole in an electromagnetic environment relative to free space. Designing this factor is at the heart of photonics technology, striving to develop ever smaller or less lossy optical resonators. The Purcell factor can be expressed using the electromagnetic eigenmodes of the resonators, introducing the notion of a mode volume for each mode. This approach allows an analytic treatment, reducing the Purcell factor and other observables to sums over eigenmode resonances. Calculating the mode volumes requires a correct normalization of the modes. We introduce an exact normalization of modes, not relying on perfectly matched layers. We present an analytic theory of the Purcell effect based on this exact mode normalization and the resulting effective mode volume. We use a homogeneous dielectric sphere in vacuum, which is analytically solvable, to exemplify these findings. We furthermore verify the applicability of the normalization to numerically determined modes of a finite dielectric cylinder.

  10. Local Mode Axis Tilting in H(sub 2)S

    NASA Technical Reports Server (NTRS)

    Brown, L. R.

    1997-01-01

    Despite the computational efficiency of conventional normal mode techniques for the analysis of rotational-vibrational spectra, the overtone bands of small symmetrical hydrides have certain features that favour an alternative local mode interpretation.

  11. Normal mode and experimental analysis of TNT Raman spectrum

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Perkins, Richard; Liu, Yucheng; Tzeng, Nianfeng

    2017-04-01

    In this study, a Raman spectrum of TNT was characterized through experiments and simulated using 22 hybrid density functional theory (DFT) methods. Among the different hybrid DFT methods, it was found that the most accurate simulation results of the Raman shift frequency were calculated by the O3LYP method. However, the deviations of the calculated Raman frequencies from the experimental value showed no dependency on the abilities of the DFT methods in recovering the correlation energy. The accuracies of the DFT methods in predicting the Raman bands are probably determined by the numerical grid and convergence criteria for optimizations of each DFT method. It was also decided that the prominent Raman shift 1362 cm-1 is mainly caused by symmetric stretching of the 4-nitro groups. Findings of this study can facilitate futuristic development of more effective surface enhanced Raman spectroscopy/scattering (SERS) substrates for explosive characterization and detection.

  12. Normal Modes of Vibration of the PHALANX Gun

    DTIC Science & Technology

    1993-06-01

    51 4. Stub Rotor ...................................................................................... 52 5... Rotor ............................................................................................... 52 6. Double Row Contact Bearing...possible. At the same time, to accurately represent the real gun, the expensive elements are sometimes the best choice. Hence, it is a balance that often

  13. Normal incidence reflective-mode etalons with novel spectral properties

    NASA Astrophysics Data System (ADS)

    Te Kolste, Robert D.

    2003-11-01

    Etalons having one surface which is highly reflective have been used for a variety of applications. By varying the coating type and carefully controlling the thicknesses of the coatings on the lower reflectance side, one can obtain interesting and useful properties. One example is a low finesse but highly efficient element having a reflectance which is very sinusoidal with respect to wavelength. By adding additional layers, functions which are asymmetric about the reflectance peak with respect to wavelength can be obtained, including behavior which approximates a sawtooth reflectance as a function of wavelength. Such devices are easily fabricated at the wafer scale, and can be used in wavelength monitoring and control applications such as wavelength lockers for tunable lasers.

  14. The excitation of normal modes by a curved line source

    NASA Astrophysics Data System (ADS)

    Mochizuki, E.

    1987-12-01

    The polynomial moments, up to total degree two, of the stress glut are calculated for a curved line source. The significance of the moments, whose total degree is one, is emphasized and the implication for inversion is discussed.

  15. The Effects of Internal Waves on Acoustic Normal Modes.

    DTIC Science & Technology

    1984-12-01

    of eigenrays . Now turn on the fluctuations. In the unsaturated region, - each of these equilibrium rays is still dominant although each of these rays...in the horizontal plane -- but nonstationary in depth so that homogeneity cannot be invoked to reduce the dimensionality of the problems. Also, the...wave number space. Here, a difficulty arises in describing the spectrum since the medium is not depth homogeneous . Nevertheless, the quantity can be

  16. Ionospheric Reflection and Absorption Properties of Normal Modes at ELF

    DTIC Science & Technology

    1977-09-15

    wave ELF and VLF programs such as documen- ted by SmithI 0 are the electric (E) and magnetic (H) fields both within and without the ionosphere. These...National Security Agency Cameron Station FT. George G. Meade, 14D 20755 Alexandria, VA 22314 01CY ATTN W65 12CY ATTN. TC O0CY ATTN Oliver H. Bartlett

  17. Cortical Thinning in Network-Associated Regions in Cognitively Normal and Below-Normal Range Schizophrenia

    PubMed Central

    Pinnock, Farena; Parlar, Melissa; Hawco, Colin; Hanford, Lindsay; Hall, Geoffrey B.

    2017-01-01

    This study assessed whether cortical thickness across the brain and regionally in terms of the default mode, salience, and central executive networks differentiates schizophrenia patients and healthy controls with normal range or below-normal range cognitive performance. Cognitive normality was defined using the MATRICS Consensus Cognitive Battery (MCCB) composite score (T = 50 ± 10) and structural magnetic resonance imaging was used to generate cortical thickness data. Whole brain analysis revealed that cognitively normal range controls (n = 39) had greater cortical thickness than both cognitively normal (n = 17) and below-normal range (n = 49) patients. Cognitively normal controls also demonstrated greater thickness than patients in regions associated with the default mode and salience, but not central executive networks. No differences on any thickness measure were found between cognitively normal range and below-normal range controls (n = 24) or between cognitively normal and below-normal range patients. In addition, structural covariance between network regions was high and similar across subgroups. Positive and negative symptom severity did not correlate with thickness values. Cortical thinning across the brain and regionally in relation to the default and salience networks may index shared aspects of the psychotic psychopathology that defines schizophrenia with no relation to cognitive impairment. PMID:28348889

  18. Advocating for Normal Birth With Normal Clothes

    PubMed Central

    Waller-Wise, Renece

    2007-01-01

    Childbirth educators need to be aware that the clothes they wear when teaching classes send a nonverbal message to class participants. Regardless of who wears the clothing or what is worn, clothes send a message; thus, both the advantages and disadvantages related to clothing choice should be considered. Ultimately, the message should reflect the values of supporting normal birth. For childbirth educators who are allowed to choose their own apparel to wear in their classes, street clothes may be the benchmark for which to strive. This article discusses the many nonverbal messages that clothes convey and provides support for the choice of street clothes as the dress for the professional childbirth educator; thus, “normal clothes to promote normal birth.” PMID:18408807

  19. Normal vibration frequencies of the vocal ligament

    NASA Astrophysics Data System (ADS)

    Titze, Ingo R.; Hunter, Eric J.

    2004-05-01

    The vocal ligament is the tension-bearing element in the vocal folds at high pitches. It has traditionally been treated as a vibrating string, with only length and longitudinal stress governing its normal mode frequencies. Results of this investigation show that, when bending stiffness and variable cross section are included, the lowest normal mode frequency can more than double, depending on the strain of the ligament. This suggests that much higher phonation frequencies may be achievable than heretofore thought for a given vocal fold length (e.g., nearly 1000 Hz at 50% elongation over cadaveric resting length). It also brings back into the discussion the concept of ``damping,'' an old misnomer for a reduction of the effective length of vibration of the vocal folds by relatively stiff boundary segments known as macula flavae. A formula is given for correcting the ideal string equation for the lowest mode frequency to include bending stiffness and macula flavae effects.

  20. Benchmarking all-atom simulations using hydrogen exchange

    SciTech Connect

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-10-27

    We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.

  1. Benchmarking all-atom simulations using hydrogen exchange

    DOE PAGES

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; ...

    2014-10-27

    We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability andmore » H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.« less

  2. Benchmarking all-atom simulations using hydrogen exchange

    PubMed Central

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413

  3. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations

    PubMed Central

    Lai, Peter C.; Crasto, Chiquito J.

    2012-01-01

    Olfactory receptors (ORs) are a type of GTP-binding protein-coupled receptor (GPCR). These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level beyond inferences that are drawn merely from static docking. Here we have shown the specific advantages of simulating the dynamic environment associated with OR-odorant interactions. We present a rigorous protocol which ranges from the creation of a computationally derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs. PMID:22563330

  4. Beyond modeling: all-atom olfactory receptor model simulations.

    PubMed

    Lai, Peter C; Crasto, Chiquito J

    2012-01-01

    Olfactory receptors (ORs) are a type of GTP-binding protein-coupled receptor (GPCR). These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level beyond inferences that are drawn merely from static docking. Here we have shown the specific advantages of simulating the dynamic environment associated with OR-odorant interactions. We present a rigorous protocol which ranges from the creation of a computationally derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.

  5. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

  6. Critical behavior of a passively mode-locked laser: rational harmonic mode locking.

    PubMed

    Zhan, Li; Gu, Zhaochang; Zhang, Jianwen; Xia, Yuxing

    2007-08-15

    The critical behavior of passive mode locking has been demonstrated in a figure-eight fiber laser that performs rational harmonic mode locking (RHML). On both the repetition rate and the pulse amplitude distribution, the observed pulse trains near the threshold exhibit the same regulations as the rational harmonic mode-locked ones. The theory also shows that there should be a middle status of RHML before achieving normal mode locking. It is important to note that the results provide what we believe to be the first confirmed attempt to address a fundamental question: how does a laser become mode locking with an increase of pump power?

  7. Influencing factors on the mode transition in a dual-mode scramjet

    NASA Astrophysics Data System (ADS)

    Yan, Zhang; Bing, Chen; Gang, Liu; Baoxi, Wei; Xu, Xu

    2014-10-01

    An experimental investigation was performed to characterize the effects of fuel type, injector configuration, inflow total temperature and fuel injection distribution on the mode transition in a dual-mode scramjet combustor. High enthalpy vitiated air was heated to three total temperatures by the hydrogen-oxygen combustion, entering the isolator entrance at a Mach number of 2.0. Fuel was injected through a four-hole aero-ramp or transverse injector, and ignited by a gas-pilot flame. At an inflow stagnation condition of P0=0.85 MPa and T0=1200 K, three combustion modes, namely Pure Scram Mode, Dual-Mode Scram Mode and Dual-Mode Ram Mode, were classified through the wall pressure distributions, one-dimensional performance analysis, and optical visualization. Two critical fuel equivalence ratios were selected to divide three combustion modes. At the lower transition point, ERlc, the transition from Pure Scram Mode to Dual-Mode Scram Mode occurred corresponding to a normalized wall pressure at x/H=2.5 of 0.23; while at the upper transition point, ERuc, the transition from Dual-Mode Scram Mode to Dual-Mode Ram Mode occurred corresponding to a normalized wall pressure at x/H=2.5 of 0.34. The transition width, ERw, was defined as the difference of two transition points. In this limited range, the combustor was operating in the Dual-Mode Scram Mode. The ERuc was estimated based on the Rayleigh flow relation, and the applicability of the analytic equation was testified through a series of experiments with different boundary conditions. The experimental results showed that two transition points in the ethylene case were higher in ER than in the hydrogen case, and the measured ERuc of two fuels were all 2.5 times larger than the predicted values. However, two fuels had little difference on the transition width. Due to the angled injection, two transition points in the aero-ramp case were higher in ER than in the transverse injector case; while the influence of injector

  8. Normalized medical information visualization.

    PubMed

    Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Somolinos, Roberto; Castro, Antonio; Velázquez, Iker; Moreno, Oscar; García-Pacheco, José L; Pascual, Mario; Salvador, Carlos H

    2015-01-01

    A new mark-up programming language is introduced in order to facilitate and improve the visualization of ISO/EN 13606 dual model-based normalized medical information. This is the first time that visualization of normalized medical information is addressed and the programming language is intended to be used by medical non-IT professionals.

  9. Normal Shock Vortex Interaction

    DTIC Science & Technology

    2003-03-01

    Figure 9: Breakdown map for normal-shock vortex-interaction. References [1] O. Thomer, W. Schroder and M. Meinke , Numerical Simulation of Normal...and Oblique-Shock Vortex Interaction, ZAMM Band 80, Sub. 1, pp. 181-184, 2000. [2] O. Thomer, E. Krause, W. Schroder and M. Meinke , Computational

  10. Mixed-mode fracture of ceramics

    SciTech Connect

    Petrovic, J.J.

    1985-01-01

    The mixed-mode fracture behavior of ceramic materials is of importance for monolithic ceramics in order to predict the onset of fracture under generalized loading conditions and for ceramic composites to describe crack deflection toughening mechanisms. Experimental data on surface flaw mixed-mode fracture in various ceramics indicate that the flaw-plane normal stress at fracture decreases with increasing in-flaw-plane shear stress, although present data exhibit a fairly wide range in details of this sigma - tau relationship. Fracture from large cracks suggests that Mode II has a greater effect on Mode I fracture than Mode III. A comparison of surface flaw and large crack mixed-mode I-II fracture responses indicated that surface flaw behavior is influenced by shear resistance effects.

  11. Normality in Analytical Psychology

    PubMed Central

    Myers, Steve

    2013-01-01

    Although C.G. Jung’s interest in normality wavered throughout his career, it was one of the areas he identified in later life as worthy of further research. He began his career using a definition of normality which would have been the target of Foucault’s criticism, had Foucault chosen to review Jung’s work. However, Jung then evolved his thinking to a standpoint that was more aligned to Foucault’s own. Thereafter, the post Jungian concept of normality has remained relatively undeveloped by comparison with psychoanalysis and mainstream psychology. Jung’s disjecta membra on the subject suggest that, in contemporary analytical psychology, too much focus is placed on the process of individuation to the neglect of applications that consider collective processes. Also, there is potential for useful research and development into the nature of conflict between individuals and societies, and how normal people typically develop in relation to the spectrum between individuation and collectivity. PMID:25379262

  12. Normal Pressure Hydrocephalus

    MedlinePlus

    ... techniques and neuroimaging, and finding improved treatments and preventions. Information from the National Library of Medicine’s MedlinePlus Normal Pressure Hydrocephalus × What research is being ...

  13. Normal Functioning Family

    MedlinePlus

    ... Spread the Word Shop AAP Find a Pediatrician Family Life Medical Home Family Dynamics Adoption & Foster Care ... Español Text Size Email Print Share Normal Functioning Family Page Content Article Body Is there any way ...

  14. Envelope Modes of Beams with Angular Momentum

    SciTech Connect

    Barnard, J J; Losic, B

    2000-08-21

    For a particle beam propagating in an alternating gradient focusing system, envelope equations are often employed to describe the evolution of the beam radii in the two directions transverse to the direction of propagation, and aligned with the principle axes of the alternating gradient system. When the beams have zero net angular momentum and when the alternating gradient focusing is approximated by a continuous focusing system, there are two normal modes to the envelope equations: the 'breathing' mode and a 'quadrupole' mode. In the former, the two radii oscillate in phase, and in the latter the radii oscillate 180 degrees out of phase. In this paper, we extend the analysis to include beams that have a finite angular momentum. We perturb the moment equations of ref. [1], wherein it was assumed that space charge is a distributed in a uniform density ellipse. Two additional modes are obtained. The breathing mode remains, but the quadrupole mode is split into two modes, and a new low frequency mode appears. We calculate the frequencies and eigenmodes of these four modes as a function of tune depression and a dimensionless net angular momentum. These modes can be excited by rotational errors of the quadrupoles in an alternating gradient focusing channel.

  15. List mode multichannel analyzer

    DOEpatents

    Archer, Daniel E.; Luke, S. John; Mauger, G. Joseph; Riot, Vincent J.; Knapp, David A.

    2007-08-07

    A digital list mode multichannel analyzer (MCA) built around a programmable FPGA device for onboard data analysis and on-the-fly modification of system detection/operating parameters, and capable of collecting and processing data in very small time bins (<1 millisecond) when used in histogramming mode, or in list mode as a list mode MCA.

  16. A la Mode II.

    ERIC Educational Resources Information Center

    Stowe, Richard A.

    This paper describes two modes of educational decision-making: Mode I, in which the instructor makes such decisions as what to teach, to whom, when, in what order, at what pace, and at what complexity level; and Mode II, in which the learner makes the decisions. While Mode I comprises most of what is regarded as formal education, the learner in…

  17. Apparent diffusion coefficient normalization of normal liver

    PubMed Central

    Zhu, Jie; Zhang, Jie; Gao, Jia-Yin; Li, Jin-Ning; Yang, Da-Wei; Chen, Min; Zhou, Cheng; Yang, Zheng-Han

    2017-01-01

    Abstract Apparent diffusion coefficient (ADC) measurement in diffusion-weighted imaging (DWI) has been reported to be a helpful biomarker for detection and characterization of lesion. In view of the importance of ADC measurement reproducibility, the aim of this study was to probe the variability of the healthy hepatic ADC values measured at 3 MR scanners from different vendors and with different field strengths, and to investigate the reproducibility of normalized ADC (nADC) value with the spleen as the reference organ. Thirty enrolled healthy volunteers received DWI with GE 1.5T, Siemens 1.5T, and Philips 3.0T magnetic resonance (MR) systems on liver and spleen (session 1) and were imaged again after 10 to 14 days using only GE 1.5T MR and Philips 3.0T MR systems (session 2). Interscan agreement and reproducibility of ADC measurements of liver and the calculated nADC values (ADCliver/ADCspleen) were statistically evaluated between 2 sessions. In session 1, ADC and nADC values of liver were evaluated for the scanner-related variability by 2-way analysis of variance and intraclass correlation coefficients (ICCs). Coefficients of variation (CVs) of ADCs and nADCs of liver were calculated for both 1.5 and 3.0-T MR system. Interscan agreement and reproducibility of ADC measurements of liver and related nADCs between 2 sessions were found to be satisfactory with ICC values of 0.773 to 0.905. In session 1, the liver nADCs obtained from different scanners were consistent (P = 0.112) without any significant difference in multiple comparison (P = 0.117 to >0.99) by using 2-way analysis of variance with post-hoc analysis of Bonferroni method, although the liver ADCs varied significantly (P < 0.001). nADCs measured by 3 scanners were in good interscanner agreements with ICCs of 0.685 to 0.776. The mean CV of nADCs of both 1.5T MR scanners (9.6%) was similar to that of 3.0T MR scanner (8.9%). ADCs measured at 3 MR scanners with different field strengths and vendors

  18. Gene expression during normal and malignant differentiation

    SciTech Connect

    Andersson, L.C.; Gahmberg, C.G.; Ekblom, P.

    1985-01-01

    This book contains 18 selections. Some of the titles are: Exploring Carcinogenesis with Retroviral and Cellular Oncogenes; Retroviruses, Oncogenes and Evolution; HTLV and Human Neoplasi; Modes of Activation of cMyc Oncogene in B and T Lymphoid Tumors; The Structure and Function of the Epidermal Growth Factor Receptor: Its Relationship to the Protein Product of the V-ERB-B Oncogene; and Expression of Human Retrovirus Genes in Normal and Neoplastic Epithelial Cells.

  19. Resonant mode at the band edge

    NASA Astrophysics Data System (ADS)

    Castro-Garay, P.; Vargas Hernández, D.; Manzanares-Martinez, J.; Corella-Madueño, A.; Rosas-Burgos, A.; Tanori, Dra J.; Pellat, A.; Estrada, S.

    2016-09-01

    We have found the solution of the boundary value problem for reflectance and transmittance of normal circularly polarized light impinges on a cholesteric elastomer film with a twist defect. We have found a tunable resonant mode in the reflectance band for right and left circularly polarized light. When the values of chiral twist defect are increased in the cholesteric elastomer film, the resonant modes changes to shorter wavelength until the edge band is reached.

  20. Quantifying surface normal estimation

    NASA Astrophysics Data System (ADS)

    Reid, Robert B.; Oxley, Mark E.; Eismann, Michael T.; Goda, Matthew E.

    2006-05-01

    An inverse algorithm for surface normal estimation from thermal polarimetric imagery was developed and used to quantify the requirements on a priori information. Building on existing knowledge that calculates the degree of linear polarization (DOLP) and the angle of polarization (AOP) for a given surface normal in a forward model (from an object's characteristics to calculation of the DOLP and AOP), this research quantifies the impact of a priori information with the development of an inverse algorithm to estimate surface normals from thermal polarimetric emissions in long-wave infrared (LWIR). The inverse algorithm assumes a polarized infrared focal plane array capturing LWIR intensity images which are then converted to Stokes vectors. Next, the DOLP and AOP are calculated from the Stokes vectors. Last, the viewing angles, θ v, to the surface normals are estimated assuming perfect material information about the imaged scene. A sensitivity analysis is presented to quantitatively describe the a priori information's impact on the amount of error in the estimation of surface normals, and a bound is determined given perfect information about an object. Simulations explored the impact of surface roughness (σ) and the real component (n) of a dielectric's complex index of refraction across a range of viewing angles (θ v) for a given wavelength of observation.

  1. Are Children "Normal"?

    PubMed

    Black, Dan A; Kolesnikova, Natalia; Sanders, Seth G; Taylor, Lowell J

    2013-03-01

    We examine Becker's (1960) contention that children are "normal." For the cross section of non-Hispanic white married couples in the U.S., we show that when we restrict comparisons to similarly-educated women living in similarly-expensive locations, completed fertility is positively correlated with the husband's income. The empirical evidence is consistent with children being "normal." In an effort to show causal effects, we analyze the localized impact on fertility of the mid-1970s increase in world energy prices - an exogenous shock that substantially increased men's incomes in the Appalachian coal-mining region. Empirical evidence for that population indicates that fertility increases in men's income.

  2. Polarization Dependent Whispering Gallery Modes in Microspheres

    NASA Technical Reports Server (NTRS)

    Adamovsky, Grigory (Inventor); Wrbanek, Susan Y. (Inventor)

    2016-01-01

    A tunable resonant system is provided and includes a microsphere that receives an incident portion of a light beam generated via a light source, the light beam having a fundamental mode, a waveguide medium that transmits the light beam from the light source to the microsphere, and a polarizer disposed in a path of the waveguide between the light source and the microsphere. The incident portion of the light beam creates a fundamental resonance inside the microsphere. A change in a normalized frequency of the wavelength creates a secondary mode in the waveguide and the secondary mode creates a secondary resonance inside the microsphere.

  3. Quasinormal modes of superfluid neutron stars

    NASA Astrophysics Data System (ADS)

    Gualtieri, L.; Kantor, E. M.; Gusakov, M. E.; Chugunov, A. I.

    2014-07-01

    We study nonradial oscillations of neutron stars with superfluid baryons, in a general relativistic framework, including finite temperature effects. Using a perturbative approach, we derive the equations describing stellar oscillations, which we solve by numerical integration, employing different models of nucleon superfluidity, and determining frequencies and gravitational damping times of the quasinormal modes. As expected by previous results, we find two classes of modes, associated to superfluid and non-superfluid degrees of freedom, respectively. We study the temperature dependence of the modes, finding that at specific values of the temperature, the frequencies of the two classes of quasinormal modes show avoided crossings, and their damping times become comparable. We also show that, when the temperature is not close to the avoided crossings, the frequencies of the modes can be accurately computed by neglecting the coupling between normal and superfluid degrees of freedom. Our results have potential implications on the gravitational wave emission from neutron stars.

  4. Tuning vibrational mode localization with frequency windowing

    NASA Astrophysics Data System (ADS)

    Cheng, Xiaolu; Talbot, Justin J.; Steele, Ryan P.

    2016-09-01

    Local-mode coordinates have previously been shown to be an effective starting point for anharmonic vibrational spectroscopy calculations. This general approach borrows techniques from localized-orbital machinery in electronic structure theory and generates a new set of spatially localized vibrational modes. These modes exhibit a well-behaved spatial decay of anharmonic mode couplings, which, in turn, allows for a systematic, a priori truncation of couplings and increased computational efficiency. Fully localized modes, however, have been found to lead to unintuitive mixtures of characteristic motions, such as stretches and bends, and accordingly large bilinear couplings. In this work, a very simple, tunable localization frequency window is introduced, in order to realize the transition from normal modes to fully localized modes. Partial localization can be achieved by localizing only pairs of modes within this traveling frequency window, which allows for intuitive interpretation of modes. The optimal window size is suggested to be a few hundreds of wave numbers, based on small- to medium-sized test systems, including water clusters and polypeptides. The new sets of partially localized coordinates retain their spatial coupling decay behavior while providing a reduced number of potential energy evaluations for convergence of anharmonic spectra.

  5. Microstructural effects on fracture toughness of polycrystalline ceramics in combined mode I and mode II loading

    NASA Technical Reports Server (NTRS)

    Singh, D.; Shetty, D. K.

    1988-01-01

    Fracture toughness of polycrystalline alumina and ceria partially-stabilized tetragonal zirconia (CeO2-TZP) ceramics were assessed in combined mode I and mode II loading using precracked disk specimens in diametral compression. Stress states ranging from pure mode I, combined mode I and mode II, and pure mode II were obtained by aligning the center crack at specific angles relative to the loading diameter. The resulting mixed-mode fracture toughness envelope showed significant deviation to higher fracture toughness in mode II relative to the predictions of the linear elastic fracture mechanics theory. Critical comparison with corresponding results on soda-lime glass and fracture surface observations showed that crack surface resistance arising from grain interlocking and abrasion was the main source of the increased fracture toughness in mode II loading of the polycrystalline ceramics. The normalized fracture toughness for pure mode II loading, (KII/KIc), increased with increasing grain size for the CeO2-TZP ceramics. Quantitative fractography confirmed an increased percentage of transgranular fracture of the grains in mode II loading.

  6. Normals to a Parabola

    ERIC Educational Resources Information Center

    Srinivasan, V. K.

    2013-01-01

    Given a parabola in the standard form y[superscript 2] = 4ax, corresponding to three points on the parabola, such that the normals at these three points P, Q, R concur at a point M = (h, k), the equation of the circumscribing circle through the three points P, Q, and R provides a tremendous opportunity to illustrate "The Art of Algebraic…

  7. Statokinesigram normalization method.

    PubMed

    de Oliveira, José Magalhães

    2017-02-01

    Stabilometry is a technique that aims to study the body sway of human subjects, employing a force platform. The signal obtained from this technique refers to the position of the foot base ground-reaction vector, known as the center of pressure (CoP). The parameters calculated from the signal are used to quantify the displacement of the CoP over time; there is a large variability, both between and within subjects, which prevents the definition of normative values. The intersubject variability is related to differences between subjects in terms of their anthropometry, in conjunction with their muscle activation patterns (biomechanics); and the intrasubject variability can be caused by a learning effect or fatigue. Age and foot placement on the platform are also known to influence variability. Normalization is the main method used to decrease this variability and to bring distributions of adjusted values into alignment. In 1996, O'Malley proposed three normalization techniques to eliminate the effect of age and anthropometric factors from temporal-distance parameters of gait. These techniques were adopted to normalize the stabilometric signal by some authors. This paper proposes a new method of normalization of stabilometric signals to be applied in balance studies. The method was applied to a data set collected in a previous study, and the results of normalized and nonnormalized signals were compared. The results showed that the new method, if used in a well-designed experiment, can eliminate undesirable correlations between the analyzed parameters and the subjects' characteristics and show only the experimental conditions' effects.

  8. Large mode radius resonators

    NASA Technical Reports Server (NTRS)

    Harris, Michael R.

    1987-01-01

    Resonator configurations permitting operation with large mode radius while maintaining good transverse mode discrimination are considered. Stable resonators incorporating an intracavity telescope and unstable resonator geometries utilizing an output coupler with a Gaussian reflectivity profile are shown to enable large radius single mode laser operation. Results of heterodyne studies of pulsed CO2 lasers with large (11mm e sup-2 radius) fundamental mode sizes are presented demonstrating minimal frequency sweeping in accordance with the theory of laser-induced medium perturbations.

  9. Few-mode fibers for mode division multiplexing transmission

    NASA Astrophysics Data System (ADS)

    Kubota, Hirokazu; Morioka, Toshio

    2012-01-01

    A study is presented of the fiber properties needed to achieve 10-mode multiplexing transmission. A combination of MIMO processing with optical LP mode separation is proposed to prevent the need for massive MIMO computation. The impact of mode crosstalk, differential mode delay, and the mode dependent loss of the few-mode fibers on mode multiplexing are discussed.

  10. Integrated mode converter for mode division multiplexing

    NASA Astrophysics Data System (ADS)

    Perez-Galacho, Diego; Alonso-Ramos, Carlos Alberto; Marris-Morini, Delphine; Vakarin, Vladyslav; Le Roux, Xavier; Ortega-Moñux, Alejandro; Wangüemert-Perez, Juan Gonzalo; Vivien, Laurent

    2016-05-01

    The ever growing demands of bandwidth in optical communication systems are making traditional Wavelength Division Multiplexing (WDM) based systems to reach its limit. In order to cope with future bandwidth demand is necessary to use new levels of orthogonality, such as the waveguide mode or the polarization state. Mode Division Multiplexing (MDM) has recently attracted attention as a possible solution to increase aggregate bandwidth. In this work we discuss the proposition a of mode converter that can cover the whole C-Band of optical communications. The Mode Converter is based on two Multimode Interference (MMI) couplers and a phase shifter. Insertion loss (IL) below 0.2 dB and Extinction ratio (ER) higher than 20 dB in a broad bandwidth range of 1.5 μm to 1.6 μm have been estimated. The total length of the device is less than 30 μm.

  11. Idiopathic Normal Pressure Hydrocephalus

    PubMed Central

    Nassar, Basant R.; Lippa, Carol F.

    2016-01-01

    Idiopathic normal pressure hydrocephalus (iNPH) is a potentially reversible neurodegenerative disease commonly characterized by a triad of dementia, gait, and urinary disturbance. Advancements in diagnosis and treatment have aided in properly identifying and improving symptoms in patients. However, a large proportion of iNPH patients remain either undiagnosed or misdiagnosed. Using PubMed search engine of keywords “normal pressure hydrocephalus,” “diagnosis,” “shunt treatment,” “biomarkers,” “gait disturbances,” “cognitive function,” “neuropsychology,” “imaging,” and “pathogenesis,” articles were obtained for this review. The majority of the articles were retrieved from the past 10 years. The purpose of this review article is to aid general practitioners in further understanding current findings on the pathogenesis, diagnosis, and treatment of iNPH. PMID:28138494

  12. Studies of normal hearing.

    PubMed

    Catlin, F I

    1984-01-01

    Auditory function changes continually from birth to old age. A variety of methods to assess hearing have evolved since the invention of the audiometer. Types of measurement include: electrical response in the central nervous system, cochlear acuity and speech responses. While some of these tests correlate fairly well with each other, their ability to represent overall hearing function is questionable. Other attempts to improve the assessment of hearing have been made in the area of self-appraisal, but these, too, have significant limitations. Most self-report and peer appraisal questionnaires have been established by studies of hearing-impaired populations. Norms for these techniques in normal-hearing populations need to be established. There is still room for valid tests of everyday communication. What we have in measurement procedures does not achieve this goal. Research studies of today will hopefully produce better definition of normal auditory function.

  13. Normal-reflection image

    SciTech Connect

    Huang, L.; Fehler, Michael C.

    2003-01-01

    Common-angle wave-equation migration using the double-square-root is generally less accurate than the common-shot migration because the wavefield continuation equation for thc former involves additional approximations compared to that for the latter. We present a common-angle wave-equation migration that has the same accuracy as common-shot wave-equation migration. An image obtained from common-angle migration is a four- to five-dimensional output volume for 3D cases. We propose a normal-reflection imaging condition for common-angle migration to produce a 3D output volume for 3D migration. The image is closely related to the normal-reflection coefficients at interfaces. This imaging condition will allow amplitude-preserving migration to generate an image with clear physical meaning.

  14. Neuroethics beyond Normal.

    PubMed

    Shook, John R; Giordano, James

    2016-01-01

    An integrated and principled neuroethics offers ethical guidelines able to transcend conventional and medical reliance on normality standards. Elsewhere we have proposed four principles for wise guidance on human transformations. Principles like these are already urgently needed, as bio- and cyberenhancements are rapidly emerging. Context matters. Neither "treatments" nor "enhancements" are objectively identifiable apart from performance expectations, social contexts, and civic orders. Lessons learned from disability studies about enablement and inclusion suggest a fresh way to categorize modifications to the body and its performance. The term "enhancement" should be broken apart to permit recognition of enablements and augmentations, and kinds of radical augmentation for specialized performance. Augmentations affecting the self, self-worth, and self-identity of persons require heightened ethical scrutiny. Reversibility becomes the core problem, not the easy answer, as augmented persons may not cooperate with either decommissioning or displacement into unaccommodating societies. We conclude by indicating how our four principles of self-creativity, nonobsolescence, empowerment, and citizenship establish a neuroethics beyond normal that is better prepared for a future in which humans and their societies are going so far beyond normal.

  15. Landsat-5 bumper-mode geometric correction

    USGS Publications Warehouse

    Storey, J.C.; Choate, Michael J.

    2004-01-01

    The Landsat-5 Thematic Mapper (TM) scan mirror was switched from its primary operating mode to a backup mode in early 2002 in order to overcome internal synchronization problems arising from long-term wear of the scan mirror mechanism. The backup bumper mode of operation removes the constraints on scan start and stop angles enforced in the primary scan angle monitor operating mode, requiring additional geometric calibration effort to monitor the active scan angles. It also eliminates scan timing telemetry used to correct the TM scan geometry. These differences require changes to the geometric correction algorithms used to process TM data. A mathematical model of the scan mirror's behavior when operating in bumper mode was developed. This model includes a set of key timing parameters that characterize the time-varying behavior of the scan mirror bumpers. To simplify the implementation of the bumper-mode model, the bumper timing parameters were recast in terms of the calibration and telemetry data items used to process normal TM imagery. The resulting geometric performance, evaluated over 18 months of bumper-mode operations, though slightly reduced from that achievable in the primary operating mode, is still within the Landsat specifications when the data are processed with the most up-to-date calibration parameters.

  16. Calculation of two-dimensional lambda modes

    SciTech Connect

    Belchior, A. Jr. ); Moreira, J.M.L. )

    1991-01-01

    A system for on-line monitoring of power distribution in small reactors (known as MAP) is under development at COPESP-IPEN. Signals of self-powered neutron detectors are input to a program that estimates the power distribution as an expansion of lambda modes. The modal coefficients are obtained from a least-mean-squares technique adequate for real-time analysis. Three-dimensional lambda modes are synthesized out of one- and two-dimensional lambda modes. As a part of this project, a modification of a computer code was carried out in order to obtain the lambda modes. The results of this effort are summarized. The lambda modes are the solutions of the time-independent multigroup neutron diffusion equation, an eigenvalue equation. Normally, the computer codes produce the fundamental mode corresponding to the largest eigenvalue; their respective interpretations are neutron flux distribution and effective multiplication factor. For calculating higher order lambda modes it is usually necessary to eliminate the contribution of the lower modes from the fission source.

  17. Dipole modes with depressed amplitudes in red giants are mixed modes

    NASA Astrophysics Data System (ADS)

    Mosser, B.; Belkacem, K.; Pinçon, C.; Takata, M.; Vrard, M.; Barban, C.; Goupil, M.-J.; Kallinger, T.; Samadi, R.

    2017-02-01

    Context. Seismic observations with the space-borne Kepler mission have shown that a number of evolved stars exhibit low-amplitude dipole modes, which is referred to as depressed modes. Recently, these low amplitudes have been attributed to the presence of a strong magnetic field in the stellar core of those stars. Subsequently, and based on this scenario, the prevalence of high magnetic fields in evolved stars has been inferred. It should be noted, however, that this conclusion remains indirect. Aims: We intend to study the properties of mode depression in evolved stars, which is a necessary condition before reaching conclusions about the physical nature of the mechanism responsible for the reduction of the dipole mode amplitudes. Methods: We perform a thorough characterization of the global seismic parameters of depressed dipole modes and show that these modes have a mixed character. The observation of stars showing dipole mixed modes that are depressed is especially useful for deriving model-independent conclusions on the dipole mode damping. We use a simple model to explain how mode visibilities are connected to the extra damping seen in depressed modes. Results: Observations prove that depressed dipole modes in red giants are not pure pressure modes but mixed modes. This result, observed in more than 90% of the bright stars (mV ≤ 11), invalidates the hypothesis that depressed dipole modes result from the suppression of the oscillation in the radiative core of the stars. Observations also show that, except for visibility, seismic properties of the stars with depressed modes are equivalent to those of normal stars. The measurement of the extra damping that is responsible for the reduction of mode amplitudes, without any prior on its physical nature, potentially provides an efficient tool for elucidating the mechanism responsible for the mode depression. Conclusions: The mixed nature of the depressed modes in red giants and their unperturbed global seismic

  18. Streaming tearing mode

    NASA Technical Reports Server (NTRS)

    Shigeta, M.; Sato, T.; Dasgupta, B.

    1985-01-01

    The magnetohydrodynamic stability of streaming tearing mode is investigated numerically. A bulk plasma flow parallel to the antiparallel magnetic field lines and localized in the neutral sheet excites a streaming tearing mode more strongly than the usual tearing mode, particularly for the wavelength of the order of the neutral sheet width (or smaller), which is stable for the usual tearing mode. Interestingly, examination of the eigenfunctions of the velocity perturbation and the magnetic field perturbation indicates that the streaming tearing mode carries more energy in terms of the kinetic energy rather than the magnetic energy. This suggests that the streaming tearing mode instability can be a more feasible mechanism of plasma acceleration than the usual tearing mode instability.

  19. Temperature modes for nonlinear Gaussian beams.

    PubMed

    Myers, Matthew R; Soneson, Joshua E

    2009-07-01

    In assessing the influence of nonlinear acoustic propagation on thermal bioeffects, approximate methods for quickly estimating the temperature rise as operational parameters are varied can be very useful. This paper provides a formula for the transient temperature rise associated with nonlinear propagation of Gaussian beams. The pressure amplitudes for the Gaussian modes can be obtained rapidly using a method previously published for simulating nonlinear propagation of Gaussian beams. The temperature-mode series shows that the nth temperature mode generated by nonlinear propagation, when normalized by the fundamental, is weaker than the nth heat-rate mode (also normalized by the fundamental in the heat-rate series) by a factor of log(n)/n, where n is the mode number. Predictions of temperature rise and thermal dose were found to be in close agreement with full, finite-difference calculations of the pressure fields, temperature rise, and thermal dose. Applications to non-Gaussian beams were made by fitting the main lobe of the significant modes to Gaussian functions.

  20. The plucked string: An example of non-normal dynamics

    NASA Astrophysics Data System (ADS)

    Politzer, David

    2015-05-01

    The motion of a single Fourier mode of the plucked string is an example of transient, free decay of linear, coupled, damped oscillators. It shares the rarely discussed features of the generic case, e.g., possessing a complete set of non-orthogonal eigenvectors and no normal modes, but it can be analyzed and solved analytically by hand in an approximation that is appropriate to musical instruments' plucked strings.

  1. Single-Mode VCSELs

    NASA Astrophysics Data System (ADS)

    Larsson, Anders; Gustavsson, Johan S.

    The only active transverse mode in a truly single-mode VCSEL is the fundamental mode with a near Gaussian field distribution. A single-mode VCSEL produces a light beam of higher spectral purity, higher degree of coherence and lower divergence than a multimode VCSEL and the beam can be more precisely shaped and focused to a smaller spot. Such beam properties are required in many applications. In this chapter, after discussing applications of single-mode VCSELs, we introduce the basics of fields and modes in VCSELs and review designs implemented for single-mode emission from VCSELs in different materials and at different wavelengths. This includes VCSELs that are inherently single-mode as well as inherently multimode VCSELs where higher-order modes are suppressed by mode selective gain or loss. In each case we present the current state-of-the-art and discuss pros and cons. At the end, a specific example with experimental results is provided and, as a summary, the most promising designs based on current technologies are identified.

  2. Ordinary electromagnetic mode instability

    NASA Technical Reports Server (NTRS)

    Cheng, C. Z.

    1974-01-01

    The instability of the ordinary electromagnetic mode propagating perpendicular to an external magnetic field is studied for a single-species plasma with ring velocity distribution. The marginal instability boundaries for both the purely growing mode and the propagating growing modes are calculated from the instability criteria. The dispersion characteristics for various sets of plasma parameters are also given. The typical growth rates are of the order of the cyclotron frequency.

  3. Acoustics measurements in normal jet impingement

    NASA Technical Reports Server (NTRS)

    Kleis, S. J.

    1977-01-01

    The dependence of far field acoustic measurements for a uniform jet on nozzle to plate spacing for small dimensionless spacings (h/d - 0.75 to 3.0) was investigated. Spectra from a real time analyzer were read and processed by an HP 2116 minicomputer in on-line mode. Similar data was generated for a fully developed pipe flow exit condition jet to compare with other investigations. The data base for normal jet impingement was extended to smaller values of nozzle to plate spacing. The effects of slight noise heating (30 deg rise) of the jet on the far field noise produced by the impinging jet are demonstrated.

  4. Normal osteoid tissue

    PubMed Central

    Raina, Vinita

    1972-01-01

    The results of a histological study of normal osteoid tissue in man, the monkey, the dog, and the rat, using thin microtome sections of plastic-embedded undecalcified bone, are described. Osteoid tissue covers the entire bone surface, except for areas of active resorption, although the thickness of the layer of osteoid tissue varies at different sites and in different species of animals. The histological features of osteoid tissue, apart from its amount, are the same in the different species studied. Distinct bands or zones are recognizable in some layers of osteoid tissue, particularly those of greatest thickness, and their significance is discussed. Some of the histological features of the calcification front are described. Images PMID:4111820

  5. Normal Untreated Jurkat Cells

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Biomedical research offers hope for a variety of medical problems, from diabetes to the replacement of damaged bone and tissues. Bioreactors, which are used to grow cells and tissue cultures, play a major role in such research and production efforts. The objective of the research was to define a way to differentiate between effects due to microgravity and those due to possible stress from non-optimal spaceflight conditions. These Jurkat cells, a human acute T-cell leukemia was obtained to evaluate three types of potential experimental stressors: a) Temperature elevation; b) Serum starvation; and c) Centrifugal force. The data from previous spaceflight experiments showed that actin filaments and cell shape are significantly different for the control. These normal cells serve as the baseline for future spaceflight experiments.

  6. Pornography, normalization, and empowerment.

    PubMed

    Weinberg, Martin S; Williams, Colin J; Kleiner, Sibyl; Irizarry, Yasmiyn

    2010-12-01

    Opponents and proponents of erotic representations (referred to hereafter as "pornography") have described the effects of pornography from their perspective. Little, however, has been done in the way of research to investigate these claims from the consumer's point of view. This especially has been so regarding the positive impact of such consumption on a person's sex life. Using a study group of 245 college students, we examined this question in a framework of scripting theory. We wanted to see whether viewing pornography appeared to expand sexual horizons through normalization and facilitate a willingness to explore new sexual behaviors and sexual relationships through empowerment. The data supported this viewpoint and further showed the effects to be mediated by gender and sexual preference identity. They suggested, however, that established scripts were extended rather than abandoned. We conclude with connections between our findings and the widespread viewing of pornography in contemporary society.

  7. Dual-Mode Combustor

    NASA Technical Reports Server (NTRS)

    Trefny, Charles J (Inventor); Dippold, Vance F (Inventor)

    2013-01-01

    A new dual-mode ramjet combustor used for operation over a wide flight Mach number range is described. Subsonic combustion mode is usable to lower flight Mach numbers than current dual-mode scramjets. High speed mode is characterized by supersonic combustion in a free-jet that traverses the subsonic combustion chamber to a variable nozzle throat. Although a variable combustor exit aperture is required, the need for fuel staging to accommodate the combustion process is eliminated. Local heating from shock-boundary-layer interactions on combustor walls is also eliminated.

  8. SAMPEX special pointing mode

    NASA Technical Reports Server (NTRS)

    Markley, F. Landis; Flatley, Thomas W.; Leoutsakos, Theodore

    1995-01-01

    A new pointing mode has been developed for the Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX) spacecraft. This pointing mode orients the instrument boresights perpendicular to the field lines of the Earth's magnetic field in regions of low field strength and parallel to the field lines in regions of high field strength, to allow better characterization of heavy ions trapped by the field. The new mode uses magnetometer signals and is algorithmically simpler than the previous control mode, but it requires increased momentum wheel activity. It was conceived, designed, tested, coded, uplinked to the spacecraft, and activated in less than seven months.

  9. New Measurements of Radial Mode Eigenfrequencies

    NASA Astrophysics Data System (ADS)

    Laske, G.; Masters, G.; Dziewonski, A. M.

    2001-12-01

    Radial mode eigenfrequencies are commonly thought to be measured with great ease and precision. The reason for this is that these modes have no geographic pattern so one should be able to measure frequencies from a spectrum observed at any station in the world. Yet, radial modes often seem inconsistent with spherical Earth models that fit all other mode frequencies. It turns out that radial modes are sometimes strongly coupled. The strongest coupling is predicted to be with l=2 modes which is caused by the Earth's hydrostatic ellipticity and aspherical structure of harmonic degree 2. In such cases, mode-coupling due to ellipticity alone can cause a frequency shift for the radial modes by more than 4 microHz. Given that mode frequencies can be measured to within 0.1 microHz, this shift is significant, and some singlets of l=2 modes have indeed been misidentified as the radial mode in the past. Including the spectra of the June 23, 2001 Southern Peru Earthquake we have re-analyzed radial mode eigenfrequencies and present a mode dataset that is internally more consistent than previous ones. We construct spherical Earth models that are consistent with our new data, the Earth's mass and moment of inertia and the current best estimates of ``Reference Normal Mode Data'' (available on the Reference Earth Model web site: //mahi.ucsd.edu/Gabi/rem.html). We seek the smallest perturbation to PREM but update the Q-structure as well as the depths of the upper mantle discontinuities (418~km and 660~km as first order discontinuities; 520~km as change in gradient). The best fitting 1D model is transversely isotropic but we also show isotropic models that fit the data to within their errors. We show that the 220~km discontinuity is not required in the isotropic model but that there exists a trade-off between high shear-velocities in the lid and a low-density zone beneath it. We also investigate ways of truncating transverse isotropy without the 220.

  10. A method for normalization of X-ray absorption spectra

    SciTech Connect

    Weng, T.-C.; Waldo, G.S.; Penner-Hahn, J.E.

    2010-07-20

    Accurate normalization of X-ray absorption data is essential for quantitative analysis of near-edge features. A method, implemented as the program MBACK, to normalize X-ray absorption data to tabulated mass absorption coefficients is described. Comparison of conventional normalization methods with MBACK demonstrates that the new normalization method is not sensitive to the shape of the background function, thus allowing accurate comparison of data collected in transmission mode with data collected using fluorescence ion chambers or solid-state fluorescence detectors. The new method is shown to have better reliability and consistency and smaller errors than conventional normalization methods. The sensitivity of the new normalization method is illustrated by analysis of data collected during an equilibrium titration.

  11. VSCF calculations for the intra- and intermolecular vibrational modes of the water dimer and its isotopologs

    NASA Astrophysics Data System (ADS)

    Monteiro, João G. S.; Barbosa, André G. H.

    2016-11-01

    In this work we show how the VSCF method may be successfully used to describe all fundamental vibrational transitions of several isotopologs of water dimer. By expressing the normal mode displacements in terms of appropriate delocalized internal coordinates we are able to minimize the mode-mode coupling in the PES and thus yield PT2-VSCF frequencies in good agreement with the experiment. The use of curvilinear normal modes is of paramount importance to describe vibrational transitions of the very soft intermolecular modes. Within our approach the maximum calculated error for the (H2O)2 intermolecular frequencies are reduced from 311 cm-1 (Cartesian normal modes) to just 56 cm-1 (curvilinear normal modes). Plots of the diagonal intermolecular potential and of the vibrational wave function illustrate the remarkable effect of different coordinate systems. In conclusion, our PT2-VSCF calculations provide a fair anharmonic description of the fundamental transitions of water dimers.

  12. Role of the normal gut microbiota

    PubMed Central

    Jandhyala, Sai Manasa; Talukdar, Rupjyoti; Subramanyam, Chivkula; Vuyyuru, Harish; Sasikala, Mitnala; Reddy, D Nageshwar

    2015-01-01

    Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual’s life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool. PMID:26269668

  13. [Normal aging and cognition].

    PubMed

    Ska, Bernadette; Joanette, Yves

    2006-03-01

    It is now well documented that normal aging modifies the cognitive functioning and most observations suggest that cognition evolves in the direction of deterioration. The more frequently impaired functions are memory, attention and visual-spatial abilities. On the other hand, some abilities seem to increase, such as vocabulary. Considering the aging effect on cognition, questions remain regarding directionality, universality and reversibility. A great variability in aged related impacts is observed among subjects and among cognitive domains. Some individuals evolved more rapidly than others. Some cognitive functions are more affected by aging than others. General and specific factors are hypothesized to explain the aged related cognitive decline. Among them, educational level, health, cognitive style, life style, personality, are likely to modulate the aged related cognitive evolution by influencing attentional resources and cerebral plasticity. Cognitive resources are essential to develop adaptative strategies. During the life span, resources are activated and increased by learning and training. Considering the role of cognitive resources, successful aging is dependent on several conditions : absence of disease leading to a loss of autonomy, maintenance of cognitive and physical activities, and active and social engaged lifestyle.

  14. Mode decomposition evolution equations

    PubMed Central

    Wang, Yang; Wei, Guo-Wei; Yang, Siyang

    2011-01-01

    Partial differential equation (PDE) based methods have become some of the most powerful tools for exploring the fundamental problems in signal processing, image processing, computer vision, machine vision and artificial intelligence in the past two decades. The advantages of PDE based approaches are that they can be made fully automatic, robust for the analysis of images, videos and high dimensional data. A fundamental question is whether one can use PDEs to perform all the basic tasks in the image processing. If one can devise PDEs to perform full-scale mode decomposition for signals and images, the modes thus generated would be very useful for secondary processing to meet the needs in various types of signal and image processing. Despite of great progress in PDE based image analysis in the past two decades, the basic roles of PDEs in image/signal analysis are only limited to PDE based low-pass filters, and their applications to noise removal, edge detection, segmentation, etc. At present, it is not clear how to construct PDE based methods for full-scale mode decomposition. The above-mentioned limitation of most current PDE based image/signal processing methods is addressed in the proposed work, in which we introduce a family of mode decomposition evolution equations (MoDEEs) for a vast variety of applications. The MoDEEs are constructed as an extension of a PDE based high-pass filter (Europhys. Lett., 59(6): 814, 2002) by using arbitrarily high order PDE based low-pass filters introduced by Wei (IEEE Signal Process. Lett., 6(7): 165, 1999). The use of arbitrarily high order PDEs is essential to the frequency localization in the mode decomposition. Similar to the wavelet transform, the present MoDEEs have a controllable time-frequency localization and allow a perfect reconstruction of the original function. Therefore, the MoDEE operation is also called a PDE transform. However, modes generated from the present approach are in the spatial or time domain and can be

  15. Excursions through KK modes

    NASA Astrophysics Data System (ADS)

    Furuuchi, Kazuyuki

    2016-07-01

    In this article we study Kaluza-Klein (KK) dimensional reduction of massive Abelian gauge theories with charged matter fields on a circle. Since local gauge transformations change position dependence of the charged fields, the decomposition of the charged matter fields into KK modes is gauge dependent. While whole KK mass spectrum is independent of the gauge choice, the mode number depends on the gauge. The masses of the KK modes also depend on the field value of the zero-mode of the extra dimensional component of the gauge field. In particular, one of the KK modes in the KK tower of each massless 5D charged field becomes massless at particular values of the extra-dimensional component of the gauge field. When the extra-dimensional component of the gauge field is identified with the inflaton, this structure leads to recursive cosmological particle productions.

  16. Zero-mode waveguides

    DOEpatents

    Levene, Michael J.; Korlach, Jonas; Turner, Stephen W.; Craighead, Harold G.; Webb, Watt W.

    2007-02-20

    The present invention is directed to a method and an apparatus for analysis of an analyte. The method involves providing a zero-mode waveguide which includes a cladding surrounding a core where the cladding is configured to preclude propagation of electromagnetic energy of a frequency less than a cutoff frequency longitudinally through the core of the zero-mode waveguide. The analyte is positioned in the core of the zero-mode waveguide and is then subjected, in the core of the zero-mode waveguide, to activating electromagnetic radiation of a frequency less than the cut-off frequency under conditions effective to permit analysis of the analyte in an effective observation volume which is more compact than if the analysis were carried out in the absence of the zero-mode waveguide.

  17. Excursions through KK modes

    SciTech Connect

    Furuuchi, Kazuyuki

    2016-07-07

    In this article we study Kaluza-Klein (KK) dimensional reduction of massive Abelian gauge theories with charged matter fields on a circle. Since local gauge transformations change position dependence of the charged fields, the decomposition of the charged matter fields into KK modes is gauge dependent. While whole KK mass spectrum is independent of the gauge choice, the mode number depends on the gauge. The masses of the KK modes also depend on the field value of the zero-mode of the extra dimensional component of the gauge field. In particular, one of the KK modes in the KK tower of each massless 5D charged field becomes massless at particular values of the extra-dimensional component of the gauge field. When the extra-dimensional component of the gauge field is identified with the inflaton, this structure leads to recursive cosmological particle productions.

  18. Mode couplings and resonance instabilities in dust clusters.

    PubMed

    Qiao, Ke; Kong, Jie; Oeveren, Eric Van; Matthews, Lorin S; Hyde, Truell W

    2013-10-01

    The normal modes for three to seven particle two-dimensional (2D) dust clusters in a complex plasma are investigated using an N-body simulation. The ion wakefield downstream of each particle is shown to induce coupling between horizontal and vertical modes. The rules of mode coupling are investigated by classifying the mode eigenvectors employing the Bessel and trigonometric functions indexed by order integers (m, n). It is shown that coupling only occurs between two modes with the same m and that horizontal modes having a higher shear contribution exhibit weaker coupling. Three types of resonances are shown to occur when two coupled modes have the same frequency. Discrete instabilities caused by both the first and third type of resonances are verified and instabilities caused by the third type of resonance are found to induce melting. The melting procedure is observed to go through a two-step process with the solid-liquid transition closely obeying the Lindemann criterion.

  19. On Mode Correlation of Solar Acoustic Oscillations

    NASA Astrophysics Data System (ADS)

    Chang, Heon-Young

    2009-09-01

    In helioseismology it is normally assumed that p-mode oscillations are excited in a statistically independent fashion. Unfortunately, however, this issue is not clearly settled down in that two experiments exist, which apparently look in discrepancy. That is, Appourchaux et al.~(2000) looked at bin-to-bin correlation and found no evidence that the assumption is invalid. On the other hand, Roth (2001) reported that p-mode pairs with nearby frequencies tend to be anti-correlated, possibly by a mode-coupling effect. This work is motivated by an idea that one may test if there exists an excess of anticorrelated power variations of pairs of solar p-modes. We have analyzed a 72-day MDI spherical-harmonic time series to examine temporal variations of p-mode power and their correlation. The power variation is computed by a running-window method after the previous study by Roth (2001), and then distribution function of power correlation between mode pairs is produced. We have confirmed Roth's result that there is an excess of anti-correlated p-mode pairs with nearby frequencies. On the other hand, the amount of excess was somewhat smaller than the previous study. Moreover, the distribution function does not exhibit significant change when we paired modes with non-nearby frequencies, implying that the excess is not due to mode coupling. We conclude that the origin of this excess of anticorrelations may not be a solar physical process, by pointing out the possibility of statistical bias playing the central role in producing the excess.

  20. Normal Conducting CLIC Technology

    SciTech Connect

    Jensen, Erk

    2006-01-03

    The CLIC (Compact Linear Collider) multi-lateral study group based at CERN is studying the technology for an electron-positron linear collider with a centre-of-mass energy up to 5 TeV. In contrast to the International Linear Collider (ILC) study which has chosen to use super-conducting cavities with accelerating gradients in the range of 30-40 MV/m to obtain centre-of-mass collision energies of 0.5-1 TeV, the CLIC study aims to use a normal-conducting system based on two-beam technology with gradients of 150 MV/m. It is generally accepted that this change in technology is not only necessary but the only viable choice for a cost-effective multi-TeV collider. The CLIC study group is studying the technology issues of such a machine, and is in particular developing state-of-the-art 30 GHz molybdenum-iris accelerating structures and power extraction and transfer structures (PETS). The accelerating structure has a new geometry which includes fully-profiled RF surfaces optimised to minimize surface fields, and hybrid damping using both iris slots and radial waveguides. A newly-developed structure-optimisation procedure has been used to simultaneously balance surface fields, power flow, short and long-range transverse wakefields, RF-to-beam efficiency and the ratio of luminosity to input power. The slotted irises allow a simple structure fabrication by high-precision high-speed 3D milling of just four pieces, and an even easier bolted assembly in a vacuum chamber.

  1. Normal Conducting CLIC Technology

    NASA Astrophysics Data System (ADS)

    Jensen, Erk

    2006-01-01

    The CLIC (Compact Linear Collider) multi-lateral study group based at CERN is studying the technology for an electron-positron linear collider with a centre-of-mass energy up to 5 TeV. In contrast to the International Linear Collider (ILC) study which has chosen to use super-conducting cavities with accelerating gradients in the range of 30-40 MV/m to obtain centre-of-mass collision energies of 0.5-1 TeV, the CLIC study aims to use a normal-conducting system based on two-beam technology with gradients of 150 MV/m. It is generally accepted that this change in technology is not only necessary but the only viable choice for a cost-effective multi-TeV collider. The CLIC study group is studying the technology issues of such a machine, and is in particular developing state-of-the-art 30 GHz molybdenum-iris accelerating structures and power extraction and transfer structures (PETS). The accelerating structure has a new geometry which includes fully-profiled RF surfaces optimised to minimize surface fields, and hybrid damping using both iris slots and radial waveguides. A newly-developed structure-optimisation procedure has been used to simultaneously balance surface fields, power flow, short and long-range transverse wakefields, RF-to-beam efficiency and the ratio of luminosity to input power. The slotted irises allow a simple structure fabrication by high-precision high-speed 3D milling of just four pieces, and an even easier bolted assembly in a vacuum chamber.

  2. Onset and Saturation of a Non-resonant Internal Mode in NSTX and Implications For AT Modes in ITER

    SciTech Connect

    J.A. Breslau, M.S. Chance, J. Chen, G.Y. Fu, S,. Gerhardt, N. Gorelenkov, S.C. Jardin and J. Manickam

    2011-08-01

    Motivated by experimental observations of apparently triggerless tearing modes, we have performed linear and nonlinear MHD analysis showing that a non-resonant mode with toroidal mode number n = 1 can develop in the National Spherical Torus eXperiment (NSTX) at moderate normalized βN when the shear is low and the central safety factor q0 is close to but greater than one. This mode, which is related to previously identified ‘infernal’ modes, will saturate and persist, and can develop poloidal mode number m = 2 magnetic islands in agreement with experiments. We have also extended this analysis by performing a free-boundary transport simulation of an entire discharge and showing that, with reasonable assumptions, we can predict the time of mode onset. __________________________________________________

  3. A numerical method for seeking the relationship between structural modes and acoustic radiation modes of complicated structures

    NASA Astrophysics Data System (ADS)

    Chang-wei, SU; Hai-chao, ZHU; Chang-geng, SHUAI; Rong-fu, MAO

    2016-09-01

    Both structural modes and acoustic radiation modes play important roles in the investigation of structure-borne sound. However, little work has been done for inherent relations between these two kinds of modes. Previous work has mainly dealt with simple and regular structures such as rectangular plates and single-layer cylindrical shells. Therefore, the relationship between structural modes and acoustic radiation modes of complicated structures which has great theory significance and utility value is an important problem that must be studied. This paper presents a numerical method for seeking the relationship between structural modes and acoustic radiation modes of complicated structures. First, a governing equation for relating these two kinds of modes is given based on the characteristics of the modes. Then, substitute the normal structural mode shape matrix and the acoustic radiation mode shape matrix which are obtained by FEM into the governing equation, the modal participating coefficients can be solved, thus we can get the corresponding relations between these two kinds of modes. Using the model of a simply supported truncated conical shell, a numerical example is presented with the numerical method which this paper has proposed. And then, the radiated sound power is calculated to verify the effectiveness of this method and the correctness of this conclusion. The results show that the numerical method proposed in this paper is feasible.

  4. Observations of core-mantle boundary Stoneley modes

    NASA Astrophysics Data System (ADS)

    Koelemeijer, Paula; Deuss, Arwen; Ritsema, Jeroen

    2013-06-01

    Core-mantle boundary (CMB) Stoneley modes represent a unique class of normal modes with extremely strong sensitivity to wave speed and density variations in the D" region. We measure splitting functions of eight CMB Stoneley modes using modal spectra from 93 events with Mw> 7.4 between 1976 and 2011. The obtained splitting function maps correlate well with the predicted splitting calculated for S20RTS+Crust5.1 structure and the distribution of Sdiff and Pdiff travel time anomalies, suggesting that they are robust. We illustrate how our new CMB Stoneley mode splitting functions can be used to estimate density variations in the Earth's lowermost mantle.

  5. Mode II fatigue crack propagation.

    NASA Technical Reports Server (NTRS)

    Roberts, R.; Kibler, J. J.

    1971-01-01

    Fatigue crack propagation rates were obtained for 2024-T3 bare aluminum plates subjected to in-plane, mode I, extensional loads and transverse, mode II, bending loads. These results were compared to the results of Iida and Kobayashi for in-plane mode I-mode II extensional loads. The engineering significance of mode I-mode II fatigue crack growth is considered in view of the present results. A fatigue crack growth equation for handling mode I-mode II fatigue crack growth rates from existing mode I data is also discussed.

  6. Dominant modes via model error

    NASA Technical Reports Server (NTRS)

    Yousuff, A.; Breida, M.

    1992-01-01

    Obtaining a reduced model of a stable mechanical system with proportional damping is considered. Such systems can be conveniently represented in modal coordinates. Two popular schemes, the modal cost analysis and the balancing method, offer simple means of identifying dominant modes for retention in the reduced model. The dominance is measured via the modal costs in the case of modal cost analysis and via the singular values of the Gramian-product in the case of balancing. Though these measures do not exactly reflect the more appropriate model error, which is the H2 norm of the output-error between the full and the reduced models, they do lead to simple computations. Normally, the model error is computed after the reduced model is obtained, since it is believed that, in general, the model error cannot be easily computed a priori. The authors point out that the model error can also be calculated a priori, just as easily as the above measures. Hence, the model error itself can be used to determine the dominant modes. Moreover, the simplicity of the computations does not presume any special properties of the system, such as small damping, orthogonal symmetry, etc.

  7. Edge chlorination of hexa-peri-hexabenzocoronene investigated by density functional theory and vibrational spectroscopy† †Electronic supplementary information (ESI) available: Description and animations of the vibrational normal modes of HBC and HBC-Cl discussed in the text. See DOI: 10.1039/c5cp07755a Click here for additional data file. Click here for additional data file.

    PubMed Central

    Maghsoumi, Ali; Narita, Akimitsu; Dong, Renhao; Feng, Xinliang; Castiglioni, Chiara

    2016-01-01

    We investigate the molecular structure and vibrational properties of perchlorinated hexa-peri-hexabenzocoronene (HBC-Cl) by density functional theory (DFT) calculations and IR and Raman spectroscopy, in comparison to the parent HBC. The theoretical and experimental IR and Raman spectra demonstrated very good agreement, elucidating a number of vibrational modes corresponding to the observed peaks. Compared with the parent HBC, the edge chlorination significantly alters the planarity of the molecule. Nevertheless, the results indicated that such structural distortion does not significantly impair the π-conjugation of such polycyclic aromatic hydrocarbons. PMID:26912311

  8. WMAP normalization of inflationary cosmologies

    SciTech Connect

    Liddle, Andrew R.; Parkinson, David; Mukherjee, Pia; Leach, Samuel M.

    2006-10-15

    We use the three-year WMAP observations to determine the normalization of the matter power spectrum in inflationary cosmologies. In this context, the quantity of interest is not the normalization marginalized over all parameters, but rather the normalization as a function of the inflationary parameters n{sub S} and r with marginalization over the remaining cosmological parameters. We compute this normalization and provide an accurate fitting function. The statistical uncertainty in the normalization is 3%, roughly half that achieved by COBE. We use the k-l relation for the standard cosmological model to identify the pivot scale for the WMAP normalization. We also quote the inflationary energy scale corresponding to the WMAP normalization.

  9. Supersymmetric mode converters

    NASA Astrophysics Data System (ADS)

    Heinrich, Matthias; Miri, Mohammad-Ali; Stützer, Simon; Nolte, Stefan; Szameit, Alexander; Christodoulides, Demetrios N.

    2015-08-01

    In recent years, the ever-increasing demand for high-capacity transmission systems has driven remarkable advances in technologies that encode information on an optical signal. Mode-division multiplexing makes use of individual modes supported by an optical waveguide as mutually orthogonal channels. The key requirement in this approach is the capability to selectively populate and extract specific modes. Optical supersymmetry (SUSY) has recently been proposed as a particularly elegant way to resolve this design challenge in a manner that is inherently scalable, and at the same time maintains compatibility with existing multiplexing strategies. Supersymmetric partners of multimode waveguides are characterized by the fact that they share all of their effective indices with the original waveguide. The crucial exception is the fundamental mode, which is absent from the spectrum of the partner waveguide. Here, we demonstrate experimentally how this global phase-matching property can be exploited for efficient mode conversion. Multimode structures and their superpartners are experimentally realized in coupled networks of femtosecond laser-written waveguides, and the corresponding light dynamics are directly observed by means of fluorescence microscopy. We show that SUSY transformations can readily facilitate the removal of the fundamental mode from multimode optical structures. In turn, hierarchical sequences of such SUSY partners naturally implement the conversion between modes of adjacent order. Our experiments illustrate just one of the many possibilities of how SUSY may serve as a building block for integrated mode-division multiplexing arrangements. Supersymmetric notions may enrich and expand integrated photonics by versatile optical components and desirable, yet previously unattainable, functionalities.

  10. Analysis of MHD instabilities limiting high normalized beta operation in KSTAR

    NASA Astrophysics Data System (ADS)

    Park, Y. S.; Sabbagh, S. A.; Berkery, J. W.; Bialek, J. M.; Yoon, S. W.; Kim, J.; Jeon, Y. M.; Bak, J. G.; Ko, W. H.; Hahn, S. H.; in, Y. K.; Choi, M. J.; Lee, S. G.; Kwak, J. G.; Oh, Y. K.; Park, H. K.; Yun, G. S.; Jardin, S. C.

    2016-10-01

    H-mode plasma operation in KSTAR reached high normalized beta up to 4.3 that significantly surpassed the computed n = 1 ideal no-wall beta limit by a factor of 1.6. Pulse lengths at maximum normalized beta were extended to longer pulses by new, more rapid equilibrium control resulting in normalized beta greater than 3 sustained for 1 s. Analysis of these plasmas shows that low- n global kink/ballooning or resistive wall modes (RWMs) were not the cause of the plasma termination. Kinetic modification of the ideal MHD n = 1 stability criterion computed by the MISK code shows the kinetic RWM to be stable, which is consistent with the observed high normalized beta operation. An m/ n = 2/1 tearing mode onsets at high normalized beta greater than 3 that experimentally reduces normalized beta by more than 30%. The stability of the observed 2/1 tearing mode examined by using the M3D-C1 code coupled with the EFIT reconstruction shows a stable 2/1 mode while the equilibrium is experimentally unstable to the 2/1 mode This result may imply that the mode is classically stable, and the pressuredriven neoclassical terms dominate over the current gradient term. Advances in the analysis from the recent run campaign will be reported. Supported by U.S. DOE Grant DE-FG02-99ER54524.

  11. The use of normal forms for analysing nonlinear mechanical vibrations

    PubMed Central

    Neild, Simon A.; Champneys, Alan R.; Wagg, David J.; Hill, Thomas L.; Cammarano, Andrea

    2015-01-01

    A historical introduction is given of the theory of normal forms for simplifying nonlinear dynamical systems close to resonances or bifurcation points. The specific focus is on mechanical vibration problems, described by finite degree-of-freedom second-order-in-time differential equations. A recent variant of the normal form method, that respects the specific structure of such models, is recalled. It is shown how this method can be placed within the context of the general theory of normal forms provided the damping and forcing terms are treated as unfolding parameters. The approach is contrasted to the alternative theory of nonlinear normal modes (NNMs) which is argued to be problematic in the presence of damping. The efficacy of the normal form method is illustrated on a model of the vibration of a taut cable, which is geometrically nonlinear. It is shown how the method is able to accurately predict NNM shapes and their bifurcations. PMID:26303917

  12. Forest canopy interactions with nucleation mode particles

    NASA Astrophysics Data System (ADS)

    Pryor, S. C.; Hornsby, K. E.; Novick, K. A.

    2014-11-01

    Ultrafine particle size distributions through a deciduous forest canopy indicate that nucleation mode particle concentrations decline with depth into the canopy, such that number concentrations at the bottom of the canopy are an average of 16% lower than those at the top. However, growth rates of nucleation mode particles (diameters 6-30 nm) are invariant with height within the canopy, which implies that the semi-volatile gases contributing to their growth are comparatively well-mixed through the canopy. Growth rates of nucleation mode particles during a meteorological drought year (2012) were substantially lower than during a meteorologically normal year with high soil water potential (2013). This may reflect suppression of actual biogenic volatile organic compound (BVOC) emissions by drought and thus a reduction in the production of condensable products during the drought-affected vegetation season. This hypothesis is supported by evidence that growth rates during the normal year exhibit a positive correlation with emissions of BVOC modeled on observed forest composition, leaf area index, temperature and photosynthetically active radiation (PAR), but particle growth rates during the drought-affected vegetation season are not correlated with modeled BVOC emissions. These data thus provide indirect evidence that drought stress in forests may reduce BVOC emissions and limit growth of nucleation mode particles to climate-relevant sizes.

  13. H-mode plasma transport simulation in ITER with effect of neoclassical tearing mode

    NASA Astrophysics Data System (ADS)

    Takahashi, Y.; Yamazaki, K.; Arimoto, H.; Shoji, T.

    2008-07-01

    For the prediction of the ITER plasmas, the effect of the neoclassical tearing mode (NTM) on the plasma confinement has been calculated using the 1.5-dimensional equilibrium and transport simulation code TOTAL. The time evolution of the NTM magnetic island has been analyzed using the modified Rutherford equation for ITER normal shear plasmas. The anomalous transport model used here is GLF23. The saturated magnetic island widths are w/a ~ 0.048 at 3/2 mode and w/a~0.21 at 2/1 mode, and the reduction in fusion power output by NTM is 27% at the 3/2 mode, and 82% at the 2/1 mode. The stabilization effect of the electron cyclotron current drive (ECCD) with EC is also clarified. The threshold of ECCD power for the full stabilization at high beta NTM island formation is ~10 MW against the 3/2 mode, and ~23 MW against the 2/1 mode.

  14. Ductile fracture in HY100 steel under mixed mode I/mode II loading

    SciTech Connect

    Bhattacharjee, D. . Dept. of Materials Science and Metallurgy); Knott, J.F. . School of Metallurgy and Materials)

    1994-05-01

    A number of criteria have been proposed which predict the direction of cracking under mixed Mode 1/Mode 2 loading. All have been evaluated for brittle materials, in which a crack subjected to tension and shear propagates normal to the maximum tensile stress (i.e. fracture is of the Mode 1 type). In a ductile material, however, a notch subjected to mixed Mode 1/Mode 2 loading may initiate a crack in the direction of maximum shear. This paper shows that the profile of the notch tip changes with increasing mixed mode load in such a way that one side of the tip blunts while the other sharpens. Various specimens, subjected to the same mixed mode ratio, were unloaded from different points on the load-displacement curves to study the change in notch-tip profile. Studies under the Scanning Electron Microscope (SEM) have shown that cracks initiate at the sharpened end, along a microscopic shear band. Using a dislocation pile-up model for decohesion of the carbide-matrix interface, a micromechanical model has been proposed for crack initiation in the shear band. It is shown that a theoretical prediction of the shear strain required for decohesion gives a result that is, of magnitude, similar to that of the shear strain at crack initiation measured in the experiments.

  15. Unidirectional dissipative soliton operation in an all-normal-dispersion Yb-doped fiber laser without an isolator.

    PubMed

    Li, Daojing; Shen, Deyuan; Li, Lei; Chen, Hao; Tang, Dingyuan; Zhao, Luming

    2015-09-10

    We demonstrate self-started unidirectional dissipative soliton operation and noise-like pulse operation in an all-normal-dispersion bidirectional Yb-doped fiber laser mode-locked by nonlinear polarization rotation. The laser works unidirectionally once mode-locking is achieved due to the cavity directional nonlinearity asymmetry along with the nonlinear polarization rotation mode-locking mechanism.

  16. Efficient femtosecond pulse generation in an all-normal-dispersion Yb:fiber ring laser at 605 MHz repetition rate.

    PubMed

    Yang, Hongyu; Wang, Aimin; Zhang, Zhigang

    2012-03-01

    We report a 1030 nm-wavelength Yb:fiber laser that produces the shortest/direct output pulse duration (502 fs) among all-normal-dispersion fiber lasers at the highest repetition rate (605 MHz) among the passively fundamentally mode-locked fiber lasers. The laser also exhibits an optical efficiency of 70% at CW and 65% at mode-locking modes.

  17. Violin plate modes.

    PubMed

    Gough, Colin

    2015-01-01

    As the first step toward developing a generic model for the acoustically radiating vibrational modes of the violin and related instruments, the modes of both freely supported and edge-constrained top and back plates have been investigated as functions of shape, arching height, elastic anisotropy, the f-holes and associated island area, thickness graduations, and the additional boundary constraints of the ribs, soundpost, and bass-bar present in the assembled instrument. Comsol shell structure finite element software has been used as a quasi-experimental tool, with physical and geometric properties varied smoothly, often over several orders of magnitude, allowing the development of the plate modes to be followed continuously from those of an initially square plate to those of doubly-arched, guitar-shaped, orthotropic plates and their dependence on all the above factors.

  18. Whispering Bloch modes

    PubMed Central

    Craster, R. V.

    2016-01-01

    We investigate eigenvalue problems for the planar Helmholtz equation in open systems with a high order of rotational symmetry. The resulting solutions have similarities with the whispering gallery modes exploited in photonic micro-resonators and elsewhere, but unlike these do not necessarily require a surrounding material boundary, with confinement instead resulting from the geometry of a series of inclusions arranged in a ring. The corresponding fields exhibit angular quasi-periodicity reminiscent of Bloch waves, and hence we refer to them as whispering Bloch modes (WBMs). We show that if the geometry of the system is slightly perturbed such that the rotational symmetry is broken, modes with asymmetric field patterns can be observed, resulting in field enhancement and other potentially desirable effects. We investigate the WBMs of two specific geometries first using expansion methods and then by applying a two-scale asymptotic scheme. PMID:27493564

  19. Infernal Fishbone Mode

    SciTech Connect

    Ya.I. Kolesnichenko; V.S. Marchenko; R.B. White

    2003-02-11

    A new kind of fishbone instability associated with circulating energetic ions is predicted. The considered instability is essentially the energetic particle mode; it is characterized by m/n not equal to 1 (m and n are the poloidal and toroidal mode numbers, respectively). The mode is localized inside the flux surface where the safety factor (q) is q* = m/n, its amplitude being maximum near q*. The instability arises in plasmas with small shear inside the q* surface and q(0) > 1. A possibility to explain recent experimental observations of the m = 2 fishbone oscillations accompanied by strong changes of the neutron emission during tangential neutral-beam injection in the National Spherical Torus Experiment [M. Ono, et al., Nucl. Fusion 40 (2000) 557] is shown.

  20. Normal matter storage of antiprotons

    SciTech Connect

    Campbell, L.J.

    1987-01-01

    Various simple issues connected with the possible storage of anti p in relative proximity to normal matter are discussed. Although equilibrium storage looks to be impossible, condensed matter systems are sufficiently rich and controllable that nonequilibrium storage is well worth pursuing. Experiments to elucidate the anti p interactions with normal matter are suggested. 32 refs.