Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: From “protein quakes” to ligand escape for myoglobin

Ligand transport through myoglobin (Mb) has been observed by using optically heterodyne-detected transient grating spectroscopy. Experimental implementation using diffractive optics has provided unprecedented sensitivity for the study of protein motions by enabling the passive phase locking of the four beams that constitute the experiment, and an unambiguous separation of the Real and Imaginary parts of the signal. Ligand photodissociation of carboxymyoglobin (MbCO) induces a sequence of events involving the relaxation of the protein structure to accommodate ligand escape. These motions show up in the Real part of the signal. The ligand (CO) transport process involves an initial, small amplitude, change in volume, reflecting the transit time of the ligand through the protein, followed by a significantly larger volume change with ligand escape to the surrounding water. The latter process is well described by a single exponential process of 725 ± 15 ns at room temperature. The overall dynamics provide a distinctive signature that can be understood in the context of segmental protein fluctuations that aid ligand escape via a few specific cavities, and they suggest the existence of discrete escape pathways.

Ultrafast diffraction and structural dynamics: The nature of complex molecules far from equilibrium

Studies of molecular structures at or near their equilibrium configurations have long provided information on their geometry in terms of bond distances and angles. Far-from-equilibrium structures are relatively unknown—especially for complex systems—and generally, neither their dynamics nor their average geometries can be extrapolated from equilibrium values. For such nonequilibrium structures, vibrational amplitudes and bond distances play a central role in phenomena such as energy redistribution and chemical reactivity. Ultrafast electron diffraction, which was developed to study transient molecular structures, provides a direct method for probing the nature of complex molecules far from equilibrium. Here we present our ultrafast electron diffraction observations of transient structures for two cyclic hydrocarbons. At high internal energies of ≈4 eV, these molecules display markedly different behavior. For 1,3,5-cycloheptatriene, excitation results in the formation of hot ground-state structures with bond distances similar to those of the initial structure, but with nearly three times the average vibrational amplitude. Energy is redistributed within 5 ps, but with a negative temperature characterizing the nonequilibrium population. In contrast, the ring-opening reaction of 1,3-cyclohexadiene is shown to result in hot structures with a C—C bond distance of over 1.7 Å, which is 0.2 Å away from any expected equilibrium value. Even up to 400 ps, energy remains trapped in large-amplitude motions comprised of torsion and asymmetric stretching. These studies promise a new direction for studying structural dynamics in nonequilibrium complex systems.

Functional dynamics in the active site of the ribonuclease binase

Binase, a member of a family of microbial guanyl-specific ribonucleases, catalyzes the endonucleotic cleavage of single-stranded RNA. It shares 82% amino acid identity with the well-studied protein barnase. We used NMR spectroscopy to study the millisecond dynamics of this small enzyme, using several methods including the measurement of residual dipolar couplings in solution. Our data show that the active site of binase is flanked by loops that are flexible at the 300-μs time scale. One of the catalytic residues, His-101, is located on such a flexible loop. In contrast, the other catalytic residue, Glu-72, is located on a β-sheet, and is static. The residues Phe-55, part of the guanine base recognition site, and Tyr-102, stabilizing the base, are the most dynamic. Our findings suggest that binase possesses an active site that has a well-defined bottom, but which has sides that are flexible to facilitate substrate access/egress, and to deliver one of the catalytic residues. The motion in these loops does not change on complexation with the inhibitor d(CGAG) and compares well with the maximum kcat (1,500 s−1) of these ribonucleases. This observation indicates that the NMR-measured loop motions reflect the opening necessary for product release, which is apparently rate limiting for the overall turnover.

Direct observation of fast protein folding: the initial collapse of apomyoglobin.

The rapid refolding dynamics of apomyoglobin are followed by a new temperature-jump fluorescence technique on a 15-ns to 0.5-ms time scale in vitro. The apparatus measures the protein-folding history in a single sweep in standard aqueous buffers. The earliest steps during folding to a compact state are observed and are complete in under 20 micros. Experiments on mutants and consideration of steady-state CD and fluorescence spectra indicate that the observed microsecond phase monitors assembly of an A x (H x G) helix subunit. Measurements at different viscosities indicate diffusive behavior even at low viscosities, in agreement with motions of a solvent-exposed protein during the initial collapse.

Hydrated myoglobin's anharmonic fluctuations are not primarily due to dihedral transitions.

To characterize the functionally important anharmonic motions of proteins, simulations of carboxymyoglobin (MbCO) dynamics have been performed during which dihedral transitions were prohibited. Comparison of torsionally restrained and unrestrained protein dynamics simulated at three levels of hydration and at temperatures ranging from 100 to 400 K suggests that hydration "catalyzes" protein mobility by facilitating collective anharmonic motions that do not require dihedral transitions. When dihedral transitions were prohibited, dehydrated MbCO, to a good approximation, exhibited only harmonic fluctuations, whereas hydrated MbCO exhibited both harmonic and anharmonic motions. The fluctuation of helix centers of mass also remained highly anharmonic in the torsionally restrained hydrated system. Atomic mean-square fluctuation at 300 K was reduced upon prohibition of dihedral transitions by only 28% and 10% for MbCO hydrated by 350 and 3830 water molecules, respectively.

Structure and evolution of the compact radio source in NGC 1275.

Investigations of the fine-scale structure in the compact nucleus of the radio source 3C 84 in NGC 1275 (New General Catalogue number) are reported. Structural monitoring observations beginning as early as 1976, and continuing to the present, revealed subluminal motions in a jet-like relatively diffuse region extending away from a flat-spectrum core. A counterjet feature was discovered in 1993, and very recent nearly simultaneous studies have detected the same feature at five frequencies ranging from 5 to 43 GHz. The counterjet exhibits a strong low-frequency cutoff, giving this region of the source an inverted spectrum. The observations are consistent with a physical model in which the cutoff arises from free-free absorption in a volume that surrounds the core but obscures only the counterjet feature. If such a model is confirmed, very-long-baseline radio interferometry observations can then be used to probe the accretion region, outside the radio jet, on parsec scales.

Bidirectional motion observed in the compact symmetric object 1946+708.

We present the first direct measurements of bidirectional motions in an extragalactic radio jet. The radio source 1946+708 is a compact symmetric object with striking S-symmetry identified with a galaxy at a redshift of 0.101. From observations 2 years apart we have determined the velocities of four compact components in the jet, the fastest of which has an apparent velocity of 1.09 h-1c. By pairing up the components, assuming they were simultaneously ejected in opposite directions, we derive a 1 lower limit on the Hubble constant, H0 > 42 km.s-1.Mpc-1.

Grs 1915+105: a superluminal source in the Galaxy.

We present the results of additional observations of the high energy source GRS 1915+105, which produces ejecta with apparent superluminal motions. The observations reported here were carried out with the Very Large Array at 3.5 cm and 20 cm. The 3.5-cm observations made during 1994 May allowed us to continue following the proper motions of the bright 1994 March 19 ejecta, as well as those of a subsequent, fainter ejection. The proper motions of the 1994 March 19 ejecta continued to be ballistic (i.e., constant) over the period of about 75 days where they remained detectable. From the observations in 1994 March-May we have identified three ejections of pairs of plasma clouds moving ballistically in approximately the same direction on the sky with similar proper motions. The 20-cm observations made during 1994 November and December were used to search, yet unsuccessfully, for extended jets or lobes associated with GRS 1915+105.

Probing active galactic nuclei with H2O megamasers.

We describe the characteristics of the rapidly rotating molecular disk in the nucleus of the mildly active galaxy NGC4258. The morphology and kinematics of the disk are delineated by the point-like watervapor emission sources at 1.35-cm wavelength. High angular resolution [200 microas where as is arcsec, corresponding to 0.006 parsec (pc) at 6.4 million pc] and high spectral resolution (0.2 km.s-1 or nu/Deltanu = 1.4 x 10(6)) with the Very-Long-Baseline Array allow precise definition of the disk. The disk is very thin, but slightly warped, and is viewed nearly edge-on. The masers show that the disk is in nearly perfect Keplerian rotation within the observable range of radii of 0.13-0.26 pc. The approximately random deviations from the Keplerian rotation curve among the high-velocity masers are approximately 3.5 km.s-1 (rms). These deviations may be due to the masers lying off the midline by about +/-4 degrees or variations in the inclination of the disk by +/-4 degrees. Lack of systematic deviations indicates that the disk has a mass of <4 x 10(6) solar mass (M[symbol: see text]). The gravitational binding mass is 3.5 x 10(7) M[symbol: see text], which must lie within the inner radius of the disk and requires that the mass density be >4 x 10(9) M[symbol: see text].pc-3. If the central mass were in the form of a star cluster with a density distribution such as a Plummer model, then the central mass density would be 4 x 10(12) M[symbol: see text].pc-3. The lifetime of such a cluster would be short with respect to the age of the galaxy [Maoz, E. (1995) Astrophys. J. Lett. 447, L91-L94]. Therefore, the central mass may be a black hole. The disk as traced by the systemic velocity features is unresolved in the vertical direction, indicating that its scale height is <0.0003 pc (hence the ratio of thickness to radius, H/R, is <0.0025). For a disk in hydrostatic equilibrium the quadrature sum of the sound speed and Alfven velocity is <2.5 km.s-1, so that the temperature of the disk must be <1000 K and the toroidal magnetic field component must be <250 mG. If the molecular mass density in the disk is 10(10) cm-3, then the disk mass is approximately 10(4) M[symbol: see text], and the disk is marginally stable as defined by the Toomre stability parameter Q (Q = 6 at the inner edge and 1 at the outer edge). The inward drift velocity is predicted to be <0.007 km.s-1, for a viscosity parameter of 0.1, and the accretion rate is <7 x 10(-5) M[symbol: see text].yr-1. At this value the accretion would be sufficient to power the nuclear x-ray source of 4 x 10(40) ergs-1 (1 erg = 0.1 microJ). The volume of individual maser components may be as large as 10(46) cm3, based on the velocity gradients, which is sufficient to supply the observed luminosity. The pump power undoubtedly comes from the nucleus, perhaps in the form of x-rays. The warp may allow the pump radiation to penetrate the disk obliquely [Neufeld, D. A. & Maloney, P. R. (1995) Astrophys. J. Lett. 447, L17-L19]. A total of 15 H2O megamasers have been identified out of >250 galaxies searched. Galaxy NGC4258 may be the only case where conditions are optimal to reveal a well-defined nuclear disk. Future measurement of proper motions and accelerations for NGC4258 will yield an accurate distance and a more precise definition of the dynamics of the disk

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

A Monte Carlo simulation method for globular proteins, called extended-scaled-collective-variable (ESCV) Monte Carlo, is proposed. This method combines two Monte Carlo algorithms known as entropy-sampling and scaled-collective-variable algorithms. Entropy-sampling Monte Carlo is able to sample a large configurational space even in a disordered system that has a large number of potential barriers. In contrast, scaled-collective-variable Monte Carlo provides an efficient sampling for a system whose dynamics is highly cooperative. Because a globular protein is a disordered system whose dynamics is characterized by collective motions, a combination of these two algorithms could provide an optimal Monte Carlo simulation for a globular protein. As a test case, we have carried out an ESCV Monte Carlo simulation for a cell adhesive Arg-Gly-Asp-containing peptide, Lys-Arg-Cys-Arg-Gly-Asp-Cys-Met-Asp, and determined the conformational distribution at 300 K. The peptide contains a disulfide bridge between the two cysteine residues. This bond mimics the strong geometrical constraints that result from a protein's globular nature and give rise to highly cooperative dynamics. Computation results show that the ESCV Monte Carlo was not trapped at any local minimum and that the canonical distribution was correctly determined.

Repacking protein cores with backbone freedom: structure prediction for coiled coils.

Progress in homology modeling and protein design has generated considerable interest in methods for predicting side-chain packing in the hydrophobic cores of proteins. Present techniques are not practically useful, however, because they are unable to model protein main-chain flexibility. Parameterization of backbone motions may represent a general and efficient method to incorporate backbone relaxation into such fixed main-chain models. To test this notion, we introduce a method for treating explicitly the backbone motions of alpha-helical bundles based on an algebraic parameterization proposed by Francis Crick in 1953 [Crick, F. H. C. (1953) Acta Crystallogr. 6, 685-689]. Given only the core amino acid sequence, a simple calculation can rapidly reproduce the crystallographic main-chain and core side-chain structures of three coiled coils (one dimer, one trimer, and one tetramer) to within 0.6-A root-mean-square deviations. The speed of the predictive method [approximately 3 min per rotamer choice on a Silicon Graphics (Mountain View, CA) 4D/35 computer] permits it to be used as a design tool.

A spectroscopy study of nearby late-type stars, possible members of stellar kinematic groups

Context. Nearby late-type stars are excellent targets for seeking young objects in stellar associations and moving groups. The origin of these structures is still misunderstood, and lists of moving group members often change with time and also from author to author. Most members of these groups have been identified by means of kinematic criteria, leading to an important contamination of previous lists by old field stars. Aims. We attempt to identify unambiguous moving group members among a sample of nearby-late type stars by studying their kinematics, lithium abundance, chromospheric activity, and other age-related properties. Methods. High-resolution echelle spectra (R ~ 57 000) of a sample of nearby late-type stars are used to derive accurate radial velocities that are combined with the precise Hipparcos parallaxes and proper motions to compute galactic-spatial velocity components. Stars are classified as possible members of the classical moving groups according to their kinematics. The spectra are also used to study several age-related properties for young late-type stars, i.e., the equivalent width of the lithium Li i 6707.8 Å line or the R'_HK index. Additional information like X-ray fluxes from the ROSAT All-Sky Survey or the presence of debris discs is also taken into account. The different age estimators are compared and the moving group membership of the kinematically selected candidates are discussed. Results. From a total list of 405 nearby stars, 102 have been classified as moving group candidates according to their kinematics. i.e., only ~25.2% of the sample. The number reduces when age estimates are considered, and only 26 moving group candidates (25.5% of the 102 candidates) have ages in agreement with the star having the same age as an MG member.

Calibração de redes de distribuição de água pelo método inverso aplicado a escoamento transiente

Desenvolve-se um método para estimar os parâmetros de uma rede hidráulica a partir de dados observados de cargas hidráulicas transientes. Os parâmetros físicos da rede como fatores de atrito, rugosidades absolutas, diâmetros e a identificação e quantificação de vazamentos são as grandezas desconhecidas. O problema transiente inverso é resolvido utilizando uma abordagem indireta que compara os dados disponíveis de carga hidráulica transiente observados com os calculados através de um método matemático. O Método Transiente Inverso (MTI) com um Algoritmo Genético (AG) emprega o Método das Características (MOC) na solução das equações do movimento para escoamento transiente em redes de tubos. As condições de regime permanente são desconhecidas. Para avaliar a confiabilidade do MTI-AG desenvolvido aqui, uma rede-exemplo é usada para os vários problemas de calibração propostos. O comportamento transiente é imposto por duas manobras distintas de uma válvula de controle localizada em um dos nós da rede. Analisam-se, ainda, o desempenho do método proposto mediante a variabilidade do tamanho do registro transiente e de possíveis erros de leitura nas cargas hidráulicas. Ensaios numéricos realizados mostram que o método é viável e aplicável à solução de problema inverso em redes hidráulicas, sobretudo recorrendo-se a poucos dados observados e ao desconhecimento das condições iniciais de estado permanente. Nos diversos problemas de identificação, as informações transientes obtidas da manobra mais brusca produziu estimações mais eficientes.

Human Motion Analysis Based on Sequential Modeling of Radar Signal and Stereo Image Features

Falls are one of the greatest threats to elderly health in their daily living routines and activities. Therefore, it is very important to detect falls of an elderly in a timely and accurate manner, so that immediate response and proper care can be provided, by sending fall alarms to caregivers. Radar is an effective non-intrusive sensing modality which is well suited for this purpose, which can detect human motions in all types of environments, penetrate walls and fabrics, preserve privacy, and is insensitive to lighting conditions. Micro-Doppler features are utilized in radar signal corresponding to human body motions and gait to detect falls using a narrowband pulse-Doppler radar. Human motions cause time-varying Doppler signatures, which are analyzed using time-frequency representations and matching pursuit decomposition (MPD) for feature extraction and fall detection. The extracted features include MPD features and the principal components of the time-frequency signal representations. To analyze the sequential characteristics of typical falls, the extracted features are used for training and testing hidden Markov models (HMM) in different falling scenarios. Experimental results demonstrate that the proposed algorithm and method achieve fast and accurate fall detections. The risk of falls increases sharply when the elderly or patients try to exit beds. Thus, if a bed exit can be detected at an early stage of this motion, the related injuries can be prevented with a high probability. To detect bed exit for fall prevention, the trajectory of head movements is used for recognize such human motion. A head detector is trained using the histogram of oriented gradient (HOG) features of the head and shoulder areas from recorded bed exit images. A data association algorithm is applied on the head detection results to eliminate head detection false alarms. Then the three dimensional (3D) head trajectories are constructed by matching scale-invariant feature transform (SIFT) keypoints in the detected head areas from both the left and right stereo images. The extracted 3D head trajectories are used for training and testing an HMM based classifier for recognizing bed exit activities. The results of the classifier are presented and discussed in the thesis, which demonstrates the effectiveness of the proposed stereo vision based bed exit detection approach.