Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/ PBE/.

Behaviour of autonomous mobile agents using linear cyclic pursuit laws

In this paper, the behaviour of a group of autonomous mobile agents under cyclic pursuit is studied. Cyclic pursuit is a simple distributed control law, in which the agent i pursues agent i + 1 modulo n.. The equations of motion are linear, with no kinematic constraints on motion. Behaviourally, the agents are identical, but may have different controller gains. We generalize existing results in the literature and show that by selecting these gains, the behavior of the agents can be controlled. They can be made to converge at a point or be directed to move in a straight line. The invariance of the point of convergence with the sequence of pursuit is also shown.

Limit Analysis of Slabs with Free Edge

The general method earlier developed by the writers for obtaining valid lower bound solutions to slabs under uniformly distributed load and supported along all edges is extended to the slabs with a free edge. Lower bound solutions with normal moment criterion are presented for six cases of orthotropically reinforced slabs, with one of the short edges being free and the other three edges being any combination of fixed and simply supported conditions. The expressions for moment field and collapse load are given for each slab. The lower bounds have been compared with the corresponding upper bound values obtained from the yield line theory with simple straight yield line modes of failure. They are also compared with Nielsen’s solutions available for two cases with isotropic reinforcement.

Terahertz Spectroscopy of Single-Walled Carbon Nanotubes in a Polymer Film: Observation of Low-Frequency Phonons

We investigate the dielectric response of single-walled carbon nanotubes dispersed in poly(vinyl alcohol) matrix by using terahertz time domain spectroscopy. Frequency-dependent real and imaginary parts of the complex dielectric function are measured experimentally in the terahertz regime. The low-frequency phonons of carbon nanotubes, though predicted theoretically, are directly observed for the first time at frequencies 0.26, 0.60, and 0.85 THz. Further, a broad resonance is observed at 1.15 THz associated with the longitudinal acoustic mode of vibration of straight-chain segments of the long polymeric molecules in the film. The latter is observed at 1.24 THz for a pristine polymer film and has been used to derive the size of crystalline lamellae in the film.

Development of twist in an emerging magnetic flux tube by poloidal field accretion

Aims. Following an earlier proposal for the origin of twist in the magnetic fields of solar active regions, we model the penetration of a wrapped up background poloidal field into a toroidal magnetic flux tube rising through the solar convective zone.Methods. The rise of the straight, cylindrical flux tube is followed by numerically solving the induction equation in a comoving Lagrangian frame, while an external poloidal magnetic field is assumed to be radially advected onto the tube with a speed corresponding to the rise velocity.Results. One prediction of our model is the existence of a ring of reverse current helicity on the periphery of active regions. On the other hand, the amplitude of the resulting twist depends sensitively on the assumed structure ( diffuse vs. concentrated/intermittent) of the active region magnetic field right before its emergence, and on the assumed vertical profile of the poloidal field. Nevertheless, in the model with the most plausible choice of assumptions a mean twist comparable to the observations results.Conclusions. Our results indicate that the contribution of this mechanism to the twist can be quite significant, and under favourable circumstances it can potentially account for most of the current helicity observed in active regions.

Hormones andCuscuta development: interaction of cytokinin and indole-3-acetic acid in the growth and curvature of subapical stem segments

Cuscuta stem (vines) exhibits two modes of growth—longitudinal elongation forming free-hanging vines, or coiling growth to twine around the host. The elongation zone of free-hanging vine extended up to 160 mm from the stem apex and in vivo growth rate (during 8 h of growth) was maximal in the 20-to-40-mm region. While gibberellic acid (GA3) or fusicoccin (FC) could maintain (GA3) or enhance (FC) the growth rate of apical (10 or 25 mm) segments, indole-3-acetic acid (IAA) (10 mgrM) induced growth only in subapical (5–160 mm) segments. In vitro growth rate induced by IAA (10 mgrM) was similar to the in vivo growth rate up to 40 mm. Thereafter, up to 100 mm, IAA induced growth rate exceeded in vivo growth. p ]Subapical segments (sim13 mm) from 5- to 40-mm regions responded to a cytokinin (BA, Z, or iP) or to low IAA (0.1 mgrM) with curved growth, whereas the segments grew straight in the presence of high IAA (10 mgrM). Curvature (measured as the angle subtended at the center of the circle of which the segment formed an arc) induced by BA and low (0.1 mgrM) IAA was greater than either added separately. Besides, segments induced to curve in BA + low-IAA solution could be made to straighten out by transferring to a solution containing high IAA (10 mgrM) with or without BA. Thus in vivo patterns of straight and coiling growth could be mimicked reversibly in vitro by adjusting the relative concentrations of cytokinin and auxin; low auxin and cytokinin induced coiling growth, whereas high auxin and cytokinin induced straight growth. p ]Beyond 40 mm, BA had no growth-promoting or curvative-inducing effect.Cuscuta vine segments thus showed sequential sensitivity to applied hormones, the apical region (0–25 mm) to GA3, the subapical (5–40 mm) region to BA and IAA and the region beyond (40–160 mm) to IAA alone.

Hot gaseous coronae of early-type galaxies and their radio luminosity function

Recent X-ray observations have revealed that early-type galaxies (which usually produce extended double radio sources) generally have hot gaseous haloes extending up to approx102kpc1,2. Moreover, much of the cosmic X-ray background radiation is probably due to a hotter, but extremely tenuous, intergalactic medium (IGM)3. We have presented4–7 an analytical model for the propagation of relativistic beams from galactic nuclei, in which the beams' crossing of the pressure-matched interface between the IGM and the gaseous halo, plays an important role. The hotspots at the ends of the beams fade quickly when their advance becomes subsonic with respect to the IGM. This model has successfully predicted (for typical double radio sources) the observed8 current mean linear-size (approx2Dsime350 kpc)4,5, the observed8–11 decrease in linear-size with cosmological redshift4–6 and the slope of the linear-size versus radio luminosity10,12–14 relation6. We have also been able to predict the redshift-dependence of observed numbers and radio luminosities of giant radio galaxies7,15. Here, we extend this model to include the propagation of somewhat weaker beams. We show that the observed flattening of the local radio luminosity function (LRLF)16–20 for radio luminosity Papproximately 1024 W Hz-1 at 1 GHz can be explained without invoking ad hoc a corresponding break in the beam power function Phi(Lb), because the heads of the beams with Lb < 1025 W Hz-1 are decelerated to sonic velocity within the halo itself, which leads to a rapid decay of radio luminosity and a reduced contribution of these intrinsically weaker sources to the observed LRLF.

How the development of condensation particle counters is reforming our view on atmospheric nucleation

Aerosol particles deteriorate air quality, atmospheric visibility and our health. They affect the Earth s climate by absorbing and scattering sunlight, forming clouds, and also via several feed-back mechanisms. The net effect on the radiative balance is negative, i.e. cooling, which means that particles counteract the effect of greenhouse gases. However, particles are one of the poorly known pieces in the climate puzzle. Some of the airborne particles are natural, some anthropogenic; some enter the atmosphere in particle form, while others form by gas-to-particle conversion. Unless the sources and dynamical processes shaping the particle population are quantified, they cannot be incorporated into climate models. The molecular level understanding of new particle formation is still inadequate, mainly due to the lack of suitable measurement techniques to detect the smallest particles and their precursors. This thesis has contributed to our ability to measure newly formed particles. Three new condensation particle counter applications for measuring the concentration of nano-particles were developed. The suitability of the methods for detecting both charged and electrically neutral particles and molecular clusters as small as 1 nm in diameter was thoroughly tested both in laboratory and field conditions. It was shown that condensation particle counting has reached the size scale of individual molecules, and besides measuring the concentration they can be used for getting size information. In addition to atmospheric research, the particle counters could have various applications in other fields, especially in nanotechnology. Using the new instruments, the first continuous time series of neutral sub-3 nm particle concentrations were measured at two field sites, which represent two different kinds of environments: the boreal forest and the Atlantic coastline, both of which are known to be hot-spots for new particle formation. The contribution of ions to the total concentrations in this size range was estimated, and it could be concluded that the fraction of ions was usually minor, especially in boreal forest conditions. Since the ionization rate is connected to the amount of cosmic rays entering the atmosphere, the relative contribution of neutral to charged nucleation mechanisms extends beyond academic interest, and links the research directly to current climate debate.

Nonlinear programming solutions for controlling the vibration pattern of stretched strings

The problem of controlling the vibration pattern of a driven string is considered. The basic question dealt with here is to find the control forces which reduce the energy of vibration of a driven string over a prescribed portion of its length while maintaining the energy outside that length above a desired value. The criterion of keeping the response outside the region of energy reduction as close to the original response as possible is introduced as an additional constraint. The slack unconstrained minimization technique (SLUMT) has been successfully applied to solve the above problem. The effect of varying the phase of the control forces (which results in a six-variable control problem) is then studied. The nonlinear programming techniques which have been effectively used to handle problems involving many variables and constraints therefore offer a powerful tool for the solution of vibration control problems.

Position-sensitive silicon strip detector characterization using particle beams

Silicon strip detectors are fast, cost-effective and have an excellent spatial resolution. They are widely used in many high-energy physics experiments. Modern high energy physics experiments impose harsh operation conditions on the detectors, e.g., of LHC experiments. The high radiation doses cause the detectors to eventually fail as a result of excessive radiation damage. This has led to a need to study radiation tolerance using various techniques. At the same time, a need to operate sensors approaching the end their lifetimes has arisen. The goal of this work is to demonstrate that novel detectors can survive the environment that is foreseen for future high-energy physics experiments. To reach this goal, measurement apparatuses are built. The devices are then used to measure the properties of irradiated detectors. The measurement data are analyzed, and conclusions are drawn. Three measurement apparatuses built as a part of this work are described: two telescopes measuring the tracks of the beam of a particle accelerator and one telescope measuring the tracks of cosmic particles. The telescopes comprise layers of reference detectors providing the reference track, slots for the devices under test, the supporting mechanics, electronics, software, and the trigger system. All three devices work. The differences between these devices are discussed. The reconstruction of the reference tracks and analysis of the device under test are presented. Traditionally, silicon detectors have produced a very clear response to the particles being measured. In the case of detectors nearing the end of their lifefimes, this is no longer true. A new method benefitting from the reference tracks to form clusters is presented. The method provides less biased results compared to the traditional analysis, especially when studying the response of heavily irradiated detectors. Means to avoid false results in demonstrating the particle-finding capabilities of a detector are also discussed. The devices and analysis methods are primarily used to study strip detectors made of Magnetic Czochralski silicon. The detectors studied were irradiated to various fluences prior to measurement. The results show that Magnetic Czochralski silicon has a good radiation tolerance and is suitable for future high-energy physics experiments.

Nonsingular cosmological models: the massive scalar field case

The nonminimal coupling of a massive self-interacting scalar field with a gravitational field is studied. Spontaneous symmetry breaking occurs in the open universe even when the sign on the mass term is positive. In contrast to grand unified theories, symmetry breakdown is more important for the early universe and it is restored only in the limit of an infinite expansion. Symmetry breakdown is shown to occur in flat and closed universes when the mass term carries a wrong sign. The model has a naturally defined effective gravitational coupling coefficient which is rendered time-dependent due to the novel symmetry breakdown. It changes sign below a critical value of the cosmic scale factor indicating the onset of a repulsive field. The presence of the mass term severely alters the behaviour of ordinary matter and radiation in the early universe. The total energy density becomes negative in a certain domain. These features make possible a nonsingular cosm

Stereochemistry of collagen

This review article, based on a lecture delivered in Madras in 1985, is an account of the author's experience in the working out of the molecular structure and conformation of the collagen triple-helix over the years 1952–78. It starts with the first proposal of the correct triple-helix in 1954, but with three residues per turn, which was later refined in 1955 into a coiled-coil structure with approximately 3.3 residues per turn. The structure readily fitted proline and hydroxyproline residues and required glycine as every third residue in each of the three chains. The controversy regarding the number of hydrogen bonds per tripeptide could not be resolved by X-ray diffraction or energy minimization, but physicochemical data, obtained in other laboratories during 1961–65, strongly pointed to two hydrogen bonds, as suggested by the author. However, it was felt that the structure with one straight NH … O bond was better. A reconciliation of the two was obtained in Chicago in 1968, by showing that the second hydrogen bond is via a water molecule, which makes it weaker, as found in the physicochemical studies mentioned above. This water molecule was also shown, in 1973, to take part in further cross-linking hydrogen bonds with the OH group of hydroxyproline, which occurred always in the location previous to glycine, and is at the right distance from the water. Thus, almost all features of the primary structure, X-ray pattern, optical and hydrodynamic data, and the role of hydroxyproline in stabilising the triple helical structure, have been satisfactorily accounted for. These also lead to a confirmation of Pauling's theory that vitamin C improves immunity to diseases, as explained in the last section.

Tyrphostin-A47 inhibitable tyrosine phosphorylation of flagellar proteins is associated with distinct alteration of motility pattern in hamster spermatozoa

To acquire fertilizing potential, mammalian spermatozoa must undergo capacitation and acrosome reaction. Our earlier work showed that pentoxifylline (0.45 mM), a sperm motility stimulant, induced an early onset of hamster sperm capacitation associated with tyrosine phosphorylation of 45-80 kDa proteins, localized to the mid-piece of the sperm tail. To assess the role of protein tyrosine phosphorylation in sperm capacitation, we used tyrphostin-A47 (TP-47), a specific protein tyrosine kinase inhibitor. The dose-dependent (0.1-0.5 mM) inhibition of tyrosine phosphorylation by TP-47 was associated with inhibition of hyperactivated motility and 0.5 mM TP-47-treated spermatozoa exhibited a distinct circular motility pattern. This was accompanied by hypo-tyrosine phosphorylation of 45-60 kDa proteins, localized to the principal piece of the intact-sperm and the outer dense fiber-like structures in detergent treated-sperm. Sperm kinematic analysis (by CASA) of spermatozoa, exhibiting circular motility (at 1st hr), showed lower values of straight line velocity, curvilinear velocity and average path velocity, compared to untreated controls. Other TP-47 analogues, tyrphostin-AG1478 and -AG1296, had no effect either on kinematic parameters or sperm protein tyrosine phosphorylation. These studies indicate that TP-47-induced circular motility of spermatozoa is compound-specific and that the tyrosine phosphorylation status of 45-60 kDa flagellum-localized proteins could be key regulators of sperm flagellar bending pattern, associated with the hyperactivation of hamster spermatozoa.

Time Dependent Operator-split and Unsplit Schemes for One Dimensional Premixed Flames

This paper is concerned with a study of an operator split scheme and unsplit scheme for the computation of adiabatic freely propagating one-dimensional premixed flames. The study uses unsteady method for both split and unsplit schemes employing implicit chemistry and explicit diffusion, a combination which is stable and convergent. Solution scheme is not sensitive to the initial starting estimate and provides steady state even with straight line profiles (far from steady state) in small number of time steps. Two systems H2-Air and H2-NO (involving complex nitrogen chemistry) are considered in presentinvestigation. Careful comparison shows that the operator split approach is slightly superior than the unsplit when chemistry becomes complex. Comparison of computational times with those of existing steady and unsteady methods seems to suggest that the method employing implicit-explicit algorithm is very efficient and robust.

News Media, Crime and Fear of Violence

Finland witnessed a surge in crime news reporting during the 1990s. At the same time, there was a significant rise in the levels of fear of crime reported by surveys. This research examines whether and how the two phenomena: news media and fear of violence were associated with each other. The dissertation consists of five sub-studies and a summary article. The first sub-study is a review of crime reporting trends in Finland, in which I have reviewed prior research and used existing Finnish datasets on media contents and crime news media exposure. The second study examines the association between crime media consumption and fear of crime when personal and vicarious victimization experiences have been held constant. Apart from analyzing the impact of crime news consumption on fear, media effects on general social trust are analyzed in the third sub-study. In the fourth sub-study I have analyzed the contents of the Finnish Poliisi-TV programme and compared the consistency of the picture of violent crime between official data sources and the programme. In the fifth and final sub-study, the victim narratives of Poliisi-TV s violence news contents have been analyzed. The research provides a series of results which are unprecedented in Finland. First, it observes that as in many other countries, the quantity of crime news supply has increased quite markedly in Finland. Second, it verifies that exposure to crime news is related to being worried about violent victimization and avoidance behaviour. Third, it documents that exposure to TV crime reality-programming is associated with reduced social trust among Finnish adolescents. Fourth, the analysis of Poliisi-TV shows that it transmits a distorted view of crime when contrasted with primary data sources on crime, but that this distortion is not as big as could be expected from international research findings and epochal theories of sociology. Fifth, the portrayals of violence victims in Poliisi-TV do not fit the traditional ideal types of victims that are usually seen to dominate crime media. The fact that the victims of violence in Poliisi-TV are ordinary people represents a wider development of the changing significance of the crime victim in Finland. The research concludes that although the media most likely did have an effect on the rising public fears in the 1990s, the mechanism was not as straight forward as has often been claimed. It is likely that there are other factors in the fear-media equation that are affecting both fear levels and crime reporting and that these factors are interactive in nature. Finally, the research calls for a re-orientation of media criminology and suggests more emphasis on the positive implications of crime in the media. Keywords: crime, media, fear of crime, violence, victimization, news