An incipient 310 helix in Piv-Pro-Pro-Ala-NHMe as a model for peptide folding

The molecular mechanism of helix nucleation in peptides and proteins is not yet understood and the question of whether sharp turns in the polypeptide backbone serve as nuclei for protein folding has evoked controversy1,2. A recent study of the conformation of a tetrapeptide containing the stereochemically constrained residue alpha-aminoisobutyric acid, both in solution and the solid state, yielded a structure consisting of two consecutive beta-turns, leading to an incipient 310 helical conformation3,4. This led us to speculate that specific tri- and tetra-peptide sequences may indeed provide a helical twist to the amino-terminal segment of helical regions in proteins and provide a nucleation site for further propagation. The transformation from a 310 helical structure to an alpha-helix should be facile and requires only small changes in the phi and psi conformational angles and a rearrangement of the hydrogen bonding pattern5. If such a mechanism is involved then it should be possible to isolate an incipient 310 helical conformation in a tripeptide amide or tetrapeptide sequence, based purely on the driving force derived from short-range interactions. We have synthesised and studied the model peptide pivaloyl-Pro-Pro-Ala-NHMe (compound I) and provide here spectroscopic evidence for a 310 helical conformation in compound I.

Reduced visual function and its association with physical functioning in the Finnish adult population : Prevalence, causes, and need for eye care services

The purpose of this study was to estimate the prevalence and distribution of reduced visual acuity, major chronic eye diseases, and subsequent need for eye care services in the Finnish adult population comprising persons aged 30 years and older. In addition, we analyzed the effect of decreased vision on functioning and need for assistance using the World Health Organization’s (WHO) International Classification of Functioning, Disability, and Health (ICF) as a framework. The study was based on the Health 2000 health examination survey, a nationally representative population-based comprehensive survey of health and functional capacity carried out in 2000 to 2001 in Finland. The study sample representing the Finnish population aged 30 years and older was drawn by a two-stage stratified cluster sampling. The Health 2000 survey included a home interview and a comprehensive health examination conducted at a nearby screening center. If the invited participants did not attend, an abridged examination was conducted at home or in an institution. Based on our finding in participants, the great majority (96%) of Finnish adults had at least moderate visual acuity (VA ≥ 0.5) with current refraction correction, if any. However, in the age group 75–84 years the prevalence decreased to 81%, and after 85 years to 46%. In the population aged 30 years and older, the prevalence of habitual visual impairment (VA ≤ 0.25) was 1.6%, and 0.5% were blind (VA < 0.1). The prevalence of visual impairment increased significantly with age (p < 0.001), and after the age of 65 years the increase was sharp. Visual impairment was equally common for both sexes (OR 1.20, 95% CI 0.82 – 1.74). Based on self-reported and/or register-based data, the estimated total prevalences of cataract, glaucoma, age-related maculopathy (ARM), and diabetic retinopathy (DR) in the study population were 10%, 5%, 4%, and 1%, respectively. The prevalence of all of these chronic eye diseases increased with age (p < 0.001). Cataract and glaucoma were more common in women than in men (OR 1.55, 95% CI 1.26 – 1.91 and OR 1.57, 95% CI 1.24 – 1.98, respectively). The most prevalent eye diseases in people with visual impairment (VA ≤ 0.25) were ARM (37%), unoperated cataract (27%), glaucoma (22%), and DR (7%). One-half (58%) of visually impaired people had had a vision examination during the past five years, and 79% had received some vision rehabilitation services, mainly in the form of spectacles (70%). Only one-third (31%) had received formal low vision rehabilitation (i.e., fitting of low vision aids, receiving patient education, training for orientation and mobility, training for activities of daily living (ADL), or consultation with a social worker). People with low vision (VA 0.1 – 0.25) were less likely to have received formal low vision rehabilitation, magnifying glasses, or other low vision aids than blind people (VA < 0.1). Furthermore, low cognitive capacity and living in an institution were associated with limited use of vision rehabilitation services. Of the visually impaired living in the community, 71% reported a need for assistance and 24% had an unmet need for assistance in everyday activities. Prevalence of ADL, instrumental activities of daily living (IADL), and mobility increased with decreasing VA (p < 0.001). Visually impaired persons (VA ≤ 0.25) were four times more likely to have ADL disabilities than those with good VA (VA ≥ 0.8) after adjustment for sociodemographic and behavioral factors and chronic conditions (OR 4.36, 95% CI 2.44 – 7.78). Limitations in IADL and measured mobility were five times as likely (OR 4.82, 95% CI 2.38 – 9.76 and OR 5.37, 95% CI 2.44 – 7.78, respectively) and self-reported mobility limitations were three times as likely (OR 3.07, 95% CI 1.67 – 9.63) as in persons with good VA. The high prevalence of age-related eye diseases and subsequent visual impairment in the fastest growing segment of the population will result in a substantial increase in the demand for eye care services in the future. Many of the visually impaired, especially older persons with decreased cognitive capacity or living in an institution, have not had a recent vision examination and lack adequate low vision rehabilitation. This highlights the need for regular evaluation of visual function in the elderly and an active dissemination of information about rehabilitation services. Decreased VA is strongly associated with functional limitations, and even a slight decrease in VA was found to be associated with limited functioning. Thus, continuous efforts are needed to identify and treat eye diseases to maintain patients’ quality of life and to alleviate the social and economic burden of serious eye diseases.

Jet Engine Health Signal Denoising Using Optimally Weighted Recursive Median Filters

The removal of noise and outliers from health signals is an important problem in jet engine health monitoring. Typically, health signals are time series of damage indicators, which can be sensor measurements or features derived from such measurements. Sharp or sudden changes in health signals can represent abrupt faults and long term deterioration in the system is typical of gradual faults. Simple linear filters tend to smooth out the sharp trend shifts in jet engine signals and are also not good for outlier removal. We propose new optimally designed nonlinear weighted recursive median filters for noise removal from typical health signals of jet engines. Signals for abrupt and gradual faults and with transient data are considered. Numerical results are obtained for a jet engine and show that preprocessing of health signals using the proposed filter significantly removes Gaussian noise and outliers and could therefore greatly improve the accuracy of diagnostic systems. [DOI: 10.1115/1.3200907].

Effect of Polymer Grafting on the Bilayer Gel to Liquid-Crystalline Transition

Grafted polymers oil the surface of lipid membranes have potential applications in liposome-based drug delivery and Supported membrane systems. The effect of polymer grafting on the phase behavior of bilayers made up of single-tail lipids is investigated using dissipative particle dynamics. The bilayer is maintained in a tensionless state using a barostat. Simulations are carried Out by varying the grafting fraction, G(f), defined as the ratio of the number of polymer molecules to the number of lipid molecules, and the length of the lipid tails. At low G(f), the bilayer shows I sharp transition from the gel (L-beta) to the liquid-crystalline (L-alpha) phase. This main melting transition temperature is lowered as G(f) is increased, and above a critical value of G(f), the interdigitated L-beta I phase is observed prior to the main transition. The temperature range over which the intermediate phases are observed is a function of the lipid tail length and G(f). At higher grafting fractions, the presence of the L-beta I, phase is attributed to the increase in the area per head group due to the lateral pressure exerted by the polymer brush. The areal expansion and decrease in the melting temperatures as a function of G(f) were found to follow the scalings predicted by the self-consistent mean field theories for grafted polymer membranes. Our study shows that the grafted polymer density can be used to effectively control the temperature range and occurrence of a given bilayer phase.

Electrical switching and thermal studies on Ge22Te78-xIx chalcohalide glasses: The effect of iodine on network-topology

Investigations on the electrical switching behavior and thermal studies using Alternating Differential Scanning Calorimetry have been undertaken on bulk, melt-quenched Ge22Te78-,Is (3 <= x <= 10) chalcohalide glasses. All the glasses studied have been found to exhibit memory-type electrical switching. The threshold voltages of Ge22Te78-I-x(x) glasses have been found to increase with the addition of iodine and the composition dependence of threshold voltages of Ge22Te78-xIx glasses exhibits a cusp at 5 at.% of iodine. Also, the variation with composition of the glass transition temperature (Tg) of Ge22Te78-I-x(x) glasses, exhibits a broad hump around this composition. Based on the present results, the composition x = 5 has been identified as the inverse rigidity percolation threshold at which Ge22Te78-I-x(x) glassy system exhibits a change from a stressed rigid amorphous solid to a flexible polymeric glass. Further, a sharp minimum is seen in the composition dependence of non-reversing enthalpy (Delta H-nr) of Ge22Te78-I-x(x) glasses at x = 5, which is suggestive of a thermally reversing window at this composition. (C) 2007 Elsevier Ltd. All rights reserved.

Discrete parameter simulation optimization algorithms with applications to admission control with dependent service times

We propose certain discrete parameter variants of well known simulation optimization algorithms. Two of these algorithms are based on the smoothed functional (SF) technique while two others are based on the simultaneous perturbation stochastic approximation (SPSA) method. They differ from each other in the way perturbations are obtained and also the manner in which projections and parameter updates are performed. All our algorithms use two simulations and two-timescale stochastic approximation. As an application setting, we consider the important problem of admission control of packets in communication networks under dependent service times. We consider a discrete time slotted queueing model of the system and consider two different scenarios - one where the service times have a dependence on the system state and the other where they depend on the number of arrivals in a time slot. Under our settings, the simulated objective function appears ill-behaved with multiple local minima and a unique global minimum characterized by a sharp dip in the objective function in a small region of the parameter space. We compare the performance of our algorithms on these settings and observe that the two SF algorithms show the best results overall. In fact, in many cases studied, SF algorithms converge to the global minimum.

Novel window functions for digital filters

Window technique is one of the simplest methods to design Finite Impulse Response (FIR) filters. It uses special functions to truncate an infinite sequence to a finite one. In this paper, we propose window techniques based on integer sequences. The striking feature of the proposed work is that it overcomes all the problems posed by floating point numbers and inaccuracy, as the sequences are made of only integers. Some of these integer window sequences, yield sharp transition, while some of them result in zero ripple in passband and stopband.

Melting of an Anchored Bilayer: Molecular Dynamics Simulations of the Structural Transition in (CnH2n+1NH3)(2)PbI4 (n=12, 14, 16, 18)

The thermally driven Structural phase transition in the organic-inorganic hybrid perovskite (CnH2n+1NH3)(2)PbI4 has been investigated using molecular dynamics (MD) simulations. This system consists of positively charged alkyl-amine chains anchored to a rigid negatively charged PbI4 sheet with the chains organized as bilayers with a herringbone arrangement. Atomistic simulations were performed using ail isothermal-isobaric ensemble over a wide temperature range from 65 to 665 K for different alkyl chain lengths, n = 12, 14, 16, and 18. The simulations are able to reproduce the essential Features of the experimental observations of this system, including the existence of a transition, the linear variation of the transition temperature with alkyl chain length, and the expansion of the bilayer thickness at the transition. By use of the distance fluctuation Criteria, it is Shown that the transition is associated With a Melting of the alkyl chains of the anchored bilayer. Ail analysis of the conformation of the alkyl chains shows increased disorder in the form of gauche defects above due melting transition. Simulations also show that the melting transition is characterized by the complete disappearance of all-trans alkyl chains in the anchored bilayer, in agreement with experimental observations. A conformationally disordered chain has a larger effective cross-sectional area, and above due transition a uniformly tilted arrangement of the anchored chains call no longer be Sustained. At the melt the angular distribution of the orientation of the chains are 110 longer uniform; the chains are splayed allowing for increased space for individual chains of the anchored bilayer. This is reflected in a sharp rise in the ratio of the mean head-to-head to tail-to-tail distance of the chains of the bilayer at the transition resulting in in expansion of the bilayer thickness. The present MD simulations provide a simple explanation as to how changes in conformation of individual alkyl-chains gives rise to the observed increase in the interlayer lattice spacing of (CnH2n+1NH3)(2)PbI4 at the melting transition.

Tendency toward crossover of the effective susceptibility exponent from its doubled Ising value to its doubled mean-field value near a double critical point

The critical behavior of osmotic susceptibility in an aqueous electrolyte mixture 1-propanol (1P)+water (W)+potassium chloride is reported. This mixture exhibits re-entrant phase transitions and has a nearly parabolic critical line with its apex representing a double critical point (DCP). The behavior of the susceptibility exponent is deduced from static light-scattering measurements, on approaching the lower critical solution temperatures (TL’s) along different experimental paths (by varying t) in the one-phase region. The light-scattering data analysis substantiates the existence of a nonmonotonic crossover behavior of the susceptibility exponent in this mixture. For the TL far away from the DCP, the effective susceptibility exponent γeff as a function of t displays a nonmonotonic crossover from its single limit three-dimensional (3D)-Ising value ( ∼ 1.24) toward its mean-field value with increase in t. While for that closest to the DCP, γeff displays a sharp, nonmonotonic crossover from its nearly doubled 3D-Ising value toward its nearly doubled mean-field value with increase in t. The renormalized Ising regime extends over a relatively larger t range for the TL closest to the DCP, and a trend toward shrinkage in the renormalized Ising regime is observed as TL shifts away from the DCP. Nevertheless, the crossover to the mean-field limit extends well beyond t>10−2 for the TL’s studied. The observed crossover behavior is attributed to the presence of strong ion-induced clustering in this mixture, as revealed by various structure probing techniques. As far as the critical behavior in complex or associating mixtures with special critical points (like the DCP) is concerned, our results indicate that the influence of the DCP on the critical behavior must be taken into account not only on the renormalization of the critical exponent but also on the range of the Ising regime, which can shrink with decrease in the influence of the DCP and with the extent of structuring in the system. The utility of the field variable tUL in analyzing re-entrant phase transitions is demonstrated. The effective susceptibility exponent as a function of tUL displays a nonmonotonic crossover from its asymptotic 3D-Ising value toward a value slightly lower than its nonasymptotic mean-field value of 1. This behavior in the nonasymptotic, high tUL region is interpreted in terms of the possibility of a nonmonotonic crossover to the mean-field value from lower values, as foreseen earlier in micellar systems.

Dimensional Reduction Near the Deconfinement Transition

When ordinary nuclear matter is heated to a high temperature of ~ 10^12 K, it undergoes a deconfinement transition to a new phase, strongly interacting quark-gluon plasma. While the color charged fundamental constituents of the nuclei, the quarks and gluons, are at low temperatures permanently confined inside color neutral hadrons, in the plasma the color degrees of freedom become dominant over nuclear, rather than merely nucleonic, volumes. Quantum Chromodynamics (QCD) is the accepted theory of the strong interactions, and confines quarks and gluons inside hadrons. The theory was formulated in early seventies, but deriving first principles predictions from it still remains a challenge, and novel methods of studying it are needed. One such method is dimensional reduction, in which the high temperature dynamics of static observables of the full four-dimensional theory are described using a simpler three-dimensional effective theory, having only the static modes of the various fields as its degrees of freedom. A perturbatively constructed effective theory is known to provide a good description of the plasma at high temperatures, where asymptotic freedom makes the gauge coupling small. In addition to this, numerical lattice simulations have, however, shown that the perturbatively constructed theory gives a surprisingly good description of the plasma all the way down to temperatures a few times the transition temperature. Near the critical temperature, the effective theory, however, ceases to give a valid description of the physics, since it fails to respect the approximate center symmetry of the full theory. The symmetry plays a key role in the dynamics near the phase transition, and thus one expects that the regime of validity of the dimensionally reduced theories can be significantly extended towards the deconfinement transition by incorporating the center symmetry in them. In the introductory part of the thesis, the status of dimensionally reduced effective theories of high temperature QCD is reviewed, placing emphasis on the phase structure of the theories. In the first research paper included in the thesis, the non-perturbative input required in computing the g^6 term in the weak coupling expansion of the pressure of QCD is computed in the effective theory framework at an arbitrary number of colors. The two last papers on the other hand focus on the construction of the center-symmetric effective theories, and subsequently the first non-perturbative studies of these theories are presented. Non-perturbative lattice simulations of a center-symmetric effective theory for SU(2) Yang-Mills theory show --- in sharp contrast to the perturbative setup --- that the effective theory accommodates a phase transition in the correct universality class of the full theory. This transition is seen to take place at a value of the effective theory coupling constant that is consistent with the full theory coupling at the critical temperature.

In situ transmission electron microscope study of single asperity sliding contacts

Direct observation of events taking place at the contacting interfaces is important to understand many tribological phenomena. Transmission electron microscope (TEM) has the ability to look through materials at very high magnifications. Most of the TEM observations are done long after the deforming loads and stresses have been relaxed and the material state is further disturbed during the specimen preparation. We have developed a specimen holder in which two electron transparent surfaces can be brought in contact and moved relative to each other in JEOL 2000FX microscope. This holder enables visualization of not only the contacting surfaces at nanoscale but also the subsurface deformation resulting from the contact interaction. Sliding experimentS have been carried out mimicking a single asperity sliding contact. A sharp tungsten probe is moved laterally against a tip mounted on a cantilever. Magnitude of the contact instability, when the contact is broken is found to be dependent on the local geometry of the contact.(C) 2009 Elsevier Ltd. All rights reserved.

Vibrational dynamics and boson peak in a supercooled polydisperse liquid

Vibrational density of states (VDOS) in a supercooled polydisperse liquid is computed by diagonalizing the Hessian matrix evaluated at the potential energy minima for systems with different values of polydispersity. An increase in polydispersity leads to an increase in the relative population of localized high-frequency modes. At low frequencies, the density of states shows an excess compared to the Debye squared-frequency law, which has been identified with the boson peak. The height of the boson peak increases with polydispersity and shows a rather narrow sensitivity to changes in temperature. While the modes comprising the boson peak appear to be largely delocalized, there is a sharp drop in the participation ratio of the modes that exist just below the boson peak indicative of the quasilocalized nature of the low-frequency vibrations. Study of the difference spectrum at two different polydispersity reveals that the increase in the height of boson peak is due to a population shift from modes with frequencies above the maximum in the VDOS to that below the maximum, indicating an increase in the fraction of the unstable modes in the system. The latter is further supported by the facilitation of the observed dynamics by polydispersity. Since the strength of the liquid increases with polydispersity, the present result provides an evidence that the intensity of boson peak correlates positively with the strength of the liquid, as observed earlier in many experimental systems.

Anomalous Raman scattering from phonons and electrons of superconducting FeSe0.82

We report interesting anomalies in the temperature dependent Raman spectra of FeSe0.82 measured from 3 K to 300 K in the spectral range from 60 to 1800 cm(-1) and determine their origin using complementary first-principles density functional calculations. A phonon mode near 100 cm-1 exhibits a sharp increase by similar to 5% in the frequency below a temperature T-s (similar to 100 K) attributed to strong spin-phonon coupling and onset of short-range antiferromagnetic order. In addition, two high frequency modes are observed at 1350 cm-1 and 1600 cm-1, attributed to electronic Raman scattering from (x(2)-y(2)) to xz/yz d-orbitals of Fe. (C) 2010 Elsevier Ltd. All rights reserved.

Cultural Trauma and Life Stories

The purpose of this work is to use the concepts of human time and cultural trauma in a biographical study of the turning points in the recent history of Estonia. This research is primarily based on 148 in-depth biographical interviews conducted in Estonia and Sweden in 1995-2005, supplemented by excerpts from 5 collections and 10 individually published autobiographies. The main body of the thesis consists of six published and of two forthcoming separate refereed articles, summarised in the theoretical introduction, and Appendix of the full texts of three particular life stories. The topic of the first article is the generational composition and the collective action frames of anti-Soviet social mobilisation in Estonia in 1940-1990. The second article details the differentiation of the rites of passage and the calendar traditions as a strategy to adapt to the rapidly changed political realities, comparatively in Soviet Estonia and among the boat-refugees in Sweden. The third article investigates the life stories of the double-minded strategic generation of the Estonian-inclined Communists, who attempted to work within the Soviet system while professing to uphold the ideals of pre-war Estonia. The fourth article is concentrated on the problems of double mental standards as a coping strategy in a contradictory social reality. The fifth article implements the theory of cultural trauma for the social practice of singing nationalism in Estonia. The sixth article bridges the ideas of Russian theoreticians concerning cultural dialogue and the Western paradigm of cultural trauma, with examples from Estonian Russian life stories. The seventh article takes a biographical look at the logic of the unraveling of cultural trauma through four Soviet decades. The eighth article explores the re-shaping of citizen activities as a strategy of coping with the loss of the independent nation state, comparatively in Soviet Estonia and among Swedish Estonians. Cultural trauma is interpreted as the re-ordering of the society s value-normative constellation due to sharp, violent, usually political events. The first one under consideration was caused by the occupations of the Republic of Estonia by the Soviet army in 1940-45. After half a century of suppression the memories of these events resurfaced as different stories describing the long-term, often inter-generational strategies of coping with the value collapse. The second cultural trauma is revealed together with the collapse of the Soviet power and ideology in Estonia in 1991. According to empirical data, the following three trauma discourses have been reconstructed: - the forced adaptation to Soviet order of the homeland Estonians; - the difficulty of preserving Estonian identity in exile (Sweden); - the identity crisis of the Russian population of Estonia. Comparative analyses of these discourses have shown that opposing experiences and worldviews cause conflicting interpretations of the past. Different social and ethnic groups consider coping with cultural trauma as a matter of self-defence and create appropriate usable pasts to identify with. Keywords: human time, cultural trauma, frame analysis, discourse, life stories

Interactions of linear dicationic molecules with lipid A: structural requisites for optimal binding affinity

The structural determinants of the binding affinity of linear dicationic molecules toward lipid A have been examined with respect to the distance between the terminal cationic functions, the basicity, and the type of cationic moieties using a series of spermidine derivatives and pentamidine analogs by fluorescence spectroscopic methods, The presence of two terminal cationic groups corresponds to enhanced affinity, A distinct sigmoidal relationship between the intercationic distance and affinity was observed with a sharp increase at 11 Angstrom, levelling off at about 13 Angstrom. The basicity (pK) and nature of the cationic functions are poor correlates of binding potency, since molecules bearing primary amino, imidazolino, or guanido termini are equipotent, The interaction of pentamidine, a bisamidine drug, with lipid A, characterized in considerable detail employing the putative intermolecular excimerization of the drug, suggests a stoichiometry of 1:1 in the resultant complex, The binding is driven almost exclusively by electrostatic forces, and is dependent on the ionization states of both lipid A and the drug, Under conditions when lipid A is highly disaggregated, pentamidine binds specifically to bis-phosphoryl- but not to monophosphoryl-lipid A indicating that both phosphate groups of lipid A are necessary for electrostatic interactions by the terminal amidininium groups of the drug, Based on these data, a structural model is proposed for the pentamidine-lipid A complex, which may be of value in designing endotoxin antagonists from first principles.