Conformational characteristics of asparaginyl residues in proteins

Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed x-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi,psi) regions of left-handed alpha-helix, right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha(L), which seems to be characteristic of non-glycyl residues at that position. In the linkers connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha(L) or alpha(R) conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein. (C) Munksgaard 1994.

Sanat kivettyvät kaupungiksi

Tutkimuksessa selvitetään, mitkä ovat Helsingin kaupunkisuunnittelua koskevat tärkeimmät puhetavat, miten kaupunkisuunnittelijat ymmärtävät ne ja miten ne konkretisoituvat kaupunkisuunnitteluksi. Tarkoituksena on tuottaa ajankohtaista tietoa Helsingin kaupunkisuunnittelun toimintaympäristöstä, kuvata suunnittelun prosessia siihen osallistuvien henkilöiden näkökulmasta sekä analysoida vallitsevia suunnitteluideologioita ja -ihanteita. Tutkimusta varten haastateltiin 15 kaupunkisuunnitteluun osallistuvaa keskeistä henkilöä.

Safeguarding against new privacy threats in inter-enterprise collaboration environments

Inter-enterprise collaboration has become essential for the success of enterprises. As competition increasingly takes place between supply chains and networks of enterprises, there is a strategic business need to participate in multiple collaborations simultaneously. Collaborations based on an open market of autonomous actors set special requirements for computing facilities supporting the setup and management of these business networks of enterprises. Currently, the safeguards against privacy threats in collaborations crossing organizational borders are both insufficient and incompatible to the open market. A broader understanding is needed of the architecture of defense structures, and privacy threats must be detected not only on the level of a private person or enterprise, but on the community and ecosystem levels as well. Control measures must be automated wherever possible in order to keep the cost and effort of collaboration management reasonable. This article contributes to the understanding of the modern inter-enterprise collaboration environment and privacy threats in it, and presents the automated control measures required to ensure that actors in inter-enterprise collaborations behave correctly to preserve privacy.

Organisaatioiden kehittäminen yhteiskunnallisen työnjaon muutoksessa

Organisaatioiden kehittäminen yhteiskunnallisen työnjaon muutoksessa –julkaisu esittelee kuvauksen yhteiskunnallisen työnjaon eli julkisen, yksityisen ja kolmannen sektorin välisen työnjaon muutosprosessissa syntyneiden hybridiorganisaatioiden (mm. tilaaja-tuottajamalli) ominaisuuksista. Toiseksi julkaisu esittelee kehittävän työntutkimuksen metodologian inspiroiman kehittämismenetelmän hybridilaboratorion, jota pilotoitiin Tampereen kaupungin päivähoidossa ja esiopetuksessa sekä Työvalmennussäätiö Tekevässä.. Hybridilaboratoriomenetelmän tavoitteena on kollektiivisesti paljastaa päätöksentekojärjestelmän rakenteita sekä luoda osallistumisen paikkoja perinteisiä hierarkiasuhteita ja organisaatiorajoja ylittävällä tavalla. Julkaisu on Yksityistämisen ja yhteisvastuun ylisektoraaliset vaihtoehdot –menetelmäkehitysprojektin loppuraportti ja sen kirjoittajat projektin tutkijoita Helsingin yliopiston Toiminnan teorian ja kehittävän työntutkimuksen yksiköstä. Projekti toteutettiin kokonaisuudessaan Tykes-ohjelman rahoituksella.

Cooperative Replies to Unbelievable Assertions

We propose a dialogue protocol for situations in which an agent makes to another agent an assertion that the other agent finds impossible to believe. In this interaction, unbelievable assertions are rejected using explanations formed by logical interpolation and new assertions are being made such that all previous rebuttals are taken into account.

Ambiguity-free polarization measurements from mixture initial preparations

Starting from beam and target spin systems which are polarized in the usual way by applying external magnetic fields, measurements of appropriate final state tensor parameters, viz., {t0,1k, k=1,...,2j} of particle d with spin j in a reaction a+b→d+c1+c2+. . .are suggested to determine the reaction amplitudes in spin space free from any associated discrete ambiguity.

Density-wave theory of dislocations in crystals

The density-wave theory of Ramakrishnan and Yussouff is extended to provide a scheme for describing dislocations and other topological defects in crystals. Quantitative calculations are presented for the order-parameter profiles, the atomic configuration, and the free energy of a screw dislocation with Burgers vector b=(a/2, a/2, a/2) in a bcc solid. These calculations are done using a simple parametrization of the direct correlation function and a gradient expansion. It is conventional to express the free energy of the dislocation in a crystal of size R as (λb2/4π)ln(αR/‖b‖), where λ is the shear elastic constant, and α is a measure of the core energy. Our results yield for Na the value α≃1.94a/(‖c1’’‖)1/2 (≃1.85) at the freezing temperature (371 K) and α≃2.48a/(‖c1’’‖)1/2 at 271 K, where c1’’ is the curvature of the first peak of the direct correlation function c(q). Detailed results for the density distribution in the dislocation, particularly the core region, are also presented. These show that the dislocation core has a columnar character. To our knowledge, this study represents the first calculation of dislocation structure, including the core, within the framework of an order-parameter theory and incorporating thermal effects.

An accurate numerical integration scheme for finite rotations using rotation vector parametrization

A numerical integration procedure for rotational motion using a rotation vector parametrization is explored from an engineering perspective by using rudimentary vector analysis. The incremental rotation vector, angular velocity and acceleration correspond to different tangent spaces of the rotation manifold at different times and have a non-vectorial character. We rewrite the equation of motion in terms of vectors lying in the same tangent space, facilitating vector space operations consistent with the underlying geometric structure. While any integration algorithm (that works within a vector space setting) may be used, we presently employ a family of explicit Runge-Kutta algorithms to solve this equation. While this work is primarily motivated out of a need for highly accurate numerical solutions of dissipative rotational systems of engineering interest, we also compare the numerical performance of the present scheme with some of the invariant preserving schemes, namely ALGO-C1, STW, LIEMIDEA] and SUBCYC-M. Numerical results show better local accuracy via the present approach vis-a-vis the preserving algorithms. It is also noted that the preserving algorithms do not simultaneously preserve all constants of motion. We incorporate adaptive time-stepping within the present scheme and this in turn enables still higher accuracy and a `near preservation' of constants of motion over significantly longer intervals. (C) 2010 The Franklin Institute. Published by Elsevier Ltd. All rights reserved.

Thermal and electrical switching studies on Ge20Se80-xBix (1 <= x <= 13) ternary chalcogenide glassy system

Alternating Differential Scanning Calorimetric (ADSC) and electrical switching studies have been undertaken on Ge20Se80-xBix glasses (1 <= x <= 13), to understand the effect of topological thresholds on thermal properties and electrical switching behavior. It is found that the compositional dependence of glass transition temperature (Tg), crystallization temperature (T-c1) and thermal stability (AT) of Ge20Se80-xBix glasses show anomalies at a composition x= 5, the rigidity percolation/stiffness threshold of the system. Further, unusual variations are also observed in different thermal properties, such as T-g, T-c1, Delta T, Delta C-p and Delta H-NR, at the composition x= 10, which indicates the occurrence of chemical threshold in these glasses at this composition. Electrical switching studies indicate that Ge20Se8o_RBig glasses with 5 11 exhibit threshold switching behavior and those with x = 12 and 13 show memory switching. A sharp decrease has been noticed in the switching voltages with bismuth concentration, which is due to the more metallic nature of bismuth and the presence of Bi+ ions. Further, a saturation is seen in the decrease in V-T around x = 6, which is related to bismuth phase percolation at higher concentrations of Bi. (C) 2010 Elsevier B.V. All rights reserved.

Disorder-driven electronic localization and phase separation in superconducting Fe1+yTe0.5Se0.5 single crystals

We have investigated the influence of Fe excess on the electrical transport and magnetism of Fe1+yTe0.5Se0.5 (y=0.04 and 0.09) single crystals. Both compositions exhibit resistively determined superconducting transitions (T-c) with an onset temperature of about 15 K. From the width of the superconducting transition and the magnitude of the lower critical field H-c1, it is inferred that excess of Fe suppresses superconductivity. The linear and nonlinear responses of the ac susceptibility show that the superconducting state for these compositions is inhomogeneous. A possible origin of this phase separation is a magnetic coupling between Fe excess occupying interstitial sites in the chalcogen planes and those in the Fe-square lattice. The temperature derivative of the resistivity d(rho)/d(T) in the temperature range T-c < T < T-a with T-a being the temperature of a magnetic anomaly, changes from positive to negative with increasing Fe. A log 1/T divergence of the resistivity above T-c in the sample with higher amount of Fe suggests a disorder-driven electronic localization.