Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Macroscopic model of city traffic using bond graph modelling

Modelling of city traffic involves capturing of all the dynamics that exist in real-time traffic. Probabilistic models and queuing theory have been used for mathematical representation of the traffic system. This paper proposes the concept of modelling the traffic system using bond graphs wherein traffic flow is based on energy conservation. The proposed modelling approach uses switched junctions to model complex traffic networks. This paper presents the modelling, simulation and experimental validation aspects.

Seasonal fluctuations in blue-green algae, especially in heterocystous species in polluted coastal waters off Helsinki city, in the northern part of the Gulf of Finland

Tiivistelmä

Discriminating between natural and anthropogenic aerosol contributions to optical depth over Afro-Asian region

To accurately assess the impact of anthropogenic aerosols on climate, spatial and temporal distribution of its radiative properties is essential. The first step towards separating the radiative impact of natural aerosol from its anthropogenic counterparts is to gather information on natural aerosols. In this paper, we have used data from multiple satellites to derive the anthropogenic aerosol fraction (AAF) over the Afro-Asian region. The AAF was largest during the pre-monsoon season (May-June) and lowest during winter. We have shown that over desert locations the AAF was unexpectedly large (>0.4) and the regionally (and annually) averaged anthropogenic fraction over the Afro-Asian region was 0.54 +/- 0.12. Copyright (C) 2010 Royal Meteorological Society

Frequency-comb-referenced molecular spectroscopy in the mid-infrared region

A simple method for absolute frequency measurements of molecular transitions in the mid-infrared region is reported. The method is based on a cw singly-resonant optical parametric oscillator (SRO), which is tunable from 3.2 to 3.45 µm. The mid- infrared frequency of the SRO is referenced to an optical frequency comb through its pump and signal beams. Sub-Doppler spectroscopy and absolute frequency measurement of the P(7) transition of the ν3 band of CH4 are demonstrated.

Studies on Unsteady Pressure Fields in the Region of Separating and Reattaching Flows

Experimental studies on the measurement of pressure fields in the region of separating and reattaching flows behind several two-dimensional fore-bodies and one axisymmetric body are reported. In particular, extensive measurements of mean pressure, surface pressure fluctuation, and pressure fluctuation within the flow were made for a series of two-dimensional fore-body shapes consisting of triangular nose with varying included angle. The measurements from different bodies are compared and one of the important findings is that the maximum values of rms pressure fluctuation levels in the shear layer approaching reattachment are almost equal to the maximum value of the surface fluctuation levels.

A sufficient criterion for Kelvin–Helmholtz instability in the magnetopause boundary‐layer region

The Kelvin–Helmholtz instability has been investigated for the magnetopause boundary‐layer region by the linearized method. The plasma in magnetosheath and magnetopause is assumed to be semi‐infinitely extended homogeneous, nondissipative, and incompressible. It is observed that, if one relation of two plasma speeds on the two sides of the magnetopause, wave number, and boundary‐layer thickness exceeds a certain threshold, the instability sets in. This new analytically sufficient criterion for excitation of instability in the three‐layer plasma flow generalizes the corresponding Chandrasekhar’s instability criterion for two‐layer plasma flow. The known results have been recovered and modified, the new results have been discovered. It is proved that the velocity threshold for the onset of instability is low when the magnitude of the magnetosheath and boundary‐layer region magnetic field and the angle between them are small. Also the threshold depends on the direction of plasma flow. The following results are observed numerically. The growth of the instability is sensitive to the magnetic field direction in the magnetosheath. A slight variation in the magnetic field direction in the second region can substantially change the relative velocity threshold for instability. When the ratio of the density of the second and third layer (magnetosphere) increases or that of the first and third layer decreases, the threshold decreases. Apart from this a necessary criterion for instability is obtained for a particular case.

Compressible MHD boundary layer in the stagnation region of a sphere

The steady laminar compressible boundary layer flow of an electrically conducting fluid in the stagnation region of a sphere with an applied magnetic field has been studied. The effects of the induced magnetic field, mass transfer, and viscous dissipation have been taken into account. Both isothermal and adiabatic wall conditions have been considered. The governing equations have been solved numerically using a shooting method. The skin friction and heat transfer are found to be strongly affected by the magnetic field, mass transfer, wall temperature and Mach number. It is found that the magnetic field reduces the heat transfer. This is a significant result which can be used in controlling the heat transfer rate. The boundary layer solutions break down as the magnetic parameter tends to a certain critical value.

Coherent rainfall zones of the Indian region

We have delineated rainfall zones for the Indian region that are coherent with respect to the variations of the summer monsoon rainfall. Within each zone, the time series of the summer monsoon rainfall at every pair of stations are significantly positively correlated, and the mean interseries correlation for each zone is high. The interseries correlation data set is analysed in order to delineate the rainfall zones, using an objective method specifically developed for the purpose. Each of the zonal averages are shown to be representative of the zone as a whole. We suggest that this regionalization is appropriate for study of the variation of the summer monsoon rainfall over the Indian region on interannual and larger scales.

Valikoiva muuttoliike Uudellamaalla

This thesis explores selective migration in Greater Helsinki region from the perspective of counterurbanisation. The aim of the study is to research whether the migration is selective by migrants age, education, income level or the rate of employment and to study any regional patterns formed by the selectivity. In the Helsinki region recent migratory developments have been shifting the areas of net migration gain away from the city of Helsinki to municipalities farther off on the former countryside. There has been discussion about Helsinki s decaying tax revenue base and whether the city s housing policy has contributed to the exodus of wealthier households. The central question of the discussion is one of selective migration: which municipalities succeed in capturing the most favourable migrants and which will lose in the competition. Selective migration means that region s in-migrants and out-migrants significantly differ from each other demographically, socially and economically. Sometimes selectivity is also understood as some individuals greater propensity to migrate than others but the proper notion for this would be differential migration. In Finnish parlance these two concepts have tended to get mixed up. The data of the study covers the total migration of the 34 municipalities of Uusimaa provinces during the years 2001 to 2003. The data was produced by Statistics Finland. Two new methods of representing the selectivity of migration as a whole were constructed during the study. Both methods look at the proportions of favourably selected migrants in regions inward and outward migrant flow. A large share in the inward flow and a small share in the outward flow is good for region s economy and demography. The first method calculates the differences of the proportions of favourably selected four migrant groups and sums the differences up. The other ranks the same proportions between regions giving value 1 to the largest proportion in inward flow and 34 to the smallest, and respectively in outward flow the smallest proportion gets value 1 and the largest 34. The total sum of the ranks or differences in proportions represents region s selectivity of migration. The results show that migration is indeed selective in the Greater Helsinki region. There also seems to be a spatial pattern centred around the Helsinki metropolitan region. The municipalities surrounding the four central communes are generally better of than those farther away. Not only these eight municipalities of the so called capital region benefit from the selective migration, but the favourable structure of migration extends to some of the small municipalities farther away. Some municipalities situated along the main northbound railway line are not coming through as well as other municipalities of the capital region. The selectivity of migration in Greater Helsinki region shows signs of counter-urbanisation. People look for suburban or small-town lifestyle no longer from Espoo or Vantaa, the neighbouring municipalities to Helsinki, but from the municipalities surrounding these two or even farther off. This kind of pattern in selective migration leads to unbalanced development in population structure and tax revenue base in the region. Migration to outskirts of the urban area also leads to urban sprawl and fragmentation of the urban structure: these issues have ecological implications. Selective migration should be studied more. Also the concept itself needs clearer definition and so do the methods to study the selectivity of migration.

Accessibility as a determinant of opportunities : A case study from Peruvian Amazonia

Accessibility is a crucial factor for interaction between areas in economic, cultural, political and environmental terms. Therefore, information concerning accessibility is relevant for informed decision making, planning and research. The Loreto region in the Peruvian Amazonia provides an interesting scene for an accessibility study. Loreto is sparsely populated and because there are few roads in the region, in practice all movement and transportation happens along the river network. Due to the proximity of the Andes, river dynamics are strong and annual changes in water level combined with these dynamic processes constantly reshape accessibility patterns of the region. Selling non-timber forest products (NTFP) and agricultural products (AP) in regional centres is an important income source for local rain forest dwellers. Thus, accessibility to the centres is crucial for the livelihood of local population. -- In this thesis I studied how accessible the regional centre Iquitos is from other parts of Loreto. In addition, I studied the regional NTFP/AP trade patterns and compared them with patterns of accessibility. Based on GPS-measurements, using GIS, I created a time-distance surface covering Loreto. This surface describes the time-distance to Iquitos, along the river network. Based on interview material, I assessed annual changes to accessibility patterns in the region. The most common regional NTFP/AP were classified according to the amount of time they can be preserved, and based on the accessibility surface, I modelled a catchment area for each of these product classes. -- According to my results, navigation speeds vary considerably in different parts of the river network, depending on river types, vessels, flow direction and season. Navigating downstream is, generally, faster than upstream navigation. Thus, Iquitos is better accessible from areas situated south and south west of the city, like along the rivers Ucayali and Marañon. Differences in accessibility between different seasons are also substantial: during the dry season navigation is slower due to lower water levels and emerging sand bars. Regularly operating boats follow routes only along certain rivers and close to Iquitos transport facilities are more abundant than in more distant areas. Most of the products present in Iquitos market places are agricultural products, and the share of NTFP is significantly smaller. Most of the products were classified in product class 2, and the catchment area for these products is rather small. Many products also belonged to class 5, and the catchment area for these products reaches up to the edges of my study area, following the patterns of the river network. -- The accessibility model created in this study predicts travel times relatively well, although in some cases the modelled time-distances are substantially shorter than observed time-distances. This is partly caused by the fact that real-life navigation routes are more complicated than the modelled routes. Rain forest dwellers having easier access to Iquitos have more opportunities in terms of the products they decide to market. Thus, they can better take advantage of other factors affecting the market potential of different products. -- In all, understanding spatial variation in accessibility is important. In the Amazonian context it is difficult to combine the accessibility-related needs of the local dwellers with conservation purposes and the future challenge lies in finding solution that satisfy both of these needs.

Polarimetric Signatures in the Stratiform Region of a Mesoscale Convective System

Four polarimetric measurands were collected in the stratiform region of a mesoscale convective system. The four are the reflectivity factor, the differential reflectivity, the correlation coefficient between orthogonal copolar echoes, and the differential propagation constant. Most striking is a signature of large aggregates (about 10 mm in size) seen in the differential phase through the melting layer. Another significant feature is an abrupt notch in the correlation coefficient that occurs towards the bottom of the bright band. Aircraft observations and a one-dimensional cloud model are used to explain some polarimetric measurements and to infer the presence of aggregates, graupel, and supercooled cloud water in the stratiform region. These unique observations and model data provide inferences concerning the presence of graupel and the growth of large aggregates in the melting layer.

Specific-heat measurements during cooling through the glass-transition region

In this paper we report the measurements of specific heats of five glass formers as they are cooled through the glass-transition region. The measurements are compared with other specific-heat measurements such as adiabatic-calorimetry and ac-calorimetry measurements. The data are then analyzed using a model of enthalpy relaxation and nonequilibrium cooling, which can track the nonequilibrium relaxation time tau(S). The relevant parameters that describe tau(S) are obtained, allowing us to compare the enthalpy-relaxation times obtained from this method with other methods. We display the clear connection of the unrelaxed enthalpy with the nonequilibrium relaxation time and also show the role played by the delayed heat release from the unrelaxed enthalpy in the glass-transition region. We have also made certain definite observations regarding the equilibrium configurational specific heat and the Vogel-Fulcher law, which describes tau(S).

Elämää keskustassa ja kaupunkiseudun reunoilla. Urbaani ja jälkiesikaupungillinen elämäntyyli asumisen valinnoissa ja arkiliikkumisessa Helsingin seudulla.

The lifestyles of people living in single-family housing areas on the outskirts of the Greater Helsinki Region (GHR) are different from those living in inner city area. The urban structure of the GHR is concentrated in the capital on the one hand, and spread out across the outskirts on the other. Socioeconomic spatial divisions are evident as well-paid and educated residents move to the inner city or the single-family house dominated suburban neighbourhoods depending on their housing preferences and life situations. The following thesis explores how these lifestyles have emerged through the housing choices and daily mobility of the residents living in the new single-family housing areas on the outskirts of the GHR and the inner city. The study shows that, when it comes to lifestyles, residents on the outskirts of the region have different housing preferences and daily mobility patterns when compared with their inner city counterparts. Based on five different case study areas my results show that these differences are related to residents values, preferences and attitudes towards the neighbourhood, on the one hand, and limited by urban structure on the other. This also confirms earlier theoretical analyses and findings from the GHR. Residents who moved to the outskirts of Greater Helsinki Region and the apartment buildings of the inner city were similar in the basic elements of their housing preferences: they sought a safe and peaceful neighbourhood close to the natural environment. However, where housing choices, daily mobility and activities vary different lifestyles develop in both the outskirts and the inner city. More specifically, lifestyles in the city apartment blocks were inherently urban. Liveliness and highest order facilities were appreciated and daily mobility patterns were supported by diverse modes of transportation for the purposes of work, shopping and leisure time. On the outskirts, by contrast, lifestyles were largely post-suburban and child-friendliness appreciated. Due to the heterachical urban structure, daily mobility was more car-dependent since work, shopping and free time activities of the residents are more spread around the region. The urban structure frames the daily mobility on the outskirts of the region, but this is not to say that short local trips replace longer regional ones. This comparative case study was carried out in the single-family housing areas of Sundsberg in Kirkkonummi, Landbo in Helsinki and Ylästö in Vantaa, as well as in the inner city apartment building areas of Punavuori and Katajanokka in Helsinki. The data is comprised of residential surveys, interviews, and statistics and GIS data sets that illustrate regional daily mobility, socio-economic structure and vis-à-vis housing stock.