Low-lying states of transverse substituted trans-polyacetylene and trans-polyacetylene: A comparative DMRG study

The density-matrix renormalization group (DMRG) method is used for a comparative study of low-lying excitations in trans-polyacetylene (t-PA) and transversely substituted t-PA (TS-t-PA). We have employed the Pariser-Parr-Pople model Hamiltonian which incorporates long-range electronic correlations to model these systems. We find some fundamental differences in the excited states of the t-PA and TS-t-PA. We find that the lowest two-photon allowed excited state in TS-t-PA is not made up of two triplet excitons and the gap to this state is nonzero even for undimerized chains in the thermodynamic limit. Contrary to earlier results for the Hubbard model, we find that the lowest two-photon state is always below the first optically allowed state in all the systems studied here making TS-t-PA systems only weakly fluorescent materials. Nonresonant tumbling averaged linear and third harmonic generation optic coefficients of TS-t-PA systems are also much smaller than that of t-PA.

Crystallite size effects in stacking faulted nickel hydroxide and its electrochemical behaviour

P-Nickel hydroxide comprises a long range periodic arrangement of atoms with a stacking sequence of AC AC AC-having an ideal composition Ni(OH)(2). Variation in the preparative conditions can lead to the changes in the stacking sequence (AC AC BA CB AC AC or AC AC AB AC AC) This type of variation in stacking sequence can result in the formation of stacking fault in nickel hydroxide. The stability of the stacking fault depends on the free energy content of the sample. Stacking faults in nickel hydroxide is essential for better electrochemical activity. Also there are reports correlating particle size to the better electrochemical activity. Here we present the effect of crystallite size on the stacking faulted nickel hydroxide samples. The electrochemical performance of stacking faulted nickel hydroxide with small crystallite size exchanges 0.8e/Ni, while the samples with larger crystallite size exchange 0.4e/Ni. Hence a right combination of crystallite size and stacking fault content has to be controlled for good electrochemical activity of nickel hydroxide. (C) 2008 Elsevier B.V. All rights reserved.

Structural Insights into the acyl-intermediates of plasmodium falciparum fatty acid synthesis pathway; the mechanism of expansion of acyl carrier protein core

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.

A dynamic renormalization group study of active nematics

We carry out a systematic construction of the coarse-grained dynamical equation of motion for the orientational order parameter for a two-dimensional active nematic, that is a nonequilibrium steady state with uniaxial, apolar orientational order. Using the dynamical renormalization group, we show that the leading nonlinearities in this equation are marginally irrelevant. We discover a special limit of parameters in which the equation of motion for the angle field bears a close relation to the 2d stochastic Burgers equation. We find nevertheless that, unlike for the Burgers problem, the nonlinearity is marginally irrelevant even in this special limit, as a result of a hidden fluctuation-dissipation relation. 2d active nematics therefore have quasi-long-range order, just like their equilibrium counterparts.

Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins

Molten globule-like intermediates have been shown to occur during protein folding and are thought to be involved in protein translocation and membrane insertion. However, the determinants of molten globule stability and the extent of specific packing in molten globules is currently unclear. Using far- and near-UV CD and intrinsic and ANS fluorescence, we show that four periplasmic binding proteins (LBP, LIVBP, MBP, and RBP) form molten globules at acidic pH values ranging from 3.0 to 3.4. Only two of these (LBP and LIVBP) have similar sequences, but all four proteins adopt similar three-dimensional structures. We found that each of the four molten globules binds to its corresponding ligand without conversion to the native state. Ligand binding affinity measured by isothermal titration calorimetry for the molten globule state of LIVBP was found to be comparable to that of the corresponding native state, whereas for LBP, MBP, and RBP, the molten globules bound ligand with approximately 5-30-fold lower affinity than the corresponding native states. All four molten globule states exhibited cooperative thermal unfolding assayed by DSC. Estimated values of Delta C-p of unfolding show that these molten globule states contain 28-67% of buried surface area relative to the native states. The data suggest that molten globules of these periplasmic binding proteins retain a considerable degree of long range order. The ability of these sequentially unrelated proteins to form highly ordered molten globules may be related to their large size as well as an intrinsic property of periplasmic binding protein folds.

Turbulence-induced melting of a nonequilibrium vortex crystal in a forced thin fluid film

To gain a better understanding of recent experiments on the turbulence-induced melting of a periodic array of vortices in a thin fluid film, we perform a direct numerical simulation of the two-dimensional Navier-Stokes equations forced such that, at low Reynolds numbers, the steady state of the film is a square lattice of vortices. We find that as we increase the Reynolds number, this lattice undergoes a series of nonequilibrium phase transitions, first to a crystal with a different reciprocal lattice and then to a sequence of crystals that oscillate in time. Initially, the temporal oscillations are periodic; this periodic behaviour becoming more and more complicated with increasing Reynolds number until the film enters a spatially disordered nonequilibrium statistical steady state that is turbulent. We study this sequence of transitions using fluid-dynamics measures, such as the Okubo-Weiss parameter that distinguishes between vortical and extensional regions in the flow, ideas from nonlinear dynamics, e.g. Poincare maps, and theoretical methods that have been developed to study the melting of an equilibrium crystal or the freezing of a liquid and that lead to a natural set of order parameters for the crystalline phases and spatial autocorrelation functions that characterize short- and long-range order in the turbulent and crystalline phases, respectively.

Manifestation of geometric frustration on magnetic and thermodynamic properties of the pyrochlores Sm2X2O7 (X=Ti,Zr)

We present here magnetization, specific heat, and Raman studies on single-crystalline specimens of the first pyrochlore member Sm2Ti2O7 of the rare-earth titanate series. Its analogous compound Sm2Zr2O7 in the rare-earth zirconate series is also investigated in the polycrystalline form. The Sm spins in Sm2Ti2O7 remain unordered down to at least T=0.5 K. The absence of magnetic ordering is attributed to very small values of exchange (θcw∼−0.26 K) and dipolar interaction (μeff∼0.15 μB) between the Sm3+ spins in this pyrochlore. In contrast, the pyrochlore Sm2Zr2O7 is characterized by a relatively large value of Sm-Sm spin exchange (θcw∼−10 K); however, long-range ordering of the Sm3+ spins is not established at least down to T=0.67 K due to frustration of the Sm3+ spins on the pyrochlore lattice. The ground state of Sm3+ ions in both pyrochlores is a well-isolated Kramers doublet. The higher-lying crystal field excitations are observed in the low-frequency region of the Raman spectra of the two compounds recorded at T=10 K. At higher temperatures, the magnetic susceptibility of Sm2Ti2O7 shows a broad maximum at T=140 K, while that of Sm2Zr2O7 changes monotonically. Whereas Sm2Ti2O7 is a promising candidate for investigating spin fluctuations on a frustrated lattice, as indicated by our data, the properties of Sm2Zr2O7 seem to conform to a conventional scenario where geometrical frustration of the spin excludes their long-range ordering.

On measurements of formation, growth, hygroscopicity, and volatility of atmospheric ultrafine particles

Atmospheric aerosol particles affect the global climate as well as human health. In this thesis, formation of nanometer sized atmospheric aerosol particles and their subsequent growth was observed to occur all around the world. Typical formation rate of 3 nm particles at varied from 0.01 to 10 cm-3s-1. One order of magnitude higher formation rates were detected in urban environment. Highest formation rates up to 105 cm-3s-1 were detected in coastal areas and in industrial pollution plumes. Subsequent growth rates varied from 0.01 to 20 nm h-1. Smallest growth rates were observed in polar areas and the largest in the polluted urban environment. This was probably due to competition between growth by condensation and loss by coagulation. Observed growth rates were used in the calculation of a proxy condensable vapour concentration and its source rate in vastly different environments from pristine Antarctica to polluted India. Estimated concentrations varied only 2 orders of magnitude, but the source rates for the vapours varied up to 4 orders of magnitude. Highest source rates were in New Delhi and lowest were in the Antarctica. Indirect methods were applied to study the growth of freshly formed particles in the atmosphere. Also a newly developed Water Condensation Particle Counter, TSI 3785, was found to be a potential candidate to detect water solubility and thus indirectly composition of atmospheric ultra-fine particles. Based on indirect methods, the relative roles of sulphuric acid, non-volatile material and coagulation were investigated in rural Melpitz, Germany. Condensation of non-volatile material explained 20-40% and sulphuric acid the most of the remaining growth up to a point, when nucleation mode reached 10 to 20 nm in diameter. Coagulation contributed typically less than 5%. Furthermore, hygroscopicity measurements were applied to detect the contribution of water soluble and insoluble components in Athens. During more polluted days, the water soluble components contributed more to the growth. During less anthropogenic influence, non-soluble compounds explained a larger fraction of the growth. In addition, long range transport to a measurement station in Finland in a relatively polluted air mass was found to affect the hygroscopicity of the particles. This aging could have implications to cloud formation far away from the pollution sources.

Molecular dynamics studies of nanoparticle impacts

This thesis concerns the dynamics of nanoparticle impacts on solid surfaces. These impacts occur, for instance, in space, where micro- and nanometeoroids hit surfaces of planets, moons, and spacecraft. On Earth, materials are bombarded with nanoparticles in cluster ion beam devices, in order to clean or smooth their surfaces, or to analyse their elemental composition. In both cases, the result depends on the combined effects of countless single impacts. However, the dynamics of single impacts must be understood before the overall effects of nanoparticle radiation can be modelled. In addition to applications, nanoparticle impacts are also important to basic research in the nanoscience field, because the impacts provide an excellent case to test the applicability of atomic-level interaction models to very dynamic conditions. In this thesis, the stopping of nanoparticles in matter is explored using classical molecular dynamics computer simulations. The materials investigated are gold, silicon, and silica. Impacts on silicon through a native oxide layer and formation of complex craters are also simulated. Nanoparticles up to a diameter of 20 nm (315000 atoms) were used as projectiles. The molecular dynamics method and interatomic potentials for silicon and gold are examined in this thesis. It is shown that the displacement cascade expansionmechanism and crater crown formation are very sensitive to the choice of atomic interaction model. However, the best of the current interatomic models can be utilized in nanoparticle impact simulation, if caution is exercised. The stopping of monatomic ions in matter is understood very well nowadays. However, interactions become very complex when several atoms impact on a surface simultaneously and within a short distance, as happens in a nanoparticle impact. A high energy density is deposited in a relatively small volume, which induces ejection of material and formation of a crater. Very high yields of excavated material are observed experimentally. In addition, the yields scale nonlinearly with the cluster size and impact energy at small cluster sizes, whereas in macroscopic hypervelocity impacts, the scaling 2 is linear. The aim of this thesis is to explore the atomistic mechanisms behind the nonlinear scaling at small cluster sizes. It is shown here that the nonlinear scaling of ejected material yield disappears at large impactor sizes because the stopping mechanism of nanoparticles gradually changes to the same mechanism as in macroscopic hypervelocity impacts. The high yields at small impactor size are due to the early escape of energetic atoms from the hot region. In addition, the sputtering yield is shown to depend very much on the spatial initial energy and momentum distributions that the nanoparticle induces in the material in the first phase of the impact. At the later phases, the ejection of material occurs by several mechanisms. The most important mechanism at high energies or at large cluster sizes is atomic cluster ejection from the transient liquid crown that surrounds the crater. The cluster impact dynamics detected in the simulations are in agreement with several recent experimental results. In addition, it is shown that relatively weak impacts can induce modifications on the surface of an amorphous target over a larger area than was previously expected. This is a probable explanation for the formation of the complex crater shapes observed on these surfaces with atomic force microscopy. Clusters that consist of hundreds of thousands of atoms induce long-range modifications in crystalline gold.

Graphene Analogues of BN: Novel Synthesis and Properties

Enthused by the fascinating properties of graphene, we have prepared graphene analogues of BN by a chemical method with a control on the number of layers. The method involves the reaction of boric acid with urea, wherein the relative proportions of the two have been varied over a wide range. Synthesis with a high proportion of urea yields a product with a majority of 1-4 layers. The surface area of BN increases progressively with the decreasing number of layers, and the high surface area BN exhibits high CO, adsorption, but negligible H, adsorption. Few-layer BN has been solubilized by interaction with Lewis bases. We have used first-principles simulations to determine structure, phonon dispersion, and elastic properties of BN with planar honeycomb lattice-based n-layer forms. We find that the mechanical stability of BN with respect to out-of-plane deformation is quite different from that of graphene, as evident in the dispersion of their flexural modes. BN is softer than graphene and exhibits signatures of long-range ionic interactions in its optical phonons. Finally, structures with different stacking sequences of BN have comparable energies, suggesting relative abundance of slip faults, stacking faults, and structural inhomogeneities in multilayer BN.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease. Conclusions: The MDH1 gene is not the cause of RP28-linked arRP. Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration.

Excitation energy transfer from a fluorophore to single-walled carbon nanotubes

We study the process of electronic excitation energy transfer from a fluorophore to the electronic energy levels of a single-walled carbon nanotube. The matrix element for the energy transfer involves the Coulombic interaction between the transition densities on the donor and the acceptor. In the Foumlrster approach, this is approximated as the interaction between the corresponding transition dipoles. For energy transfer from a dye to a nanotube, one can use the dipole approximation for the dye, but not for the nanotube. We have therefore calculated the rate using an approach that avoids the dipole approximation for the nanotube. We find that for the metallic nanotubes, the rate has an exponential dependence if the energy that is to be transferred, h is less than a threshold and a d(-5) dependence otherwise. The threshold is the minimum energy required for a transition other than the k(i,perpendicular to)=0 and l=0 transition. Our numerical evaluation of the rate of energy transfer from the dye pyrene to a (5,5) carbon nanotube, which is metallic leads to a distance of similar to 165 A degrees up to which energy transfer is appreciable. For the case of transfer to semiconducting carbon nanotubes, apart from the process of transfer to the electronic energy levels within the one electron picture, we also consider the possibility of energy transfer to the lowest possible excitonic state. Transfer to semiconducting carbon nanotubes is possible only if>=epsilon(g)-epsilon(b). The long range behavior of the rate of transfer has been found to have a d(-5) dependence if h >=epsilon(g). But, when the emission energy of the fluorophore is in the range epsilon(g)>h >=epsilon(g)-epsilon(b), the rate has an exponential dependence on the distance. For the case of transfer from pyrene to the semiconducting (6,4) carbon nanotube, energy transfer is found to be appreciable up to a distance of similar to 175 A degrees.

Evaluation and modelling of the spatial and temporal variability of particulate matter in urban areas

This thesis contains three subject areas concerning particulate matter in urban area air quality: 1) Analysis of the measured concentrations of particulate matter mass concentrations in the Helsinki Metropolitan Area (HMA) in different locations in relation to traffic sources, and at different times of year and day. 2) The evolution of traffic exhaust originated particulate matter number concentrations and sizes in local street scale are studied by a combination of a dispersion model and an aerosol process model. 3) Some situations of high particulate matter concentrations are analysed with regard to their meteorological origins, especially temperature inversion situations, in the HMA and three other European cities. The prediction of the occurrence of meteorological conditions conducive to elevated particulate matter concentrations in the studied cities is examined. The performance of current numerical weather forecasting models in the case of air pollution episode situations is considered. The study of the ambient measurements revealed clear diurnal variation of the PM10 concentrations in the HMA measurement sites, irrespective of the year and the season of the year. The diurnal variation of local vehicular traffic flows seemed to have no substantial correlation with the PM2.5 concentrations, indicating that the PM10 concentrations were originated mainly from local vehicular traffic (direct emissions and suspension), while the PM2.5 concentrations were mostly of regionally and long-range transported origin. The modelling study of traffic exhaust dispersion and transformation showed that the number concentrations of particles originating from street traffic exhaust undergo a substantial change during the first tens of seconds after being emitted from the vehicle tailpipe. The dilution process was shown to dominate total number concentrations. Minimal effect of both condensation and coagulation was seen in the Aitken mode number concentrations. The included air pollution episodes were chosen on the basis of occurrence in either winter or spring, and having at least partly local origin. In the HMA, air pollution episodes were shown to be linked to predominantly stable atmospheric conditions with high atmospheric pressure and low wind speeds in conjunction with relatively low ambient temperatures. For the other European cities studied, the best meteorological predictors for the elevated concentrations of PM10 were shown to be temporal (hourly) evolutions of temperature inversions, stable atmospheric stability and in some cases, wind speed. Concerning the weather prediction during particulate matter related air pollution episodes, the use of the studied models were found to overpredict pollutant dispersion, leading to underprediction of pollutant concentration levels.

Hydrogen soil deposition and atmospheric variations in the boreal zone

This research has been prompted by an interest in the atmospheric processes of hydrogen. The sources and sinks of hydrogen are important to know, particularly if hydrogen becomes more common as a replacement for fossil fuel in combustion. Hydrogen deposition velocities (vd) were estimated by applying chamber measurements, a radon tracer method and a two-dimensional model. These three approaches were compared with each other to discover the factors affecting the soil uptake rate. A static-closed chamber technique was introduced to determine the hydrogen deposition velocity values in an urban park in Helsinki, and at a rural site at Loppi. A three-day chamber campaign to carry out soil uptake estimation was held at a remote site at Pallas in 2007 and 2008. The atmospheric mixing ratio of molecular hydrogen has also been measured by a continuous method in Helsinki in 2007 - 2008 and at Pallas from 2006 onwards. The mean vd values measured in the chamber experiments in Helsinki and Loppi were between 0.0 and 0.7 mm s-1. The ranges of the results with the radon tracer method and the two-dimensional model were 0.13 - 0.93 mm s-1 and 0.12 - 0.61 mm s-1, respectively, in Helsinki. The vd values in the three-day campaign at Pallas were 0.06 - 0.52 mm s-1 (chamber) and 0.18 - 0.52 mm s-1 (radon tracer method and two-dimensional model). At Kumpula, the radon tracer method and the chamber measurements produced higher vd values than the two-dimensional model. The results of all three methods were close to each other between November and April, except for the chamber results from January to March, while the soil was frozen. The hydrogen deposition velocity values of all three methods were compared with one-week cumulative rain sums. Precipitation increases the soil moisture, which decreases the soil uptake rate. The measurements made in snow seasons showed that a thick snow layer also hindered gas diffusion, lowering the vd values. The H2 vd values were compared to the snow depth. A decaying exponential fit was obtained as a result. During a prolonged drought in summer 2006, soil moisture values were lower than in other summer months between 2005 and 2008. Such conditions were prevailing in summer 2006 when high chamber vd values were measured. The mixing ratio of molecular hydrogen has a seasonal variation. The lowest atmospheric mixing ratios were found in the late autumn when high deposition velocity values were still being measured. The carbon monoxide (CO) mixing ratio was also measured. Hydrogen and carbon monoxide are highly correlated in an urban environment, due to the emissions originating from traffic. After correction for the soil deposition of H2, the slope was 0.49±0.07 ppb (H2) / ppb (CO). Using the corrected hydrogen-to-carbon-monoxide ratio, the total hydrogen load emitted by Helsinki traffic in 2007 was 261 t (H2) a-1. Hydrogen, methane and carbon monoxide are connected with each other through the atmospheric methane oxidation process, in which formaldehyde is produced as an important intermediate. The photochemical degradation of formaldehyde produces hydrogen and carbon monoxide as end products. Examination of back-trajectories revealed long-range transportation of carbon monoxide and methane. The trajectories can be grouped by applying cluster and source analysis methods. Thus natural and anthropogenic emission sources can be separated by analyzing trajectory clusters.

Structural Insights into the Acyl Intermediates of the Plasmodium falciparum Fatty Acid Synthesis Pathway THE MECHANISM OF EXPANSION OF THE ACYL CARRIER PROTEIN CORE

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.