Adaptive tree multigrids and simplified spherical harmonics approximation in deterministic neutral and charged particle transport

A new deterministic three-dimensional neutral and charged particle transport code, MultiTrans, has been developed. In the novel approach, the adaptive tree multigrid technique is used in conjunction with simplified spherical harmonics approximation of the Boltzmann transport equation. The development of the new radiation transport code started in the framework of the Finnish boron neutron capture therapy (BNCT) project. Since the application of the MultiTrans code to BNCT dose planning problems, the testing and development of the MultiTrans code has continued in conventional radiotherapy and reactor physics applications. In this thesis, an overview of different numerical radiation transport methods is first given. Special features of the simplified spherical harmonics method and the adaptive tree multigrid technique are then reviewed. The usefulness of the new MultiTrans code has been indicated by verifying and validating the code performance for different types of neutral and charged particle transport problems, reported in separate publications.

Studies on the Cell Wall Structure and on the Mechanical Properties of Norway Spruce

The structure and the mechanical properties of wood of Norway spruce (Picea abies [L.] Karst.) were studied using small samples from Finland and Sweden. X-ray diffraction (XRD) was used to determine the orientation of cellulose microfibrils (microfibril angle, MFA), the dimensions of cellulose crystallites and the average shape of the cell cross-section. X-ray attenuation and x-ray fluorescence measurements were used to study the chemical composition and the trace element content. Tensile testing with in situ XRD was used to characterise the mechanical properties of wood and the deformation of crystalline cellulose within the wood cell walls. Cellulose crystallites were found to be 192 284 Å long and 28.9 33.4 Å wide in chemically untreated wood and they were longer and wider in mature wood than in juvenile wood. The MFA distribution of individual Norway spruce tracheids and larger samples was asymmetric. In individual cell walls, the mean MFA was 19 30 degrees, while the mode of the MFA distribution was 7 21 degrees. Both the mean MFA and the mode of the MFA distribution decreased as a function of the annual ring. Tangential cell walls exhibited smaller mean MFA and mode of the MFA distribution than radial cell walls. Maceration of wood material caused narrowing of the MFA distribution and removed contributions observed at around 90 degrees. In wood of both untreated and fertilised trees, the average shape of the cell cross-section changed from circular via ambiguous to rectangular as the cambial age increased. The average shape of the cell cross-section and the MFA distribution did not change as a result of fertilisation. The mass absorption coefficient for x-rays was higher in wood of fertilised trees than in that of untreated trees and wood of fertilised trees contained more of the elements S, Cl, and K, but a smaller amount of Mn. Cellulose crystallites were longer in wood of fertilised trees than in that of untreated trees. Kraft cooking caused widening and shortening of the cellulose crystallites. Tensile tests parallel to the cells showed that if the mean MFA is initially around 10 degrees or smaller, no systematic changes occur in the MFA distribution due to strain. The role of mean MFA in defining the tensile strength or the modulus of elasticity of wood was not as dominant as that reported earlier. Crystalline cellulose elongated much less than the entire samples. The Poisson ratio νca of crystalline cellulose in Norway spruce wood was shown to be largely dependent on the surroundings of crystalline cellulose in the cell wall, varying between -1.2 and 0.8. The Poisson ratio was negative in kraft cooked wood and positive in chemically untreated wood. In chemically untreated wood, νca was larger in mature wood and in latewood compared to juvenile wood and earlywood.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Observations on the first steps of atmospheric particle formation and growth

Atmospheric aerosol particles have a significant impact on air quality, human health and global climate. The climatic effects of secondary aerosol are currently among the largest uncertainties limiting the scientific understanding of future and past climate changes. To better estimate the climatic importance of secondary aerosol particles, detailed information on atmospheric particle formation mechanisms and the vapours forming the aerosol is required. In this thesis we studied these issues by applying novel instrumentation in a boreal forest to obtain direct information on the very first steps of atmospheric nucleation and particle growth. Additionally, we used detailed laboratory experiments and process modelling to determine condensational growth properties, such as saturation vapour pressures, of dicarboxylic acids, which are organic acids often found in atmospheric samples. Based on our studies, we came to four main conclusions: 1) In the boreal forest region, both sulphurous compounds and organics are needed for secondary particle formation, the previous contributing mainly to particle formation and latter to growth; 2) A persistent pool of molecular clusters, both neutral and charged, is present and participates in atmospheric nucleation processes in boreal forests; 3) Neutral particle formation seems to dominate over ion-mediated mechanisms, at least in the boreal forest boundary layer; 4) The subcooled liquid phase saturation vapour pressures of C3-C9 dicarboxylic acids are of the order of 1e-5 1e-3 Pa at atmospheric temperatures, indicating that a mixed pre-existing particulate phase is required for their condensation in atmospheric conditions. The work presented in this thesis gives tools to better quantify the aerosol source provided by secondary aerosol formation. The results are particularly useful when estimating, for instance, anthropogenic versus biogenic influences and the fractions of secondary aerosol formation explained by neutral or ion-mediated nucleation mechanisms, at least in environments where the average particle formation rates are of the order of some tens of particles per cubic centimeter or lower. However, as the factors driving secondary particle formation are likely to vary depending on the environment, measurements on atmospheric nucleation and particle growth are needed from around the world to be able to better describe the secondary particle formation, and assess its climatic effects on a global scale.