Skogen som ämnesövergripande tema : För en hållbar och ljusnande framtid

I denna uppsats undersöks möjligheterna att införa skogen som ett ämnesövergripande tema inomramen för gymnasieskolans naturvetenskapliga program. Det föreslagna arbetssättet innehållerutomhusundervisning såväl som klassrumsbaserad undervisning. Ämnena som ingår i arbetssättet är idetta förslag biologi, kemi och fysik. Fokus på det ämnesövergripande ligger därför pånaturvetenskapens karaktär och arbetssätt, något som dessa ämnen har som gemensamt centraltinnehåll. Med temat skogen ges möjlighet att se skogen både ur ett biologiskt perspektiv, somekosystem och viktig pusselbit i kolcykeln men också som naturresurs och råmaterial för trä, pappersochmassaindustri såväl som för avancerad materialutveckling av nya material från trä

Cellulose and the role of hydrogen bonds : not in charge of everything

In the cellulose scientific community, hydrogen bonding is often used as the explanation for a large variety of phenomena and properties related to cellulose and cellulose based materials. Yet, hydrogen bonding is just one of several molecular interactions and furthermore is both relatively weak and sensitive to the environment. In this review we present a comprehensive examination of the scientific literature in the area, with focus on theory and molecular simulation, and conclude that the relative importance of hydrogen bonding has been, and still is, frequently exaggerated

Charge State Dependence of Amino Acid Propensity at Water Surface : Mechanisms Elucidated by Molecular Dynamics Simulations

Atmospheric aerosols contain a variety of compounds, among them free amino acids and salt ions. The pH of the aerosol droplets depends on their origin and environment. Consequently, compounds like free amino acids found in the droplets will be at different charge states, since these states to a great extent depend on the surrounding pH condition. In droplets of marine origin, amino acids are believed to drive salt ions to the water surface and a pH-dependent amino acid surface propensity will, therefore, indirectly affect many processes in atmospheric chemistry and physics such as for instance cloud condensation. To understand the surface propensity of glycine, valine, and phenylalanine at acidic, neutral, and basic pH, we used molecular dynamics (MD) simulations to investigate them at three different charge states in water. Their respective surface propensities were obtained by the means of a potential of mean force (PMF) in an umbrella sampling approach. Glycine was found to have no preference for the surface, while both valine and phenylalanine showed high propensities. Among the charge states of the surface-enriched ones, the cation, representing the amino acids at low pH, was found to have the highest affinity. Free energy decomposition revealed that the driving forces depend strongly on the nature of the amino acid and its charge state. In phenylalanine, the main factor was found to be a substantial entropy gain, likely related to the side chain, whereas in valine, hydrogen bonding to the functional groups leads to favorable energies and, in turn, affects the surface propensity. A significant gain in water-water enthalpy was seen for both valine and phenylalanine

Solubility of Cellulose in Supercritical Water Studied by Molecular Dynamics Simulations

The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm^–3) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 × 4 × 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water–water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water

Microscopic computed tomography aided finiteelement modelling as a methodology to estimatehygroexpansion coefficients of wood : a case studyon opposite and compression wood in softwoodbranches

Microscopic X-ray computed tomography (XµCT) aided finite element (FE) modelling is a popular method in material science to relate material properties to heterogeneous microstructures. Recently, a methodology was developed for the XµCT aided FE modelling of wood, which characterises the process from specimen preparation to estimation of material properties. In the current research, this methodology is tested on branches of Norway spruce (Picea abies (L.) Karst.) to estimate the hygroexpansion coefficients of opposite (OW) and compression wood (CW). These properties are largely unknown and have engineering implications. The study is complemented by measurements of density, moisture content (MC) and elastic moduli. Results showed that the methodology assisted in the design of an integrated process and the identification of bottlenecks. It was seen that the level of detail of the numerical model had a strong influence on the obtained hygroexpansion properties. CW from branches showed higher density and longitudinal shrinkage coefficients, and elastic moduli less affected by MC. These differences are unlikely caused by MC, but more likely by the characteristics of the microstructure

Propensity, free energy contributions and conformation of primary : N -alcohols at a water surface

Atmospheric aerosols contain organic molecules that serve as cloud condensation nucleation sites and affect the climate. Several experimental and simulation studies have been dedicated to investigate their surface propensity, but the mechanisms that drive them to the water surface are still not fully understood. In this molecular dynamics (MD) simulation study, primary alcohols are considered as a model system representing polar organic molecules. We find that the surface affinity of n-alcohols increases linearly with the length of the hydrophobic tail. By decomposing the adsorption free energy into enthalpy and entropy contributions, we find that the transition from bulk to surface is entropically driven, compatible with the fact that the hydrophobic effect of small solutes is of entropic origin. The enthalpy of surface adsorption is nearly invariant among different n-alcohols because the loss of solvent-alcohol interactions is balanced by a gain in solvent-solvent interactions. Structural analysis shows that, at the surface, the linear alcohols prefer an orientation with the hydrophobic tail pointing out from the surface, whereas the hydroxyl group remains buried in the water. This general behaviour is likely transferable to other small molecules with similar structures but other functional groups that are present in the atmosphere. Therefore, the present study is a step forward toward a general description of organic molecules in aerosols

Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers

Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model

A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility

The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by NMR spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated and free energy maps of the φ - ψ space and hydrogen bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of hemicelluloses’ function both in the cell wall and in technical products