After use and disposal of chemical products, many types of polymer particles end up in the aquatic environment with potential toxic effects to primary producers like green algae. In this study, we... Show moreAfter use and disposal of chemical products, many types of polymer particles end up in the aquatic environment with potential toxic effects to primary producers like green algae. In this study, we have developed Quantitative Structure-Activity Relationships (QSARs) for a set of highly structural diverse polymers which are capable to estimate green algae growth inhibition (EC50). The model (N = 43, R2 = 0.73, RMSE = 0.28) is a regression-based decision tree using one structural descriptor for each of three polymer classes separated based on charge. The QSAR is applicable to linear homo polymers as well as copolymers and does not require information on the size of the polymer particle or underlying core material. Highly branched polymers, non-nitrogen cationic polymers and polymeric surfactants are not included in the model and thus cannot be evaluated. The model works best for cationic and non-ionic polymers for which cellular adsorption, disruption of the cell wall and photosynthesis inhibition were the mechanisms of action. For anionic polymers, specific properties of the polymer and test characteristics need to be known for detailed assessment. The data and QSAR results for anionic polymers, when combined with molecular dynamics simulations indicated that nutrient depletion is likely the dominant mode of toxicity. Nutrient depletion in turn, is determined by the non-linear interplay between polymer charge density and backbone flexibility. Show less
Polymers are the main building blocks of many biological systems, and thus polymer models are important tools for our understanding. One such biological system is the large scale organisation of... Show morePolymers are the main building blocks of many biological systems, and thus polymer models are important tools for our understanding. One such biological system is the large scale organisation of chromatin. A key question here, is how during cell division the chromosomes can separate without entanglement and knotting. One proposal is that this achieved by a specific spatial organisation of the chromosomes, known as the "fractal globule". Using Monte Carlo simulations, we found that fractal globules are unstable and thus cannot represent the biological system without further ingredients. Another proposal is that topological effects cause spatial separation of the chromosomes. These topological effects can be studied using simulations of nonconcatenated ring polymers. Using a compute device called the Graphics Processing Unit, very detailed and long simulations were carried out. From these a picture emerged in which ring polymers behave much slower than was found in previous studies. A second biological system studied here is the folded state of the protein. This is modeled by the Hamiltonian walk. Here, instead of simulations, we exactly enumerated all Hamiltonian walks of the 4x4x4 cube. Interestingly, simulations show that for larger systems many more walks exist than previously estimated. Show less
Of the various biomolecular building blocks in use in nature, coiled-coil forming peptides are amongst those with the most potential as building blocks for the synthetic self-assembly of... Show moreOf the various biomolecular building blocks in use in nature, coiled-coil forming peptides are amongst those with the most potential as building blocks for the synthetic self-assembly of nanostructures. Native coiled coils have the ability to function in, and influence, complex systems composed of multiple building blocks. However, there have only been a limited number of synthetic coiled-coil assemblies that mimic native coiled coils by incorporating multiple assembling components. This thesis represents efforts at extending this aspect of coiled-coil self-assembly. In order to achieve this, a range of hybrid molecules were synthesized which combine coiled-coil peptides with a hydrophobic component. In this way the highly specific coiled-coil self-assembly is juxtaposed with the non-specific, but structure-inducing aggregation of the hydrophobic section. This thesis asked simple questions: can coiled coils function when covalently attached to large hydrophobic blocks? How large can the hydrophobic blocks be? Can coiled coils function when incorporated noncovalently with a supramolecular assembly? By answering these fundamental questions the possibilities of prescriptive self-assembly have been probed and expanded, novel preparative methods have been developed, and specific applications have arisen. Show less
