The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

The assembly of clathrin triskelia into polyhedral cages during endocytosis is regulated by adaptor proteins (APs). We explore how APs achieve this by developing coarse-grained models for clathrin and AP2, employing a Monte Carlo click interaction, to simulate their collective aggregation behavior. The phase diagrams indicate that a crucial role is played by the mechanical properties of the disordered linker segment of AP. We also present a statistical-mechanical theory for the assembly behavior of clathrin, yielding good agreement with our simulations and experimental data from the literature. Adaptor proteins are found to regulate the formation of clathrin coats under certain conditions, but can also suppress the formation of cages.

Previous studies indicated that a few risk variants for autoimmune diseases are subject to pathogen-driven selection. Nonetheless, the proportion of risk loci that has been targeted by pathogens and the type of infectious agent(s) that exerted the strongest pressure remain to be evaluated. We assessed whether different pathogens exerted a pressure on known Crohn's disease (CD) risk variants and demonstrate that these single-nucleotide polymorphisms (SNPs) are preferential targets of protozoa-driven selection (P = 0.008). In particular, 19% of SNPs associated with CD have been subject to protozoa-driven selective pressure. Analysis of P values from genome-wide association studies (GWASs) and meta-analyses indicated that protozoan-selected SNPs display significantly stronger association with CD compared with nonselected variants. This same behavior was not observed for GWASs of other autoimmune diseases. Thus, we integrated selection signatures and meta-analysis results to prioritize five genic SNPs for replication in an Italian cohort. Three SNPs were significantly associated with CD risk, and combination with meta-analysis results yielded P values < 4 × 10(-6). The bona fide risk alleles are located in ARHGEF2, an interactor of NOD2, NSF, a gene involved in autophagy, and HEBP1, encoding a possible mediator of inflammation. Pathway analysis indicated that ARHGEF2 and NSF participate in a molecular network, which also contains VAMP3 (previously associated to CD) and is centered around miR-31 (known to be disregulated in CD). Thus, we show that protozoa-driven selective pressure had a major role in shaping predisposition to CD. We next used this information for the identification of three bona fide novel susceptibility loci.

Tailing wastes are by-products of mining industry and are generally mixtures of rock, sand, fine-grained solid material and in some cases relevant quantities of heavy metals and water remaining after the mineral values have been extracted from the patent ore. In recent years the amount of tailings has significantly increased to meet the growing demand for metals and minerals. Huge amounts of tailing wastes are produced and discharged inside storage facilities (TSF), also known as tailing dams. Owing to their complexity and high rate of collapses with relevant loss of human lives, economic and environmental damages, a detailed knowledge of the hydromechanical properties of tailings is essential to develop a reliable stability analysis both for new and existing structures. This research provides a preliminary parametric study aimed at investigating the impact of some fundamental design aspects. The influence of the adopted numerical method, raising techniques, distance of decant pond, hydraulic conditions, geometry of drainage systems and uncertainty of geotechnical properties on stability of an embankment have been evaluated for a simple case, providing some fundamental concepts to be considered when designing new tailing dams or performing stability analysis on existing ones.

This work is part of the research programme 'Self-assembly of protein coats at membranes' (project nr. 711.012.004) which is financed by the Netherlands Organisation for Scientific Research (NWO). The research described in this thesis was performed using the computational resources of the Computational Biophysics (CBP) group within the MESA+ Institute for Nanotechnology of the University of Twente. SummaryThe assembly of clathrin coats in the presence of adaptor proteins was studied through computer simulations using coarse-grained models and through statistical mechanics. Adopting a reductionist approach based on recent experimental results, we aimed at reproducing and studying the minimal conditions that lead to the successful formation of aggregates, and at investigating the molecular properties and mechanisms required by the assembly process both in bulk conditions and at a membranous surface. In order to tackle this challenging task, coarse-grained models were used to describe all the assembly units involved in the simulations presented in this thesis. These models are based on the available structural data and are engineered to capture the key elements and behavior of the modeled proteins.In Chapter ?? we introduce a coarse grained model of adaptor proteins, inspired by and representing the AP2 complex. The latter, the second most abundant component of endocytic coats after clathrin, is known to play a fundamental role in promoting and assisting the creation of coats at the cytosolic surface of the membrane. It is reported to be able to trigger polymerization of clathrin triskelia in physiological conditions of salt and pH, under which purified clathrin triskelia do not spontaneously self-assemble. The interaction between APs and clathrin were modeled throughout this thesis through a click potential, introduced for the first time in this chapter. The characteristics of the AP model, and of this interaction, have been tuned to reproduce the existing experimental assembly data of an AP2 and clathrin mixture. Our computer simulations provide novel insights into the role of AP2 in the self-assembly of clathrin cages and suggest that the mechanical properties of adaptor proteins are of fundamental importance. In the same chapter, we also developed a statistical mechanical theory that describes the equilibrium concentration of clathrin cages as a function of the other assembly variables and parameters, such as the protein concentrations and interaction strengths.This theoretical model has been further developed in Chapter ??, in order to explicitly take into account the effect of the flexibility of the clathrin triskelion, previously neglected. The main aim of the chapter is to investigate the equilibrium properties of clathrin cages resulting from the aggregation process, with emphasis on their size in the absence and in the presence of adaptor proteins. In order to perform this study, the essential features and characteristics of clathrin and AP2s are captured through a small number of effective parameters, an...