Electrical conductivity of dispersions: from dry foams to dilute suspensions

We present new data for the electrical conductivity of foams in which the liquid fraction ranges from two to eighty percent. We compare with a comprehensive collection of prior data, and we model all results with simple empirical formul\ae. We achieve a unified description that applies equally to dry foams and emulsions, where the droplets are highly compressed, as well as to dilute suspensions of spherical particles, where the particle separation is large. In the former limit, Lemlich's result is recovered; in the latter limit, Maxwell's result is recovered

A standardised static in vitro digestion method suitable for food – an international consensus

peer-reviewedSimulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.COST action FA1005 Infogest22 (http://www.cost-infogest.eu/) is acknowledged for providing funding for travel, meetings and conferences

White-etching matter in bearing steel. Part II: Distinguishing cause and effect in bearing steel failure

The premature failure of large bearings of the type used in wind turbines, possibly through a mechanism called “white-structure flaking”, has triggered many studies of microstructural damage associated with “white-etching areas” created during rolling contact fatigue, although whether they are symptoms or causes of failure is less clear. Therefore, some special experiments have been conducted to prove that white-etching areas are the consequence, and not the cause, of damage. By artificially introducing a fine dispersion of microcracks in the steel through heat treatment and then subjecting the sample to rolling contact fatigue, manifestations of hard white-etching matter have been created to a much greater extent than samples similarly tested without initial cracks. A wide variety of characterization tools has been used to corroborate that the white areas thus created have the same properties as reported observations on real bearings. Evidence suggests that the formation mechanism of the white-etching regions involves the rubbing and beating of the free surfaces of cracks, debonded inclusions, and voids under repeated rolling contact. It follows that the focus in avoiding early failure should be in enhancing the toughness of the bearing steel in order to avoid the initial microscopic feature event.Funding by CONACyT, the Cambridge Overseas Trust, and the Roberto Rocca Education Programme is highly appreciated and acknowledged.This is the accepted manuscript version. The final published version is available from Springer at http://link.springer.com/article/10.1007%2Fs11661-014-2431-x

Building Computational Tools for Antibody Modeling and Protein–Protein Docking

Protein-protein interactions underlie countless biological functions, the nature of which is determined by the structure of the protein complex. Computational modeling is and important resource for evaluating protein complexes, with tools like RosettaDock offering structural insights in a high-throughput and cost-efficient manner. Antibodies provide an interesting test case for computational protein-protein docking protocols; they are a highly homologous class of protein that naturally bind an enormous range of antigenic proteins. In this dissertation, I describe new computational methods I developed to model both antibodies and protein-protein complexes, as well as evaluations I made of their performance. I begin with my additions to the RosettaAntibody protocol, which were motivated by community-wide shortcomings in antibody homology modeling revealed by the Second Antibody Modeling Assessment (AMA-II). I first built the Light-Heavy Orientational Coordinates (LHOC) framework to unambiguously describe the poorly defined antibody VL-VH orientation; I then developed the multiple-template grafting protocol, which leverages the LHOC framework to correctly model the VL-VH orientation in a majority of antibody targets, tripling the accuracy of the previous RosettaAntibody version. Seeing the guidance the AMA-II provided toward improving RosettaAntibody, I participated in several rounds of the Critical Assessment of PRediction of Interactions (CAPRI) to better understand the extant deficiencies of the RosettaDock protocol. CAPRI revealed a number of weaknesses in the protocol, including an inability to fully sample anisotropic proteins. I corrected this shortcoming in my novel Ellipsoidal Dock method, with which I correctly modeleld two challenging CAPRI targets. More broadly, all protein-protein docking methods fared poorly on CAPRI targets with binding-induced conformational changes and/or large surface areas to search. Addressing these difficult docking problems requires significantly more extensive conformational sampling protocols. So that such protocols remain computationally feasible, I developed Motif Dock Score (MDS) to rapidly evaluate the expanded pools of candidate structures. With no additional runtime, MDS provides three times the near-native enrichment and nine times the near-native discrimination as the low-resolution RosettaDock mode it replaces. In summary, I built computational tools that improve the fidelity of antibody homology modeling and broaden the scope of protein-protein docking. Additionally, my contributions to the RosettaDock protocol set the stage for the next generation of computational docking protocols