Modeling and simulation of intrinsically disordered proteins

This work is primarily about the development, validation and application of computer simulation models for intrinsically disordered proteins, both in solution and in the presence of uniformly charged, ideal surfaces. The models in question are either coarse-grained or atomistic in nature, and their applications are dependent on the specific purpose of each study. Both, Metropolis Monte Carlo and molecular dynamics simulations were employed to execute them.In regard to the coarse-grained models, it was found that a simple physical model can be used to mimic the properties of flexible proteins, helping to understand how and why these proteins adsorb to surfaces under certain conditions. The same model later shown that two disordered proteins from different sources (saliva and milk) possess similar structural and thermodynamic properties in solution and when adsorbed to surfaces, thus being hypothesized that it may be possible to use one of them as a substitute for the other under a pharmaceutical context.After a first indication that the atomistic models used until recently for the simulation of well-folded proteins may not be applicable to their disordered counterparts, it was then confirmed - by evaluating several such models against experimental evidence - that these models do indeed produce overly collapsed IDP conformational ensembles. New models, favoring protein–water over protein–protein interactions, were then shown to effectively produce more extended conformations, which are in much better agreement with each other and with experimental evidence. One of the new atomistic models was then used to perform the structural characterization of a disordered peptide conjugated to a small molecule, which has been shown to possess promising therapeutical applications. The value of computer simulations is well illustrated in this study, as the insight obtainable from experiment was limited and it was only through the analysis of the simulations that a possible link between the average conjugate structure and its increased antifungal activity is established

The spectrum of gravitational waves in an f(R) model with a bounce

We present an inflationary model preceded by a bounce in a metric $f(R)$ theory. In this model, modified gravity affects only the early stages of the universe. We analyse the predicted spectrum of the gravitational waves in this scenario using the method of the Bogoliubov coefficients. We show that there are distinctive (oscillatory) signals on the spectrum for very low frequencies; i.e., corresponding to modes that are currently entering the horizon.Comment: 4 pages, 2 figures. Contribution to the Spanish Relativity Meeting in Portugal 2012 (ERE2012), Guimaraes, Portuga

Novel applications of luminescence for solar energy

Luminescent solar concentrators (LSCs) provide indirect light concentration by absorbing both direct and indirect incident light, and have applications in building-integrated photovoltaics (BIPV). Fibre LSCs were found to have a linear relationship between photon concentration and fibre lengths in scales suitable for LSC modules. Using raytrace modelling, cylindrical LSC arrays were found to exhibit light trapping properties at certain angles of incidence, which can pave the way for more efficient BIPV applications. Novel optics for a double-illuminated water splitting reactor were introduced, for the objective of solar hydrogen for energy storage and sustainable transport fuels. A reflective cone embedded in a waveguide reflects incident concentrated light into the waveguide. Raytrace modelling and practical high concentration measurements demonstrate the viability of the optical system as well as necessity for a perfectly smooth reflective cone. It was also shown that replaced the reflective cone with a quantum well solar cell (QWSC) in order to harness the photoluminescence (PL) is not a viable concept with current QWSC structures. Another form of sustainable transport fuels is to use biofuels produced by algae. Algae have evolved to absorb excess amounts of energy, even when it is detrimental to their own growth and survival. This causes inefficiencies when growing algae in raceway ponds. The luminescent solar diffuser (LSD) is an optical funnel, optimisable by use of a genetic algorithm, that can be retrofitted into an algae raceway pond in order to better distribute incident light into the pond depths. This was calculated to increase algae growth rates in the pond, thereby increasing the yield of an algae farm.Open Acces

A Light Touch Approach to Teaching Transformers Multi-view Geometry

Transformers are powerful visual learners, in large part due to their conspicuous lack of manually-specified priors. This flexibility can be problematic in tasks that involve multiple-view geometry, due to the near-infinite possible variations in 3D shapes and viewpoints (requiring flexibility), and the precise nature of projective geometry (obeying rigid laws). To resolve this conundrum, we propose a "light touch" approach, guiding visual Transformers to learn multiple-view geometry but allowing them to break free when needed. We achieve this by using epipolar lines to guide the Transformer's cross-attention maps, penalizing attention values outside the epipolar lines and encouraging higher attention along these lines since they contain geometrically plausible matches. Unlike previous methods, our proposal does not require any camera pose information at test-time. We focus on pose-invariant object instance retrieval, where standard Transformer networks struggle, due to the large differences in viewpoint between query and retrieved images. Experimentally, our method outperforms state-of-the-art approaches at object retrieval, without needing pose information at test-time

Analysis and Real-time Data of Meteorologic Impact on Home Solar Energy Harvesting

Solar energy production increased in the world from 0 TWh in 1965 to 724.09 TWh in 2019. Solar energy is adopted as a source for residential renewable energy sources because, besides Biomass sources, it’s the only one that can be installed and maintained at home. Operating efficiency is an important consideration when evaluating the application of photovoltaic panels (PV) technology. A real-time system monitoring is required to analyse the current production and understand the impact of the weather conditions on PV production. This paper extends the literature on the residence solar energy harvesting subject, by providing a scalable architecture that can be used as starting point on data analysis on PV panels efficiency and how weather conditions impact energy production. A dataset was collected related to PV panel energy production, the residence energy consumption and that’s reading weather conditions. Wind intensity and direction, temperature, precipitation, humidity, atmospheric pressure and radiation were weather conditions analysed. Moreover, this data was analysed and interpreted in order to evaluate the pros and cons of the architecture as well as how the weather impacted the energy production