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| 2. |
- Alves, Joao S., et al.
(författare)
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Experimental investigation on performance improvement by mid-plane guide-vanes in a biplane-rotor Wells turbine for wave energy conversion
- 2021
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Ingår i: Renewable & sustainable energy reviews. - : Elsevier BV. - 1364-0321 .- 1879-0690. ; 150
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Tidskriftsartikel (refereegranskat)abstract
- The Wells turbine is the most frequently used or proposed self-rectifying air turbine for oscillating-water column wave-energy converter application, largely because of its conceptual and mechanical simplicity. Biplane Wells turbines allow a higher total blade solidity to be attained than monoplane turbines do, but this results in larger aerodynamic losses associated with the swirl kinetic energy loss at turbine exit. This may be overcome by the presence of a row of guide vanes between the two rotor planes, a solution that had been proposed and investigated theoretically or by numerical modelling. Results of turbine overall performance and flow details are reported from laboratory tests of a biplane Wells turbine without guide vanes and with specially designed guide vanes. The presence of the guide vanes was found to increase the peak efficiency by seven percentual points, while reducing (for fixed rotational speed) the damping provided by the turbine. Measured losses in the guide vane row were much smaller than in the rotors. Experimental results are compared with previously published numerical results. A stochastic theoretical transform was applied to obtain averaged results for the turbine performance subject to the irregular bidirectional air flow induced by real sea waves.
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| 3. |
- Williams, James Henty, et al.
(författare)
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Roadmap for action on the environmental risk assessment of chemicals for insect pollinators (IPol-ERA)
- 2023
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Approaches integrating interdisciplinary perspectives are necessary to address current and future health and environmental challenges. Many policy initiatives have embraced more holistic approaches to tackle these challenges, e.g., the One Health concept, the Farm to Fork (F2F), Biodiversity and Chemical strategies within the European Green Deal and the global Sustainable Development Goals (SDGs). Insect pollinators are an excellent example of the One Health concept and have gained renewed focus through the EU Pollinator Initiative. Insect pollinators are essential for healthy diets by providing pollination services and maintaining biodiversity and healthy ecosystem functions. For this reason, they are part of the Environmental Risk Assessment (ERA) of chemicals, such as plant protection products (PPPs). However, an ERA of PPPs can align with and embrace these more holistic concepts and strategies by evolving towards a systems-based approach that recognises the diversity and the important role played by insect pollinators (e.g., pollination services for food security), as well as the variety of habitats and contexts they live in with their multiple stressors, and where PPPs may be used. A roadmap has been developed to determine the steps and actions needed to progress ERA methodologies and tools for insect pollinators. This roadmap is based on a review of the latest scientific knowledge, determining key areas for development to advance ERA, and identifying expertise and networks needed to foster progressive dialogue and public acceptance. The roadmap proposes several actions to generate the necessary knowledge to advance methodologies and tools within the current ERA framework, initially for chemical PPPs but extendable to other regulated chemicals. In addition, it outlines the actions needed to build the framework and the collaborative activities required to realise the transition to a systems-based ERA for insect pollinators by 2030.
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| 4. |
- Gomes, João, et al.
(författare)
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Evaluation of the impact of stagnation temperatures in different prototypes of low concentration PVT solar panels
- 2015
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Ingår i: ISES Solar World Congress 2015, Conference Proceedings. - Freiburg, Germany : International Solar Energy Society. - 9783981465952 ; , s. 993-1004
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Konferensbidrag (refereegranskat)abstract
- Photovoltaic thermal (PVT) solar panels produce both thermal and electric power from the some area. This paper concerns a PVT design where the series connected strings of cells are laminated using silicone to an aluminium receiver where the heat transfer fluid flows. An evaluation of the impact of reaching high temperatures in the cell structural integrity and performance is presented. Eight small test receivers were made in which the following properties were varied: Size of the PV cells, type of silicone used to encapsulate the PV cells, existence of a strain relief between the cells, size of the gap between cells and type of cell soldering (line or point soldering). These test receivers were placed in an oven for one hour, under eight different monitored temperatures. The temperature of the last round was set at 220°C which well exceeds the highest temperature the panel design can reach. Before and after each round in the oven, the following tests were conducted to the receivers: Electroluminescence (EL) test, IV-curve, diode function, and visual inspection. The test results showed that the receivers made with the transparent silicone and strain relief between cells experienced less micro-cracks and lower degradation in maximum power. No prototype test receiver lost more than 30% of its initial power, despite the large cell breakage shown in some receivers. Prototype receivers with transparent (softer) silicone showed much far less cracks and power decrease when compared to red (harder) silicone receivers. As expected, larger cells are more prone to develop micro-cracks after exposure to thermal stress. Additionally, existing micro-cracks tend to grow in size into larger micro-cracks relatively fast with thermal stress. The EL imaging taken during our experiment leads us to observe that it seems far easier for existing cracks to expand than for new cracks to appear.
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| 5. |
- Henriques, Joao, et al.
(författare)
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A coarse-grained model for flexible (phospho)proteins: Adsorption and bulk properties
- 2015
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Ingår i: Food Hydrocolloids. - : Elsevier BV. - 0268-005X. ; 43, s. 473-480
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Tidskriftsartikel (refereegranskat)abstract
- Protein adsorption is a complex process that it controlled by several different mechanisms, for example: (i) electrostatic interactions between the protein and the surface, and (ii) between adsorbed proteins; (iii) dispersion interactions; (iv) hydration effects; and (v) structural rearrangements of the protein to balance conformational chain entropy with energetics. The aim of this study was to develop a simple model for the adsorption of intrinsically disordered proteins onto surfaces at a mesoscopic level of detail, while retaining protein integrity. Monte Carlo simulations were used in order to study the thermodynamical and structural properties of the flexible phosphoprotein beta-casein, in bulk and adsorbed to hydrophilic silica surfaces, in order to evaluate the effect of varying pH, monovalent salt concentration, and degree of serine phosphorylation. Experimental evidence from our previous study, published in this Journal, was used to set up and tune the Hamiltonian of the model. Our simulations show that protein-surface electrostatic interactions are, indeed, not the main driving force behind adsorption under the simulated conditions. Despite its importance, when taken alone, this type of interaction is not enough to promote the adsorption of beta-casein at any salt concentration. Adsorption is only possible through the inclusion of a protein-surface short-ranged attractive interaction potential with a minimum interaction strength of 2.25 k(B)T. This represents the lowest interaction strength required to mimic experimental adsorption results. An equally important finding is that considerable protein net charge fluctuations, due to phosphorylated serine saturation, have a negligible contribution to the free energy of adsorption. (C) 2014 Elsevier Ltd. All rights reserved.
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| 6. |
- Henriques, Joao
(författare)
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Modeling and simulation of intrinsically disordered proteins
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 7. |
- Henriques, Joao, et al.
(författare)
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Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
- 2015
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:7, s. 3420-3431
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Tidskriftsartikel (refereegranskat)abstract
- An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and Size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational Class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [Best et al. J. Chem. Theory Comput. 2014, 10, 5113-5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment.
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| 8. |
- Henriques, Joao, et al.
(författare)
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Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P‐D Water Model and the Representativeness of Protein Disorder Models
- 2016
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:7, s. 3407-3415
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Tidskriftsartikel (refereegranskat)abstract
- Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [Henriques et al. J. Chem. Theory Comput. 2015, 11, 3420−3431], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.
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| 9. |
- Henriques, João, et al.
(författare)
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On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations
- 2018
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836. ; 430:16, s. 2521-2539
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Tidskriftsartikel (refereegranskat)abstract
- Solution techniques such as small-angle X-ray scattering (SAXS) play a central role in structural studies of intrinsically disordered proteins (IDPs); yet, due to low resolution, it is generally necessary to combine SAXS with additional experimental sources of data and to use molecular simulations. Computational methods for the calculation of theoretical SAXS intensity profiles can be separated into two groups, depending on whether the solvent is modeled implicitly as continuous electron density or considered explicitly. The former offers reduced computational cost but requires the definition of a number of free parameters to account for, for example, the excess density of the solvation layer. Overfitting can thus be an issue, particularly when the structural ensemble is unknown. Here, we investigate and show how small variations of the contrast of the hydration shell, δρ, severely affect the outcome, analysis and interpretation of computed SAXS profiles for folded and disordered proteins. For both the folded and disordered proteins studied here, using a default δρ may, in some cases, result in the calculation of non-representative SAXS profiles, leading to an overestimation of their size and a misinterpretation of their structural nature. The solvation layer of the different IDP simulations also impacts their size estimates differently, depending on the protein force field used. The same is not true for the folded protein simulations, suggesting differences in the solvation of the two classes of proteins, and indicating that different force fields optimized for IDPs may cause expansion of the polypeptide chain through different physical mechanisms.
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| 10. |
- Jephthah, Stephanie, et al.
(författare)
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Structural Characterization of Histatin 5-Spermidine Conjugates : A Combined Experimental and Theoretical Study
- 2017
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Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 57:6, s. 1330-1341
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Tidskriftsartikel (refereegranskat)abstract
- Histatin 5 (Hst5) is a naturally occurring antimicrobial peptide that acts as the first line of defense against oral candidiasis. It has been shown that conjugation of the active Hst5 fragment, Hst54-15, and the polyamine spermidine (Spd) improves the candidacidal effect. Knowledge about the structure of these conjugates is, however, very limited. Thus, the aim of this study was to characterize the structural properties of the Hst54-15-Spd conjugates by performing atomistic molecular dynamics simulations in combination with small-angle X-ray scattering. It was shown that the Hst54-15-Spd conjugates adopt extended and slightly rigid random coil conformations without any secondary structure in aqueous solution. It is hypothesized that the increased fungal killing potential of Hst54-15-Spd, in comparison with the Spd-Hst54-15 conjugate, is due to the more extended conformations of the former, which cause the bonded Spd molecule to be more accessible for recognition by polyamine transporters in the cell.
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