Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.

Global Sensitivity Analysis for MAP Inference in Graphical Models

We study the sensitivity of a MAP configuration of a discrete probabilistic graphical model with respect to perturbations of its parameters. These perturbations are global, in the sense that simultaneous perturbations of all the parameters (or any chosen subset of them) are allowed. Our main contribution is an exact algorithm that can check whether the MAP configuration is robust with respect to given perturbations. Its complexity is essentially the same as that of obtaining the MAP configuration itself, so it can be promptly used with minimal effort. We use our algorithm to identify the largest global perturbation that does not induce a change in the MAP configuration, and we successfully apply this robustness measure in two practical scenarios: the prediction of facial action units with posed images and the classification of multiple real public data sets. A strong correlation between the proposed robustness measure and accuracy is verified in both scenarios.

New Complexity Results for MAP in Bayesian Networks

This paper presents new results for the (partial) maximum a posteriori (MAP) problem in Bayesian networks, which is the problem of querying the most probable state configuration of some of the network variables given evidence. It is demonstrated that the problem remains hard even in networks with very simple topology, such as binary polytrees and simple trees (including the Naive Bayes structure), which extends previous complexity results. Furthermore, a Fully Polynomial Time Approximation Scheme for MAP in networks with bounded treewidth and bounded number of states per variable is developed. Approximation schemes were thought to be impossible, but here it is shown otherwise under the assumptions just mentioned, which are adopted in most applications.

New Results for the MAP Problem in Bayesian Networks

This paper presents new results for the (partial) maximum a posteriori (MAP) problem in Bayesian networks, which is the problem of querying the most probable state configuration of some of the network variables given evidence. First, it is demonstrated that the problem remains hard even in networks with very simple topology, such as binary polytrees and simple trees (including the Naive Bayes structure). Such proofs extend previous complexity results for the problem. Inapproximability results are also derived in the case of trees if the number of states per variable is not bounded. Although the problem is shown to be hard and inapproximable even in very simple scenarios, a new exact algorithm is described that is empirically fast in networks of bounded treewidth and bounded number of states per variable. The same algorithm is used as basis of a Fully Polynomial Time Approximation Scheme for MAP under such assumptions. Approximation schemes were generally thought to be impossible for this problem, but we show otherwise for classes of networks that are important in practice. The algorithms are extensively tested using some well-known networks as well as random generated cases to show their effectiveness.

NP-hardness of MAP in Ternary Tree Bayesian Networks

This paper strengthens the NP-hardness result for the (partial) maximum a posteriori (MAP) problem in Bayesian networks with topology of trees (every variable has at most one parent) and variable cardinality at most three. MAP is the problem of querying the most probable state configuration of some (not necessarily all) of the network variables given evidence. It is demonstrated that the problem remains hard even in such simplistic networks.

Anytime Marginal MAP Inference

This paper presents a new anytime algorithm for the marginal MAP problem in graphical models of bounded treewidth. We show asymptotic convergence and theoretical error bounds for any fixed step. Experiments show that it compares well to a state-of-the-art systematic search algorithm.

A solution concept for network games: The role of multilateral interactions

We propose an allocation rule that takes into account the importance of both players and their links and characterize it for a fixed network. Our characterization is along the lines of the characterization of the Position value for Network games by van den Nouweland and Slikker (2012). The allocation rule so defined admits multilateral interactions among the players through their links which distinguishes it from the other existing rules. Next, we extend our allocation rule to flexible networks à la Jackson (2005).

An analysis of stage performance in automotive turbocharger centrifugal compressors

As the concept of engine downsizing becomes ever more integrated into automotive powertrain development strategies, so too does the pressure on turbocharger manufacturers to deliver improvements in map width and a reduction in the mass flow rate at which compressor surge occurs. A consequence of this development is the increasing importance of recirculating flows, both in the impeller inlet and outlet domains, on stage performance.
The current study seeks to evaluate the impact of the inclusion of impeller inlet recirculation on a meanline centrifugal compressor design tool. Using a combination of extensive test data, single passage CFD predictions, and 1-D analysis it is demonstrated how the addition of inlet recirculation modelling impacts upon stage performance close to the surge line. It is also demonstrated that, in its current configuration, the accuracy of the 1-D model prediction diminishes significantly with increasing blade tip speed.
Having ascertained that the existing model requires further work, an evaluation of the vaneless diffuser modelling method currently employed within the existing 1-D model is undertaken. The comparison of the predicted static pressure recovery coefficient with test data demonstrated the inherent inadequacies in the resulting prediction, in terms of both magnitude and variation with flow rate. A simplified alternative method based on an equivalent friction coefficient is also presented that, with further development, could provide a significantly improved stage performance prediction.

A techno-economic feasibility study of high altitude wind power in Northern Ireland

Globally the amount of installed terrestrial wind power both onshore and offshore has grown rapidly over the last twenty years. Most large onshore and offshore wind turbines are designed to harvest winds within the atmospheric boundary layer, which can be vary variable due to terrain and weather effects. The height of the neutral atmospheric boundary layer is estimated at above 1300m. A relatively new concept is to harvest more consistent wind conditions above the atmospheric boundary layer using high altitude wind harvesting devices such as tethered kites, air foils and dirigible rotors. This paper presents a techno-economic feasibility study of high altitude wind power in Northern Ireland. First this research involved a state of the art review of the resource and the technologies proposed for high altitude wind power. Next the techno-economic analysis involving four steps is presented. In step one, the potential of high altitude wind power in Northern Ireland using online datasets (e.g. Earth System Research Laboratory) is estimated. In step two a map for easier visualisation of geographical limitations (e.g. airports, areas of scenic beauty, flight paths, military training areas, settlements etc.) that could impact on high altitude wind power is developed. In step three the actual feasible resource available is recalculated using the visualisation map to determine the ‘optimal’ high altitude wind power locations in Northern Ireland. In the last step four the list of equipment, resources and budget needed to build a demonstrator is provided in the form of a concise techno-economic appraisal using the findings of the previous three steps.