Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562

A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods

Physical problem solving: Joint planning with symbolic, geometric, and dynamic constraints

In this paper, we present a new task that investigates how people interact with and make judgments about towers of blocks. In Experiment~1, participants in the lab solved a series of problems in which they had to re-configure three blocks from an initial to a final configuration. We recorded whether they used one hand or two hands to do so. In Experiment~2, we asked participants online to judge whether they think the person in the lab used one or two hands. The results revealed a close correspondence between participants' actions in the lab, and the mental simulations of participants online. To explain participants' actions and mental simulations, we develop a model that plans over a symbolic representation of the situation, executes the plan using a geometric solver, and checks the plan's feasibility by taking into account the physical constraints of the scene. Our model explains participants' actions and judgments to a high degree of quantitative accuracy

Extended quantum portrait of MGD black holes and information entropy

The extended minimal geometric deformation (EMGD) is employed on the fluid membrane paradigm, to describe compact stellar objects as Bose--Einstein condensates (BEC) consisting of gravitons. The black hole quantum portrait, besides deriving a preciser phenomenological bound for the fluid brane tension, is then scrutinized from the point of view of the configurational entropy. It yields a range for the critical density of the EMGD BEC, whose configurational entropy has global minima suggesting the configurational stability of the EMGD BEC.Comment: 9 pages, 7 figures, matches the published versio