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

Shape-Based Models for Interactive Segmentation of Medical Images

Accurate image segmentation is one of the key problems in computer vision. In domains such as radiation treatment planning, dosimetrists must manually trace the outlines of a few critical structures on large numbers of images. Considerable similarity can be seen in the shape of these regions, both between adjacent slices in a particular patient and across the spectrum of patients. Consequently we should be able to model this similarity and use it to assist in the process of segmentation. Previous work has demonstrated that a constraint-based 2D radial model can capture generic shape information for certain shape classes, and can reduce user interaction by a factor of three over purely manual segmentation. Additional simulation studies have shown that a probabilistic version of the model has the potential to further reduce user interaction. This paper describes an implementation of both models in a general-purpose imaging and graphics framework and compares the usefulness of the models on several shape classes

The Amplitude Mode in the Quantum Phase Model

We derive the collective low energy excitations of the quantum phase model of interacting lattice bosons within the superfluid state using a dynamical variational approach. We recover the well known sound (or Goldstone) mode and derive a gapped (Higgs type) mode that was overlooked in previous studies of the quantum phase model. This mode is relevant to ultracold atoms in a strong optical lattice potential. We predict the signature of the gapped mode in lattice modulation experiments and show how it evolves with increasing interaction strength.Comment: 4 pages, 3 figure

Decay of superfluid currents in a moving system of strongly interacting bosons

We analyze the stability and decay of supercurrents of strongly interacting bosons on optical lattices. At the mean-field level, the system undergoes an irreversible dynamic phase transition, whereby the current decays beyond a critical phase gradient that depends on the interaction strength. At commensurate filling the transition line smoothly interpolates between the classical modulational instability of weakly interacting bosons and the equilibrium Mott transition at zero current. Below the mean-field instability, the current can decay due to quantum and thermal phase slips. We derive asymptotic expressions of the decay rate near the critical current. In a three-dimensional optical lattice this leads to very weak broadening of the transition. In one and two dimensions the broadening leads to significant current decay well below the mean-field critical current. We show that the temperature scale below which quantum phase slips dominate the decay of supercurrents is easily within experimental reach.Accepted manuscrip

How To Demoralize the Faculty: A Six-Step Program That Works

A satirical article discussing faculty morale