Unconventional Secondary Structure Mimics: Ladder-Rungs

Secondary structures tend to be recognizable because they have repeating structural motifs, but mimicry of these does not have to follow such well-defined patterns. Bioinformatics studies to match side-chain orientations of a novel hydantoin triazole chemotype ( 1 ) to protein-protein interfaces revealed it tends to align well across parallel and antiparallel sheets, like rungs on a ladder. One set of these overlays was observed for the protein-protein interaction uPA⋅uPAR. Consequently, chemotype 1 was made with appropriate side-chains to mimic uPA at this interface. Biophysical assays indicate these compounds did in fact bind uPAR, and elicit cellular responses that affected invasion, migration, and wound healing.     

Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.     

Sobolev Stability of Plane Wave Solutions to the Nonlinear Schrödinger Equation

This article explores the questions of long time orbital stability in high order Sobolev norms of plane wave solutions to the NLSE in the defocusing case.     

T1Effects in Sequential Dynamic Susceptibility Contrast Experiments

Residual effects of an initial bolus of gadolinium contrast agent have been previously demonstrated in sequential dynamic susceptibility contrast MR experiments. While these residual effects quickly reach a saturation steady state, their etiology is uncertain, and they can lead to spurious estimates of hemodynamic parameters in activation experiments. The possible influence ofT₁effects is now investigated with experiments in whichT₁weighting is varied as well as with serial regionalT₁measurements. Little evidence for significant residualT₁effects is found, suggesting instead that susceptibility effects underlie these observations. An initial saturation dose of contrast agent minimizes this effect.     

Heuristic Solution Methods for the Multilevel Generalized Assignment Problem

The multilevel generalized assignment problem is a problem of assigning agents to tasks where the agents can perform tasks at more than one efficiency level. A profit is associated with each assignment and the objective of the problem is profit maximization. Two heuristic solution methods are presented for the problem. The heuristics are developed from solution methods for the generalized assignment problem. One method uses a regret minimization approach whilst the other method uses a repair approach on a relaxation of the problem. The heuristics are able to solve moderately large instances of the problem rapidly and effectively. Procedures for deriving an upper bound on the solution of the problem are also described. On larger and harder instances of the problem one heuristic is particularly effective.     

On the critical exponents of random k‐SAT

There has been much recent interest in the satisfiability of random Boolean formulas. A random k‐SAT formula is the conjunction of m random clauses, each of which is the disjunction of k literals (a variable or its negation). It is known that when the number of variables n is large, there is a sharp transition from satisfiability to unsatisfiability; in the case of 2‐SAT this happens when m/n → 1, for 3‐SAT the critical ratio is thought to be m/n ≈ 4.2. The sharpness of this transition is characterized by a critical exponent, sometimes called ν = ν_k (the smaller the value of ν the sharper the transition). Experiments have suggested that ν₃ = 1.5 ± 0.1. ν₄ = 1.25 ± 0.05, ν₅ = 1.1 ± 0.05, ν₆ = 1.05 ± 0.05, and heuristics have suggested that ν_k → 1 as k → ∞. We give here a simple proof that each of these exponents is at least 2 (provided the exponent is well defined). This result holds for each of the three standard ensembles of random k‐SAT formulas: m clauses selected uniformly at random without replacement, m clauses selected uniformly at random with replacement, and each clause selected with probability p independent of the other clauses. We also obtain similar results for q‐colorability and the appearance of a q‐core in a random graph. © 2002 Wiley Periodicals, Inc. Random Struct. Alg., 21: 182–195, 2002