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.     

3-D vertical ray shooting and 2-D point enclosure, range searching, and arc shooting amidst convex fat objects

We present a new data structure for a set of n convex simply-shaped fat objects in the plane, and use it to obtain efficient and rather simple solutions to several problems including (i) vertical ray shooting—preprocess a set of n non-intersecting convex simply-shaped flat objects in 3-space, whose xy-projections are fat, for efficient vertical ray shooting queries, (ii) point enclosure—preprocess a set C of n convex simply-shaped fat objects in the plane, so that the k objects containing a query point p can be reported efficiently, (iii) bounded-size range searching— preprocess a set C of n convex fat polygons, so that the k objects intersecting a “not-too-large” query polygon can be reported efficiently, and (iv) bounded-size segment shooting—preprocess a set C as in (iii), so that the first object (if exists) hit by a “not-too-long” oriented query segment can be found efficiently. For the first three problems we construct data structures of size O(λ_s(n)log³n), where s is the maximum number of intersections between the boundaries of the (xy-projections) of any pair of objects, and λ_s(n) is the maximum length of (n, s) Davenport-Schinzel sequences. The data structure for the fourth problem is of size O(λ_s(n)log²n). The query time in the first problem is O(log⁴n), the query time in the second and third problems is O(log³n + klog²n), and the query time in the fourth problem is O(log³n).

We also present a simple algorithm for computing a depth order for a set as in (i), that is based on the solution to the vertical ray shooting problem. (A depth order for , if exists, is a linear order of , such that, if K₁, K₂ and K₁ lies vertically above K₂, then K₁ precedes K₂.) Unlike the algorithm of Agarwal et al. (1995) that might output a false order when a depth order does not exist, the new algorithm is able to determine whether such an order exists, and it is often more efficient in practical situations than the former algorithm.     

A search technique for global optimization in a chaotic environment

We describe a new algorithm which uses the trajectories of a discrete dynamical system to sample the domain of an unconstrained objective function in search of global minima. The algorithm is unusually adept at avoiding nonoptimal local minima and successfully converging to a global minimum. Trajectories generated by the algorithm for objective functions with many local minima exhibit chaotic behavior, in the sense that they are extremely sensitive to changes in initial conditions and system parameters. In this context, chaos seems to have a beneficial effect: failure to converge to a global minimum from a given initial point can often be rectified by making arbitrarily small changes in the system parameters.     

Irregularities of distribution with respect to strips

Summary A lower bound is established for the strip discrepancy of a broad class of point distributions. The bound implies unbounded strip discrepancy for equally weighted point distributions under favorable conditions. The methods of proof use notions from integral geometry.     

Buckling of a stiff thin film on a compliant substrate in large deformation

A finite-deformation theory is developed to study the mechanics of thin buckled films on compliant substrates. Perturbation analysis is performed for this highly nonlinear system to obtain the analytical solution. The results agree well with experiments and finite element analysis in wavelength and amplitude. In particular, it is found that the wavelength depends on the strain. Based on the accurate wavelength and amplitude, the membrane and peak strains in thin films, and stretchability and compressibility of the system are also obtained analytically.