Second SH3 domain of ponsin solved from powder diffraction

Determination of protein crystal structures is dependent on the growth of high-quality single crystals, a process that is not always successful. Optimum crystallization conditions must be systematically sought for, and microcrystalline powders are frequently obtained in failed attempts to grow the desired crystal. In materials science, structures of samples ranging from ceramics, pharmaceuticals, zeolites, etc., can nowadays be solved, almost routinely, from powdered samples, and there seems to be no fundamental reason, except the sheer size and complexity of the structures involved, why powder diffraction should not be employed to solve structures of small proteins. Indeed, recent work has shown that the high-quality powder diffraction data can be used in the study of protein crystal structures. We report the solution, model building, and refinement of a 67-residue protein domain crystal structure, with a cell volume of 64 879 A3, from powder diffraction. The second SH3 domain of ponsin, a protein of high biological significance due to its role in cellular processes, is determined and refined to resolution limits comparable to single-crystal techniques. Our results demonstrate the power and future applicability of the powder technique in structural biology.     

Distinguishing Linear from Star‐Branched Polystyrene Solutions with Fourier‐Transform Rheology

Summary: Fourier‐Transform rheology (FT rheology) was used to study the influence of the degree of branching on the nonlinear relaxation behaviour of polystyrene solutions. The results were compared with those obtained under oscillatory shear and step‐shear conditions. The different topologies could be distinguished using FT rheology where the other rheological measurements failed. Significant differences occurred under large amplitude oscillatory shear (LAOS) conditions as particularly reflected in the phase difference of the third harmonic, Φ₃, which could be related to strain‐softening and strain‐hardening behaviour. Currently, this work is extended towards different topologies in polyolefins (e.g. long chain branched).

Phase difference Φ₃ as a function of the Deborah number De at γ₀ = 2 for the polystyrene solutions measured at temperatures from 295 to 350.5 K.     

Block copolymers with Zwitterionic groups at specific sites: Synthesis and aggregation behavior in dilute solutions

Well‐defined linear diblock and triblock copolymers of styrene and isoprene, nearly symmetric in composition, with one or two sulfobetaine associogenic groups at the ends of the polymer chain or the junction points between blocks, were synthesized by anionic polymerization high‐vacuum techniques. The synthetic strategy used the combined initiation of polymerization with 3‐dimethylaminopropyllithium, living end‐capping with 1‐(4‐dimethylaminophenyl)‐1‐phenylethylene, and postpolymerization reaction with cyclopropanesultone. The association behavior of these macromolecules in dilute solutions in the nonpolar solvent CCl₄, good for both blocks, was studied by a number of methods, including static and dynamic light scattering and viscometry. The number and position of the associogenic groups dramatically influenced the association behavior of these model block copolymers. The end‐functionalized samples formed larger aggregates than the junction‐point‐functionalized ones. The difference was attributed to stronger excluded volume effects when the zwitterion group was located within the chain than when the group was at the chain end(s). © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3791–3801, 2000     

A kinetic study of the formation of polystyrene stars using 1,2-bis(trichlorosilyl)ethane

The kinetics of formation of a chlorosilane-linked polystyrene six-arm star is reported. The precursor arm material (M_n = 88,000) was made using anionic polymerization in benzene. Prior to addition to the 1,2-bis(trichlorosilyl) ethane linking agent, the anions were endcapped with about five units of isoprene. Size exclusion chromatography using multiangle laser light scattering and viscosity detectors was utilized for characterization. This technique has allowed the molecular weights, radii of gyration, and intrinsic viscosities to be measured for star components in aliquots taken from the reactor at various times. It was found that four-arm star is formed within 30 min after the addition of the chlorosilane linking agent. There is a linear relationship between the logarithm of molecular weight of the star samples and logarithm of time of the reaction after the formation of the four-arm star. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 587–594, 1997     

Bergman polynomials on an archipelago: Estimates, zeros and shape reconstruction

Growth estimates of complex orthogonal polynomials with respect to the area measure supported by a disjoint union of planar Jordan domains (called, in short, an archipelago) are obtained by a combination of methods of potential theory and rational approximation theory. The study of the asymptotic behavior of the roots of these polynomials reveals a surprisingly rich geometry, which reflects three characteristics: the relative position of an island in the archipelago, the analytic continuation picture of the Schwarz function of every individual boundary and the singular points of the exterior Green function. By way of explicit example, fine asymptotics are obtained for the lemniscate archipelago |z^m−1|<r^m, 0<r<1, which consists of m islands. The asymptotic analysis of the Christoffel functions associated to the same orthogonal polynomials leads to a very accurate reconstruction algorithm of the shape of the archipelago, knowing only finitely many of its power moments. This work naturally complements a 1969 study by H. Widom of Szegő orthogonal polynomials on an archipelago and the more recent asymptotic analysis of Bergman orthogonal polynomials unveiled by the last two authors and their collaborators.     

A Hardy field extension of Szemerédi's theorem

In 1975 Szemerédi proved that a set of integers of positive upper density contains arbitrarily long arithmetic progressions. Bergelson and Leibman showed in 1996 that the common difference of the arithmetic progression can be a square, a cube, or more generally of the form p(n) where p(n) is any integer polynomial with zero constant term. We produce a variety of new results of this type related to sequences that are not polynomial. We show that the common difference of the progression in Szemerédi's theorem can be of the form [nδ] where δ is any positive real number and [x] denotes the integer part of x. More generally, the common difference can be of the form [a(n)] where a(x) is any function that is a member of a Hardy field and satisfies a(x)/xk→∞ and a(x)/xk+1→0 for some non-negative integer k. The proof combines a new structural result for Hardy sequences, techniques from ergodic theory, and some recent equidistribution results of sequences on nilmanifolds.     

An argument-based approach to reasoning with clinical knowledge

Better use of biomedical knowledge is an increasingly pressing concern for tackling challenging diseases and for generally improving the quality of healthcare. The quantity of biomedical knowledge is enormous and it is rapidly increasing. Furthermore, in many areas it is incomplete and inconsistent. The development of techniques for representing and reasoning with biomedical knowledge is therefore a timely and potentially valuable goal. In this paper, we focus on an important and common type of biomedical knowledge that has been obtained from clinical trials and studies. We aim for (1) a simple language for representing the results of clinical trials and studies; (2) transparent reasoning with that knowledge that is intuitive and understandable to users; and (3) simple computation mechanisms with this knowledge in order to facilitate the development of viable implementations. Our approach is to propose a logical language that is tailored to the needs of representing and reasoning with the results of clinical trials and studies. Using this logical language, we generate arguments and counterarguments for the relative merits of treatments. In this way, the incompleteness and inconsistency in the knowledge is analysed via argumentation. In addition to motivating and formalising the logical and argumentation aspects of the framework, we provide algorithms and computational complexity results.