On the Computational Complexity of the Rooted Subtree Prune and Regraft Distance

The graph-theoretic operation of rooted subtree prune and regraft is increasingly being used as a tool for understanding and modelling reticulation events in evolutionary biology. In this paper, we show that computing the rooted subtree prune and regraft distance between two rooted binary phylogenetic trees on the same label set is NP-hard. This resolves a longstanding open problem. Furthermore, we show that this distance is fixed parameter tractable when parameterised by the distance between the two trees.Received March 16, 2004     

Sulfobetaine‐containing diblock and triblock copolymers via reversible addition‐fragmentation chain transfer polymerization in aqueous media

A novel bifunctional acrylamido‐based reversible addition–fragmentation chain transfer (RAFT) chain‐transfer agent (CTA), N,N′‐ethylenebis[2‐(thiobenzoylthio)propionamide] (CTA2), has been synthesized and used for the controlled free‐radical polymerization of N,N‐dimethylacrylamide (DMA). A comparative study of CTA2 and the monofunctional CTA N,N‐dimethyl‐s‐thiobenzoylthiopropionamide (CTA1) has been conducted. Polymerizations mediated by CTA1 result in poly(N,N‐dimethylacrylamide) (PDMA) homopolymers with unimodal molecular weight distributions, whereas CTA2 yields unimodal, bimodal, and trimodal distributions according to the extent of conversion. The multimodal nature of the PDMAs has been attributed to termination events and/or chains initiated by primary radicals. The RAFT polymerization of DMA with CTA2 also results in a prolonged induction period that may be attributed to the higher local concentration of dithioester functionalities early in the polymerization. A series of ω‐ and α,ω‐dithioester‐capped PDMAs have been prepared in organic media and subsequently employed as macro‐CTAs for the synthesis of diblock and triblock copolymers in aqueous media with the zwitterionic monomer 3‐[2‐(N‐methylacrylamido)‐ethyldimethylammonio] propane sulfonate (MAEDAPS). Additionally, an ω‐dithioester‐capped MAEDAPS homopolymer has been used as a macro‐CTA for the block polymerization of DMA. To our knowledge, this is the first example of a near‐monodisperse, sulfobetaine‐containing block copolymer prepared entirely in aqueous media. The diblock and triblock copolymers form aggregates in pure water that can be dissociated by the addition of salt, as determined by ¹H NMR spectroscopy and dynamic light scattering. In pure water, highly uniform, micellelike aggregates with hydrodynamic diameters of 71–93 nm are formed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1262–1281, 2003     

Influence of the composition of the polymer matrix on the electrooptical properties of films with a dispersed liquid crystal

Polymer films with a dispersed liquid crystal were prepared by photopolymerization of (meth)acrylic monomers. The electrooptical properties of these films were studied. The influence exerted by the composition of the monomer mixture, cross-linking agents, and chain-transfer agent on the liquid crystal drop size and on the transmission of the polymer-liquid crystal films was examined.     

Methods for implementing the stream boundary condition in DSMC computations

In the direct simulation Monte‐Carlo (DSMC) method for simulating rarefied gas flows, the velocities of simulator particles that cross a simulation boundary and enter the simulation space are typically generated using the acceptance–rejection procedure that samples the velocities from a truncated theoretical velocity distribution that excludes low and high velocities. This paper analyses an alternative technique, where the velocities of entering particles are obtained by extending the simulation procedures to a region adjacent to the simulation space, and considering the movement of particles generated within that region during the simulation time step. The alternative method may be considered as a form of acceptance–rejection procedure, and permits the generation of all possible velocities, although the population of high velocities is depleted with respect to the theoretical distribution. Nevertheless, this is an improvement over the standard acceptance–rejection method. Previous implementations of the alternative method gave a number flux lower than the theoretical number required. Two methods for obtaining the correct number flux are presented. For upstream boundaries in high‐speed flows, the alternative method is more computationally efficient than the acceptance–rejection method. However, for downstream boundaries, the alternative method is extremely inefficient. The alternative method, with the correct theoretical number flux, should therefore be used in DSMC computations in favour of the acceptance–rejection method for upstream boundaries in high‐speed flows. Copyright © 2003 John Wiley & Sons, Ltd.     

Photopolymerization of 1,6‐hexanedioldiacrylate initiated by three‐component systems based on N‐arylphthalimides

Three‐component photoinitiators comprised of an N‐arylphthalimide, a diarylketone, and a tertiary amine were investigated for their initiation efficiency of acrylate polymerization. The use of an electron‐deficient N‐arylphthalimide resulted in a greater acrylate polymerization rate than an electron‐rich N‐arylphthalimide. Triplet energies of each N‐arylphthalimide, determined from their phosphorescence spectra, and the respective rate constants for triplet quenching by the N‐arylphthalimide derivatives (acquired via laser flash photolysis) indicated that an electron–proton transfer from an intermediate radical species to the N‐arylphthalimide (not energy transfer from triplet sensitization) is responsible for generating the initiating radicals under the conditions and species concentrations used for polymerization. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4009–4015, 2004     

Thermal behavior of metallodendrimers possessing bis(terpyridinyl)Ru(II) connectivity and different surface functionality

A series of metallodendrimers, assembled by means of bis(terpyridinyl)Ru^(II) connectivity on poly(propylene imine) dendrimer scaffolds, with homogeneous or heterogeneous surfaces, were prepared. Differential scanning calorimetry and thermogravimetric analysis were used to determine their thermal behavior, glass‐transition temperatures, and the decomposition kinetics and temperatures; no synergy effects for these properties were observed for the heterogeneously surfaced constructs in contrast to the corresponding homogeneously coated materials, which exhibited different values depending on their surface functionalities. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1487–1495, 2004     

Large melting point depression of 2–3‐nm length‐scale nanocrystals formed by the self‐assembly of an associative polymer: Telechelic,pyrene‐labeled poly(dimethylsiloxane)

Large melting point depressions for organic nanocrystals, in comparison with those of the bulk, were observed in an associative polymer: telechelic, pyrene‐labeled poly(dimethylsiloxane) (Py‐PDMS‐Py). Nanocrystals formed within nanoaggregates of pyrenyl units that were immiscible in poly(dimethylsiloxane). For 5 and 7 kg/mol Py‐PDMS‐Py, physical gels resulted, with melting points exceeding 40 °C and with small‐angle X‐ray scattering peaks indicating that the crystals were nanoconfined, were 2–3 nm long, and contained roughly 18–30 pyrenyl dye end units. In contrast, 30 kg/mol Py‐PDMS‐PY was not a gel and exhibited no scattering peak at room temperature; however, after 12 h of annealing at ?5 °C, multiple melting peaks were present at 5–30 °C. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3470–3475, 2004     

Black and white local invariants of mappings from surfaces into three-space

Goryunov proved that the space of local invariants of Vassiliev type for generic maps from surfaces to three-space is three-dimensional. The basic invariants were the number of pinch points, the number of triple points and one linked to a Rokhlin type invariant. In this paper we show that, by colouring the complement of the image of the map with a chess board pattern, we can produce a six-dimensional space of local invariants. These are essentially black and white versions of the above. Simple examples show how these are more effective. This revised version was published online in August 2006 with corrections to the Cover Date.     

Using Form and Function Analogy Object Boxes to Teach Human Body Systems

This study compares the use of form and function analogy object boxes to more traditional lecture and worksheet instruction during a 10th‐grade unit on human body systems. The study was conducted with two classes (N= 32) of mixed ability students at a high‐needs rural high school in central New York State. The study used a pretest/posttest design, in which the two classes alternated between conditions for the four systems (skeletal, digestive, immune, nervous). Both conditions involved students in quality instruction addressing the same concepts for the same amount of time. Additionally, all students participated in hands‐on labs. The experimental condition presented students with a set of objects analogous in form and function to parts of a human body system. Students matched objects with cards describing body system parts, mapped the analogies on a chart, generated alternative objects that could be used for the analogy, and finally, created new analogies for other body system parts. Students made significantly higher posttest and gain scores on material learned in the experimental condition, with a mean gain score average of 12.4 points out of 25, compared to 6.2 points in the control condition. Cohen's Effect Size was large, 1.36.