Parametric multiple sequence alignment and phylogeny construction

Bounds are given on the size of the parameter-space decomposition induced by multiple sequence alignment problems where phylogenetic information may be given or inferred. It is shown that many of the usual formulations of these problems fall within the same integer parametric framework, implying that the number of distinct optima obtained as the parameters are varied across their ranges is polynomially bounded in the length and number of sequences.     

The Random Average Process and Random Walk in a Space-Time Random Environment in One Dimension

We study space-time fluctuations around a characteristic line for a one-dimensional interacting system known as the random average process. The state of this system is a real-valued function on the integers. New values of the function are created by averaging previous values with random weights. The fluctuations analyzed occur on the scale n ^1/4, where n is the ratio of macroscopic and microscopic scales in the system. The limits of the fluctuations are described by a family of Gaussian processes. In cases of known product-form invariant distributions, this limit is a two-parameter process whose time marginals are fractional Brownian motions with Hurst parameter 1/4. Along the way we study the limits of quenched mean processes for a random walk in a space-time random environment. These limits also happen at scale n ^1/4 and are described by certain Gaussian processes that we identify. In particular, when we look at a backward quenched mean process, the limit process is the solution of a stochastic heat equation.     

What do multistep methods approximate?

Summary Standard analysis of multistep methods for ODE's assumes the application of an initialization routine that generates the starting points. Here ak-step method is considered directly as a mappingR ^kn R ⁿ . It is shown to approximate a mapping which is expressible directly in terms of the flow of the vector field. Some useful properties of that mapping are shown and for strictly stable methods these are applied to the question of invariant circles near a hyperbolic periodic solution.     

IR-induced processes for allyl alcohol dimers involving an intermolecular OH...π Bond in low-temperature matrices

Sharp peaks were observed in the IR spectra of allyl alcohol dimers in the νOH and τOH regions in low-temperature Ar and N₂ matrices. In Ar a peak at 3587 cm^?1 was found to increase in intensity upon annealing and decrease upon IR irradiation; it is concluded that this peak is due to an OH...π interaction (of a cyclic structure) present in part of the dimers. This is the first time such an interaction and photoprocess have been found for an alcohol in matrices. Also a faster photo-process was found. Confomer changes in the monomers accompany the photoprocess in allyl alcohol dimers.     

Parameter Study for the Pre‐Irradiation Grafting of Styrene/Divinylbenzene onto Poly(tetrafluoroethylene‐co‐hexafluoropropylene) from Isopropanol Solution

Pre‐irradiation grafting of styrene/divinylbenzene (DVB) onto poly(tetrafluoroethylene‐co‐hexafluoropropylene) (FEP) films from isopropanol (ⁱPrOH) solution was investigated with respect to the effect of irradiation dose, film thickness, cross‐linker concentration, and reaction temperature. A mathematical model was applied to the kinetic curves to extract information on the polymerization rate, the radical‐recombination rate, and the grafting through time. It turned out that the two closely correlated reaction rates for polymerization and radical recombination can be varied over a wide range by changing the irradiation dose, the cross‐linker concentration, and the reaction temperature. On the other hand, the time until the grafting front has progressed to the center of the film is mainly affected by the film thickness and the reaction temperature. The formation of homopolymer in the grafting solution increases steeply with temperature and cross‐linker concentration.     

Nuclear amination catalyzed by fungal laccases: reaction products of p-hydroquinones and primary aromatic amines

[reaction: see text] Nuclear amination of p-hydroquinones with primary aromatic amines was catalyzed by fungal laccases (EC 1.10.3.2) from Trametes spec. and Myceliophthora thermophila. This is the first report of laccase-catalyzed synthesis of aminoquinones. Incubation of two compounds with laccase in the presence of oxygen resulted in the formation of the corresponding monoaminated or diaminated quinones. No hydroquinonoids were formed. Observed differences in the reaction courses for different p-hydroquinones and aromatic amines with different laccases are discussed.     

Biologically active compounds through catalysis: efficient synthesis of N-(heteroarylcarbonyl)-N'-(arylalkyl)piperazines

A practical route for the synthesis of new biologically active 5-HT(2 A) receptor antagonists has been developed. In only three catalytic steps, this class of central nervous system (CNS) active compounds can be synthesized efficiently with high diversity. As the initial step, an anti-Markovnikov addition of amines to styrenes provides an easy route to N-(arylalkyl)piperazines, which constitute the core structure of the active molecules. Here, base-catalyzed hydroamination reactions of styrenes with benzylated piperazine proceeded in high yield even at room temperature. After catalytic debenzylation, the free amines were successfully carbonylated with different aromatic and heteroaromatic halides and carbon monoxide to yield the desired compounds in good to excellent yields. The two key reactions, base-catalyzed hydroamination of styrenes and palladium-catalyzed aminocarbonylation of haloarenes/heterocycles, showed tolerance towards various functional groups, thereby demonstrating the potential to synthesize a wide variety of new derivatives of this promising class of pharmaceuticals.     

Evaluation of epifluorescence image analysis of biofilm growth on stainless steel surfaces

Biofilm growth of Bacillus subtilis, Pseudomonas fragi, Pediococcus inopinatus and Listeria monocytogenes was studied on stainless steel surfaces at room and low temperatures to evaluate the results of traditional hygiene measures. The results were compared with those of image analysis of stainless steel surfaces in an epifluorescence microscope. Statistical analyses were carried out to determine the variations between the conventional cultivation swab method, the glycocalyx amount obtained using swabbing, and the values of the areas of the biofilm, slime and cells. As a general rule, old biofilms showed total counts at approximately the same levels as the young biofilm. The results showed that temperature affected the results for all strains except B. subtilis. The strains of Pe. inopinatus and Ps. fragi showed increased attachment at 6°C and L. monocytogenes at 25°C. The biofilm slime was more easily detached than the cells. The results indicated that the traditional swab method is not reliable for the measurement of biofilm formation on surfaces.     

Syntheses of macrocyclic bisbibenzyls on solid support

We describe a route for the polymer supported total synthesis of the cyclic bisbibenzyls of the isoplagiochin type found in liverworts. TentaGel^® resins were used as solid support for a sequence involving Suzuki, Wittig and hydrogenation protocols. The polymer linked intermediates could be characterized by HR-MAS NMR. This route is to be extended to the synthesis of small libraries of differently halogenated derivatives.