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.     

Decomposition algorithms for the tree edit distance problem

We study the behavior of dynamic programming methods for the tree edit distance problem, such as [P. Klein, Computing the edit-distance between unrooted ordered trees, in: Proceedings of 6th European Symposium on Algorithms, 1998, p. 91–102; K. Zhang, D. Shasha, SIAM J. Comput. 18 (6) (1989) 1245–1262]. We show that those two algorithms may be described as decomposition strategies. We introduce the general framework of cover strategies, and we provide an exact characterization of the complexity of cover strategies. This analysis allows us to define a new tree edit distance algorithm, that is optimal for cover strategies.     

Synthesis of MgAl2O4 Spinel Nanometer Powder via Biology Polysaccharide Assisted Sol-Gel Process

A novel and cost-effective sol-gel process for preparation of MgAl₂O₄ spinel nanometer powders has been developed in this study. A solution of magnesium and aluminum nitrates in stoichiometric proportion was successfully embraced in the biology polysaccharide gel network, formed by the synergistic interaction between xanthan gum (XG) and locust bean gum (LBG) utilizing their broad-spectrum stability of salt tolerance and character of transformation from sol to gel on the condition of proper temperature and relative proportion of polymeric components. Dry gel could be obtained by vacuum dehydration of aqueous gel at low temperatures. Monolithic MgAl₂O₄ spinel nanometer powders were produced by calcining the dry gel above 800°C, with average crystallite size of 20 nanometers.     

Stochastic resonance in perspective

Summary We outline the historical development of stochastic resonance (SR), a phenomenon in which the signal and/or the signal-to-noise ratio in a nonlinear system increase with increasing intensity of noise. We discuss basic theoretical ideas explaining and describing SR, and we review some revealing experimental data that place SR within the wider context of statistical physics. We emphasize the close relationship of SR to some effects that are well known in condensed-matter physics. Paper presented at the International Workshop ?Fluctuations in Physics and Biology: Stochastic Resonance, Signal Processing and Related Phenomena?, Elba, 5–10 June 1994.     

Statistical mechanics of warm and cold unfolding in proteins

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm unfolding, thus qualitatively reproducing the known thermodynamics of proteins. Received: 19 March 1998 / Revised and Accepted: 25 May 1998     

The Staudinger ligation-a gift to chemical biology

Although the reaction between an azide and a phosphane to form an aza-ylide was discovered by Hermann Staudinger more than 80 years ago and has found widespread application in organic synthesis, its potential as a highly chemoselective ligation method for the preparation of bioconjugates has been recognized only recently. As the two reaction partners are bioorthogonal to almost all functionalities that exist in biological systems and react at room temperature in an aqueous environment, the Staudinger ligation has even found application in the complex environment of living cells. Herein we describe the current state of knowledge on this reaction and its application both for the preparation of bioconjugates and as a ligation method in chemical biology.     

Cross-linking chemistry and biology: development of multifunctional photoaffinity probes

An efficient method of photoaffinity labeling has been developed based on rationally designed multifunctional photoprobes. Photoaffinity techniques have been used to elucidate the protein structure at the interface of biomolecules by the photochemical labeling of interacting sites. However, the identification of labeled sites within target proteins is often difficult. Novel biotinyl bioprobes bearing a diazirine photophore have contributed significantly to the rapid elucidation of ligand binding sites within proteins, thereby extending conventional photoaffinity methods. This article discusses the synthesis and applications of various photoprobes bearing a biotin, including strategies using cleavable linkages between photophores. The combination of photoaffinity methods with chip technology is also described as a novel entry to rapid affinity-based screening of inhibitors. This review focuses on a rapid and reliable photoaffinity method utilizing diazirine-based multifunctional photoprobes with numerous potential applications in functional proteomics of biomolecular interactions.     

Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification

Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of target DNA, annealing of sequence-specific oligonucleotide primers and the enzyme-catalyzed elongation of the annealed complex (primer:DNA:polymerase). The denaturation step separates the double strands of DNA; this model assumes denaturation is complete. The annealing step describes the formation of a primer-fragment complex followed by the attachment of the polymerase to form a ternary complex. This step is complicated by competitive annealing between primers and incomplete fragments including primer-primer reactions. The elongation step is modeled by a stochastic method. Species that compete during the elongation step are deoxynucleotide triphosphates dCTP, dATP, dTTP, dGTP, dUTP, and pyrophosphate. Thermal deamination of dCTP to form dUTP is included in the model. The probability for a species to arrive at the active site is based on its molar fraction. The number of random insertion events depends on the average processing speed of the polymerase and the elongation time of the simulation. The numerical stochastic experiment is repeated a sufficient number of times to construct a probability density distribution (PDF). The moment of the PDF and the annealing step products provide the product distribution at the end of the elongation step. The overall yield is compared to six experimental values of the yield. In all cases the comparisons are very good.     

Rumer's transformation,in biology,as the negation,in classical logic

In this article, we make a connection between the Rumer transformation, used in the study of the genetic code‐doublets, and the negation of classic logic. A unified classification is given, relying on two Klein's 4‐groups describing the symmetries of the 16 doublets of nitrogenous bases and those of the 16 binary connectives of classic logic, both groups being subgroups of a larger noncommutative group with eight elements we identify as the dihedral group D₄. Also, some connections with other works are briefly considered. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003