An algebraic characterization ofB-convergent Runge-Kutta methods

Summary In the analysis of discretization methods for stiff intial value problems, stability questions have received most part of the attention in the past.B-stability and the equivalent criterion algebraic stability are well known concepts for Runge-Kutta methods applied to dissipative problems. However, for the derivation ofB-convergence results — error bounds which are not affected by stiffness — it is not sufficient in many cases to requireB-stability alone. In this paper, necessary and sufficient conditions forB-convergence are determined.This paper was written while J. Schneid was visiting the Centre for Mathematics and Computer Science with an Erwin-Schrödinger stipend from the Fonds zur Förderung der wissenschaftlichen Forschung     

Temporary attachment of carbohydrates to cyclopeptide templates: a new strategy for single-bead analysis of multivalent neoglycopeptides

Employing a cleavable carbohydrate–peptide linker, a new strategy for single-bead analysis of multivalent cyclic neoglycopeptides based on Edman degradation is described. Edman degradation of glycopeptides is hampered by the acid lability of the glycosidic bond and potential incompatibilities of phenylthiohydantoin (PTH) derivatives of glycosylated amino acids with PTH derivatives of the proteinogenic amino acids. To overcome this problem, carbohydrates are detached from the cyclopeptide templates before single-bead analysis, allowing for micro sequencing under routine conditions. With this strategy, application of multivalent cyclic neoglycopeptides in split-mix libraries with a subsequent screening process becomes possible for the first time.     

An Addendum to Birkhoff's Theorem

In spherically symmetric systems, in spite of Birkhoff's Theorem, the rates of clocks in vacuum regions on either side of moving mass shells must be continually readjusted to stay in synchrony. This shows up as time-dependence of the metric in terms of the globally meaningful time coordinate.     

Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage

Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO ₂ ^— —O— chain changed for —O—PO ₂ ^— —CH₂—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)₁₁ with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The -ggt conformation of the modified linkages is highly preferred, temporary jumps to the -g-gt and ggt conformations were, however, observed.     

On operators and search space topology in multi-objective flow shop scheduling

Multi-objective optimization using evolutionary algorithms identifies Pareto-optimal alternatives or their close approximation by means of a sequence of successive local improvement moves. While several successful applications to combinatorial optimization problems are known, studies of underlying problem structures are still scarce.