Functionalized Silver-Ion-Mediated α-dC/β-dC Hybrid Base Pairs with Exceptional Stability: α-d-5-Iodo-2′-Deoxycytidine and Its Octadiynyl Derivative in Metal DNA

Silver-mediated α-dC–Ag⁺–β-dC hybrid base pairs decorated with 5-iodo- or 5-octadiynyl residues are well accommodated in duplex DNA. A strong T_m increase and favorable thermodynamic data for duplex DNA were observed after addition of silver ions. The phenomenon is particularly obvious when both nucleobases of the base pairs are functionalized. Neither the position of the base pair, nor the type of 5-substituent had a negative influence. On the contrary, functionalization of conventional silver-mediated β-dC–Ag⁺–β-dC homo base pairs showed a negative impact induced by the bulky substituents. To this end, cytosine modified 12-mer oligodeoxynucleotides were prepared by solid-phase synthesis employing new α-anomeric 2′-deoxycytidine phosphoramidites. A multigram scale synthesis was developed for 5-iodo-α-d -2′-deoxycytidine ( 1 ) employing the direct glycosylation of cytosine with Hoffer's α-d -halogenose followed by separation of anomeric DMT nucleosides. Regarding base-pair stability and functionalization silver-mediated α/β-dC hybrid base pairs were found to be superior to β/β-dC homo pairs. According to their extraordinary properties, they might find applications in DNA diagnostics, material science, or nanotechnology.     

Spectral estimates for saddle point matrices arising in weak constraint four‐dimensional variational data assimilation

We consider the large sparse symmetric linear systems of equations that arise in the solution of weak constraint four‐dimensional variational data assimilation, a method of high interest for numerical weather prediction. These systems can be written as saddle point systems with a 3 × 3 block structure but block eliminations can be performed to reduce them to saddle point systems with a 2 × 2 block structure, or further to symmetric positive definite systems. In this article, we analyse how sensitive the spectra of these matrices are to the number of observations of the underlying dynamical system. We also obtain bounds on the eigenvalues of the matrices. Numerical experiments are used to confirm the theoretical analysis and bounds.     

Smart Geodesic Tracing in GRworkbench

We have developed a new tool for numerical work in General Relativity: GRworkbench. We discuss how GRworkbench's implementation of a numerically-amenable analogue to Differential Geometry facilitates the development of robust and chart-independent numerical algorithms. We consider, as an example, geodesic tracing on two charts covering the exterior Schwarzschild space-time.     

Transport of Neutrally Buoyant and Dense Variably Sized Colloids in a Two-Dimensional Fracture with Anisotropic Aperture

The transport of monodisperse as well as polydisperse colloid suspensions in a two-dimensional, water saturated fracture with spatially variable and anisotropic aperture is investigated with a particle tracking model. Both neutrally buoyant and dense colloid suspensions are considered. Although flow and transport in fractured subsurface formations have been studied extensively by numerous investigators, the transport of dense, polydisperse colloid suspensions in a fracture with spatially variable and anisotropic aperture has not been previously explored. Simulated snapshots and breakthrough curves of ensemble averages of several realizations of a log-normally distributed aperture field show that polydisperse colloids exhibit greater spreading than monodisperse colloids, and dense colloids show greater retardation than neutrally buoyant colloids. Moreover, it is demonstrated that aperture anisotropy oriented along the flow direction substantially increases colloid spreading; whereas, aperture anisotropy oriented transverse to the flow direction retards colloid movement.     

Application of polymer-supported triphenyl phosphine in the palladium-catalyzed cyanation reaction under microwave conditions

A variety of aryl nitriles were prepared in excellent yields from the palladium acetate catalyzed coupling of aryl halides with Zn(CN)₂ using polymer-supported triphenyl phosphine as the ligand and dimethylformamide as solvent under microwave irradiation conditions.     

Bringing the balance function into focus

Charge balance functions provide important insight concerning hadronization and charge transport in heavy ion collisions at RHIC. Unfortunately, this observable is clouded by several effects. One of these effects is resonance production. Here, we present a simple thermal model where resonance production is included via a Monte Carlo technique based on the canonical ensemble. Resonance production is not found to have a large effect on the width.