ChipCheck--a program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays

Presented here is the program ChipCheck that allows the computation of total hybridization equilibria for hybridization experiments involving small oligonucleotide arrays. The calculation requires the free energies of binding for all pairs of probes and targets as well as total strand concentrations and probe molecule numbers. ChipCheck has been tested computationally on microarrays with up to 100 spots and 42 target strands (4200 binding equilibria). It arrives at solutions through iterations employing the multidimensional Newton method. While currently running in simulation mode only, an extension of the approach to the exhaustive analysis of chip results is being outlined and may be implemented in the future. The output displays the extent of correct and cross hybridization both graphically and numerically. In principle, calculating total hybridization equilibria allows for eliminating noise from DNA chip results and thus an improvement in sensitivity and accuracy.     

Biologically active metabolites from fungi, 17. 8-alpha-acetoxyverrol,a new member of the trichothecene sesquiterpenes

8-alpha-Acetoxyverrol (4), the first open chain example of the trichothecenes with oxygenation at C-8, was isolated from cultures of Aphanocladium spectabile. The compound doses the biosynthetic gap to the macrocyclic verrucarins.     

Wavelet bases in

Some years ago, compactly supported divergence-free wavelets were constructed which also gave rise to a stable (biorthogonal) wavelet splitting of . These bases have successfully been used both in the analysis and numerical treatment of the Stokes and Navier-Stokes equations. In this paper, we construct stable wavelet bases for the stream function spaces . Moreover, -free vector wavelets are constructed and analysed. The relationship between and are expressed in terms of these wavelets. We obtain discrete (orthogonal) Hodge decompositions.

Our construction works independently of the space dimension, but in terms of general assumptions on the underlying wavelet systems in that are used as building blocks. We give concrete examples of such bases for tensor product and certain more general domains . As an application, we obtain wavelet multilevel preconditioners in and .

     

A physical model of laser-assisted blocking of blood flow: II. Pulse modulation of radiation

A method for the calculation of blocking of blood flow upon treatment of vessel pathologies by laser irradiation at a wavelength of 530 nm are considered. The model is based on the assumption that blood-vessel occlusion is a consequence of preceding photothermal coagulation of internal layers of the vessel wall. The irradiation regimes are determined that provide homogeneous and highly efficient coagulation of the vessel wall under irradiation of tissues by series of short radiation pulses.     

Numerical Simulation Studies of the Long-term Evolution of a CO<Subscript>2</Subscript> Plume in a Saline Aquifer with a Sloping Caprock

We have used the TOUGH2-MP/ECO2N code to perform numerical simulation studies of the long-term behavior of CO₂ stored in an aquifer with a sloping caprock. This problem is of great practical interest, and is very challenging due to the importance of multi-scale processes. We find that the mechanism of plume advance is different from what is seen in a forced immiscible displacement, such as gas injection into a water-saturated medium. Instead of pushing the water forward, the plume advances because the vertical pressure gradients within the plume are smaller than hydrostatic, causing the groundwater column to collapse ahead of the plume tip. Increased resistance to vertical flow of aqueous phase in anisotropic media leads to reduced speed of up-dip plume advancement. Vertical equilibrium models that ignore effects of vertical flow will overpredict the speed of plume advancement. The CO₂ plume becomes thinner as it advances, but the speed of advancement remains constant over the entire simulation period of up to 400 years, with migration distances of more than 80 km. Our simulations include dissolution of CO₂ into the aqueous phase and associated density increase, and molecular diffusion. However, no convection develops in the aqueous phase because it is suppressed by the relatively coarse (sub-) horizontal gridding required in a regional-scale model. A first crude sub-grid-scale model was developed to represent convective enhancement of CO₂ dissolution. This process is found to greatly reduce the thickness of the CO₂ plume, but, for the parameters used in our simulations, does not affect the speed of plume advancement.     

Open Chain Chiral Macrolide Building Blocks by Opening of Deoxygenated 1,6-Anhydrosugars with 1,3-Propanedithiol

Chiral building blocks for macrolides and related natural products are obtained from 1,6-anhydrosugars by conversion of the bicyclic acetals 2 or 12 into the open chain chiral 1,3-dithianes 6 and 13. Branched precursors can be obtained by opening of the ?erný epoxide 1 with the 1,3-dithiane anion to yield 7, followed by ring opening with 1,3-propanedithiol to the bis-1,3-dithiane 8.