Diamondoids are cage-like saturated hydrocarbons consisting of fused cyclohexane rings. The Diamondoids family of compounds is one of the best candidates for molecular building blocks (MBBs) in nanotechnology to construct organic nanostructures compared to other MBBs known so far. The challenge is to find a route for self-assembly of these cage hydrocarbons and their applications in the bottom-...

We have demonstrated that the DNA sequence between two triplex-forming polypurine.polypyrimidine (Pu.Py) tracts was protected from DNA modifying enzymes upon formation of triplex DNA structures with an oligodeoxyribonucleotide in which two triplex-forming Pu or Py tracts were placed at the termini (triplex-bridge formation). In model experiments, when two triplex structures were formed between ...

Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the ...

Eukaryotic DNA topoisomerase I (Top1) is a monomeric protein clamp that functions in DNA replication, transcription, and recombination. Opposable "lip" domains form a salt bridge to complete Top1 protein clamping of duplex DNA. Changes in DNA topology are catalyzed by the formation of a transient phosphotyrosyl linkage between the active-site Tyr-723 and a single DNA strand. Substantial protein...

When depth of flow past a river bridge exceeds opening under the bridge, the flow under the bridge becomes pressurized. The water is directed downward and under the bridge deck, causing increase in velocity and shear stress on the bed thereby increasing bed scour. This is termed as Pressure Flow Scour. The present study investigates the phenomenon of pressure flow scour resulting from a submerg...

We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi–site breathers in a DNA–shaped double strand. Within a network model of the double helix we take individual motions of the bases within the base pair plane into account. The resulting H-bridge deformations may be asymmetric with respect to the helix axis. Furthermore the covalent bonds may be d...

In a recent study (Moreno-Herrero et al., 2005), atomic force microscopy (AFM) imaging of the human Mre11/Rad50/Nbs1 (MRN) complex engaging substrate DNA revealed large-scale, DNA binding-induced propagation of conformational change to the distal ends of the Rad50 coiled coils and erection of a 1000 A scaffold to productively bridge DNA ends.

Bacterial histone-like DNA-binding proteins are best known for their role in compacting the genomic DNA. Of these proteins, HU is ubiquitous and highly conserved across the eubacterial kingdom. Using the HBsu (Bacillus subtilis-encoded HU homologue) as a model, we explore here the molecular basis for the ability of some HU homologues to engage a longer approx. 35 bp DNA site as opposed to the m...

three unconventional details for plastic hinges of bridge columns subjected to seismic loads were developed, designed, and implemented in a large-scale, four-span reinforced concrete bridge. shape memory alloys (sma), special engineered cementitious composites (ecc), elastomeric pads embedded into columns, and post-tensioning were used in three different piers. the bridge model was subjected to...