MOTIVATION DNA structure plays an important role in a variety of biological processes. Different di- and tri-nucleotide scales have been proposed to capture various aspects of DNA structure including base stacking energy, propeller twist angle, protein deformability, bendability, and position preference. Yet, a general framework for the computational analysis and prediction of DNA structure is ...

Fapy.dG and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) are formed in DNA by hydroxyl radical damage. In order to study replication past these lesions in cells, we constructed a single-stranded shuttle vector containing the lesion in 5'-TGT and 5'-TGA sequence contexts. Replication of the modified vector in simian kidney (COS-7) cells showed that Fapy.dG is mutagenic inducing primarily targe...

OBJECTIVES Breath-stacking asynchrony during assist-control-mode ventilation may be associated with increased tidal volume and alveolar pressure that could contribute to ventilator-induced lung injury. Methods to reduce breath stacking have not been well studied. The objective of this investigation was to evaluate 1) which interventions were used by managing clinicians to address severe breath ...

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified p...

Genomic homogeneity is investigated for a broad base of DNA sequences in terms of dinucleotide relative abundance distances (abbreviated delta-distances) and of oligonucleotide compositional extremes. It is shown that delta-distances between different genomic sequences in the same species are low, only about 2 or 3 times the distance found in random DNA, and are generally smaller than the betwe...

We study from a computational standpoint several different physical scales associated with structural features of DNA sequences, including dinucleotide scales such as base stacking energy and propeller twist, and trinucleotide scales such as bendability and nucleosome positioning. We show that these scales provide an alternative or complementary compact representation of DNA sequences. As an ex...

Magnesium alloys containing long-period-stacking ordered (LPSO) phases have attracted considerable attention because they have been reported to exhibit excellent mechanical properties, including high strength and reasonable ductility. It is thought that the LPSO phase plays a critical role in producing these favorable mechanical properties. We analyze the deformation behavior of the LPSO phases...

Stability of the ;-; stacking interactions in the substituted-coronene||cyclooctatetraene complexes wasstudied using the computational quantum chemistry methods (where || denotes ;–; stackinginteraction, and substituted-coronene is coronene which substituted with four similar X groups; X =OH, SH, H, F, CN, and NO). There are meaningful correlations between changes of geometricalparameters and t...

Graphite-like hexagonal AlN (h-AlN) multilayers have been experimentally manifested and theoretically modeled. The development of any functional electronics applications of h-AlN would most certainly require its integration with other layered materials, particularly graphene. Here, by employing vdW-corrected density functional theory calculations, we investigate structure, interaction energy, a...

Alanyl peptide nucleic acids (alanyl-PNAs) are oligomers based on a regular peptide backbone with alternating configuration of the amino acids. All side chains are modified by covalently linked nucleobases. Alanyl-PNAs form very rigid, well defined, and linear double strands based on hydrogen bonding of complementary strands, stacking, and solvation. Side chain homology was examined by comparin...