PURPOSE Atherosclerosis is classically defined as an immune-mediated disease characterized by accumulation of low-density lipoprotein cholesterol over intima in medium sized and large arteries. Recent studies have demonstrated that both innate and adaptive immune responses are involved in atherosclerosis. In addition, experimental and human models have recognized many autoantigens in pathophysi...

The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these c...

RAMACHANDRAN, SHANKAR. Stack Space Analysis for ARM Executables. (Under the direction of Dr. Alexander Dean). Bounding maximum stack depth for embedded system applications is essential in order to avoid conditions such as stack overflow. Stack usage information is useful for allocating the stack into a memory hierarchy. Prior work in stack space analysis addresses specific issues such as handli...

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we coup...

T he conformation of a polypeptide chain can be described with good accuracy in terms of a unique set of values of backbone torsion angles—two for each amino acid residue— called φ and ψ (Fig. 1); bond lengths and bond angles are given fixed canonical values, and the peptide bond linking successive residues also is fixed as a planar structure. As was shown by Ramachandran and coworkers nearly 5...

A technique by Rogers-Ramachandran and Ramachandran [Vis. Res. 38 (1998) 71-77] was adapted to evaluate magnocellular (M) and parvocellular (P) visual processing efficiency, with identical task structure, in normal and dyslexic children. A battery of phonological, orthographic and cognitive tasks was administered to assess reading ability and component reading skills in both groups. For the vis...

The Ramachandran plot is among the most central concepts in structural biology which uses torsion angles to describe polypeptide and protein conformation. To help visualize the features of high-fidelity Ramachandran plots, it is helpful to look beyond the common two-dimensional psi-phi-plot, which for a large dataset does not serve very well to convey the true nature of the distribution. In par...