The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.

Software testing is considered to be the ultimate obstacle before software can be released. Traditional approaches to testing the software revolves around capabilities of a system using various types of testing (e.g., black-box) at various level of software development process. Testing the software for system-wide qualities such as portability is very rare. The research work in this area is very limited. In this work, we discuss the importance of portability testing and attempt to explore a testing approach to test the portability of Scientific Computing (SC) software using different platforms. The main incentive for testing of SC software is that this class of software is challenging because of the elements such as computing environment, computational mathematics, languages, optimization; these elements play significant roles in success or failure of these systems.

reporter. Using the second methods we found out that the UCS domain but not the central domain prevents the thermal aggregation of the myosin motor domain. We conclude that while both the UCS domain and the central domain bind the myosin head, only the UCS domain displays chaperone activity. Funded by a grant from the American Heart Association (AHA 13GRNT17290006).

channels have been shown to be localized to the intercalated disks along with Cx43 channels. Recent evidence of reciprocity in the co-localized expression of Kir2.1 and Nav1.5 channels in cardiac myocytes suggest that ionic currents due to these two channels are in some way calibrated to each other. In isolated cells, the fast sodium current is much larger than IK1 resulting in a large depolarization reserve. Using simulations of chains of cardiac cells, we show that the depolarization reserve for conducting action potentials is significantly smaller than in isolated cells. We also studied the changes in the depolarization reserve with variations in gap junction channel density and explored the conditions under which propagation slowed or failed. These insights will allow a better understanding of the effects of Na channel blockers as well as regional differences in action potential conduction in the heart.