As a case study, we present an examination of high resolution, ultraviolet spectroscopy from Hubble Space Telescope of the photospheric spectrum of the O-supergiant in the massive X-ray binary HDE 226868 = Cyg X-1. We analyzed the ultraviolet and ground-based optical spectra to determine the effective temperature and gravity of the O9.7 Iab supergiant. Using non-LTE, line blanketed, plane parallel models from the TLUSTY grid, we obtain T_eff = 28.0 +/- 2.5 kK and log g > 3.00 +/- 0.25, both lower than found in previous studies. The optical spectrum is best fit with models that have enriched He and N abundances. We fit the model spectral energy distribution for this temperature and gravity to the UV, optical, and IR fluxes to determine the angular size of and extinction towards the binary. By assuming that the supergiant rotates synchronously with the orbit, we can use the radius - distance relation to find mass estimates for both components as a function of the distance and the ratio of stellar to Roche radius. Our results indicate masses of 23⁺⁸_-6 solarmasses for the supergiant and 11⁺⁵_-3 solarmasses for the black hole. These results agree with subsequent mass estimates Orosz et al. (2011) based on the trigonometric parallax distance measurements of Reid et al. (2011).

The results of this survey provide fundamental information on the impact of environment on massive binaries and also the role multiplicity has on massive star formation and evolution.

To provide a foundation upon which to base computational studies of pigments in protein binding sites density functional theory based calculations of the vibrational properties of neutral ubiquinone in the gas phase and in solvent were undertaken. From single point energy calculations it was shown that at least eight ubiquinone conformers, each with slightly different FTIR spectra, could be present in solvent at room temperature.

The calculated and experimental spectra for neutral ubiquinone in solution are very different from the spectra associated with ubiquinone in the Q_A binding in purple bacterial reaction centers. For this reason an ONIOM method was undertaken in which the pigment was treated using density functional theory based methods while the protein was treated using molecular mechanics. The ONIOM calculations not only modeled the experimental Q_A FTIR difference spectra but also resolved the long standing issue of whether a very strong hydrogen bond exists between the bound ubiquinone and the imidazole nitrogen of a histidine residue (HisM219).

To further validate the usefulness of the ONIOM approach experimental isotope edited FTIR spectra obtained using purple bacterial reaction centers with a range of chainless symmetrical quinones incorporated were modeled. Again, the agreement between the calculated and experimental spectra is outstanding.

We also modeled the vibrational properties of the ubisemiquinone anion radical both in solvent and in the Q_A binding site. Vibrational modes of ubisemiquinone display a greater degree of mixing of the various molecular groups of the molecule. Nonetheless the calculated FTIR spectra for ubisemiquinone in solution and in the Q_A site agree very well with that found experimentally. Vibrational frequencies of ubisemiquinone obtained from ONIOM calculated Raman spectra also agree very well with that found in experimental resonance Raman spectra associated with the ubisemiquinone anion radical in the Q_A binding site.

Several targets, with spectral types ranging from O to G and luminosity classes
from III to V, have been observed in this fashion, and orbits have been derived for the close binaries of eight targets (V819 Her B, Kappa Peg B, Eta Vir A, Eta Ori Aab, 55 UMa A, 13 Ceti A, CHARA 96 Ab, HD 129132 Aa). The derivation of an orbit has allowed for the calculation of the masses of the components in these systems. The magnitude differences between the components can also be derived, provided that the components of the close binary have a magnitude difference of Delta K < 2.5 (CHARA’s limit). Derivation of the orbit also allows for the calculation of the mutual inclination (Phi), which is the angle between the planes of the wide and close orbits. According to data from the Multiple Star Catalog, there are 34 triple systems other than the 8 studied here for which the wide and close systems both have visual orbits. Early formation scenarios for multiple systems predict coplanarity (Phi < 15 degrees), but only 6 of these 42 systems are possibly coplanar. This tendency against coplanarity may suggest that the capture method of multiple system formation is more important than previously believed.

In this work we have used FTIR microscopy to study Vero cells that have been infected with herpes simplex virus (type I) and adenovirus. We have studied cellular samples at various time intervals following exposure to the virus. Several spectral regions were identified that allow discrimination between infected and uninfected Vero cell samples at 24 hours post exposure to both HSV1 and adenovirus. Spectral features were also identified that could be used to discriminate infected cells within 2-6 hours after exposure to both viruses. FTIR microscopy is therefore a useful tool for following the kinetics of viral infection in the 2-24 hours time range, at least at the levels of infection used in this study.

In a second type of study, FTIR microscopy was used to study apoptosis induction in acute lymphoblastic leukemia T-cells. Apoptosis was induced in T-cells in three different ways. We show that FTIR microscopy can be used to distinguish T-cells in the early stages of apoptosis from normal cells. We also provide data that may suggest that FTIR microscopy can distinguish cells that have undergone apoptosis via different pathways.

For most of the FTIR microscopic studies on cellular samples we have focused on the collection of spectral data in the 1500-800 cm^-1 region. Spectra were collected for control cells and variously treated cells. The two sets of cells were then analyzed statistically using: 1) pair-wise comparison, 2) logistic regression, 3) partial least square regression, 4) principle component fed linear discriminant analysis and 5) hierarchical cluster analysis. The statistical analyses rigorously quantify to what extent treated and untreated cells can be distinguished. Since different statistical methods give differing results for the same data, it is important the right statistical method should be applied. The basis for these differences is discussed.

We investigated the low-dimensional model and identified six different types of multistability of dynamical regimes. We described six generic mechanisms underlying the co-existence of oscillatory and silent regimes. The mechanisms are based either on a saddle equilibrium or a saddle periodic orbit. The stable manifold of the saddle equilibrium or the saddle orbit sets the threshold between the regimes. In the two models of the leech interneuron the range of the controlling parameters supporting the co-existence of bursting and silence is limited by the Andronov-Hopf and homoclinic bifurcations (Malashchenko, Master Thesis 2007). The bistability was found in a narrow range of the leak currents' parameters. Here, we introduced a propensity index to bistability as the width of the range on a bifurcation diagram; we investigated how the propensity index was affected by modifications of the ionic currents, and found that conductances of only two currents substantially affected the index. The increase of the conductance of the hyperpolarization-activated current, I_h, and the reduction of the fast Ca²⁺ current, I_CaF, notably increased the propensity index. These findings define modulatory conditions under which we suggest the bistability of bursting and silence could be experimentally revealed in leech heart interneurons. We hypothesize that this mechanism could be commonly found in a large variety of neuronal models. We applied our techniques to models of vertebrate neurons controlling respiratory rhythm, which represent two types of inspiratory pacemakers of the Pre-Bӧtzinger Complex. We showed that both types of neurons could exhibit bistability of bursting and silence in accordance with the mechanism which we described.