The photoionization of the beryllium-like isoelectronic series has been studied. The bound state wave functions of the target ions were built with CIV3 program. The relativistic Breit-Pauli R-matrix method was used to calculate the cross sections in the photon energy range between the ionization threshold and 1s24f7/2 threshold for each ion. For the total cross sections of Be, B+, C+2, N+3, and O+4, our results match experiment well. The comparison between the present work and other theoretical works are also discussed. We show the comparison with our LS results as it indicates the importance of relativistic effects on different ions. In the analysis, the resonances converging to 1s22lj and 1s23lj were identified and characterized with quantum defects, energies and widths using the eigenphase sum methodology. We summarize the general appearance of resonances along the resonance series and along the isoelectronic sequence. Partial cross sections are also reported systematically along the sequence. All calculations were performed on the NERSC system.

We introduce an approach to implement full coherent control on nanometer length scales. It is based on spatiotemporal modulation of the surface plasmon polariton (SPP) fields at the thick edge of a nanowedge. The SPP wavepackets propagating toward the sharp edge of this nanowedge are compressed and adiabatically concentrated at a nanofocus, forming an ultrashort pulse of local fields. The profile of the focused waveform as a function of time and one spatial dimension is completely coherently controlled. We establish the principal limits for the nanoconcentration of the terahertz (THz) radiation in metal/dielectric waveguides and determine their optimum shapes required for this nanoconcentration. We predict that the adiabatic compression of THz radiation from the initial spot size of vacuum wavelength ~300 μm to the unprecedented final size of 100-250 nm can be achieved, while the THz radiation intensity is increased by a factor of 10 to 250. This THz energy nanoconcentration will not only improve the spatial resolution and increase the signal/noise ratio for THz imaging and spectroscopy, but in combination with the recently developed sources of powerful THz pulses, will allow the observation of nonlinear THz effects and a variety of nonlinear spectroscopies (such as two-dimensional spectroscopy), which are highly informative. This should find a wide spectrum of applications in science, engineering, biomedical research and environmental monitoring. We also develop a theory of the spoof plasmons propagating at the interface between a dielectric and a real conductor. The deviation from a perfect conductor is introduced through a finite skin depth. The possibilities of guiding and focusing of spoof plasmons are considered. Geometrical parameters of the structure are found which provide a good guiding of such modes. Moreover, the limit on the concentration by means of planar spoof plasmons in case of non-ideal metal is established. These properties of spoof plasmons are of great interest for THz technology.

We have developed a general theory of the plasmonic enhancement of many-body phenomena resulting in a closed expression for the surface plasmon-dressed Coulomb interaction. It is shown that this interaction has a resonant nature. We have also demonstrated that renormalized interaction is a long-ranged interaction whose intensity is considerably increased compared to bare Coulomb interaction over the entire region near the plasmonic nanostructure. We illustrate this theory by re-deriving the mirror charge potential near a metal sphere as well as the quasistatic potential behind the so-called perfect lens at the surface plasmon (SP) frequency. The dressed interaction for an important example of a metal–dielectric nanoshell is also explicitly calculated and analyzed. The renormalization and plasmonic enhancement of the Coulomb interaction is a universal effect, which affects a wide range of many-body phenomena in the vicinity of metal nanostructures: chemical reactions, scattering between charge carriers, exciton formation, Auger recombination, carrier multiplication, etc. We have described the nanoplasmonic-enhanced Förster resonant energy transfer (FRET) between quantum dots near a metal nanoshell. It is shown that this process is very efficient near high-aspect-ratio nanoshells. We have also obtained a general expression for the force exerted by an electromagnetic field on an extended polarizable object. This expression is applicable to a wide range of situations important for nanotechnology. Most importantly, this result is of fundamental importance for processes involving interaction of nanoplasmonic fields with metal electrons. Using the obtained expression for the force, we have described a giant surface-plasmoninduced drag-effect rectification (SPIDER), which exists under conditions of the extreme nanoplasmonic confinement. Under realistic conditions in nanowires, this giant SPIDER generates rectified THz potential differences up to 10 V and extremely strong electric fields up to 10^5-10^6 V/cm. It can serve as a powerful nanoscale source of THz radiation. The giant SPIDER opens up a new field of ultraintense THz nanooptics with wide potential applications in nanotechnology and nanoscience, including microelectronics, nanoplasmonics, and biomedicine. Additionally, the SPIDER is an ultrafast effect whose bandwidth for nanometric wires is 20 THz, which allows for detection of femtosecond pulses on the nanoscale.

This research focuses on the nanoscopic investigation of the three-dimensional surface morphology of the neural growth cones from the snail Helisoma trivolvis, and InN and InGaN semiconductor material systems using Atomic Force Microscopy (AFM). In the analysis of the growth cones, the results obtained from AFM experiments have been used to construct a 3D architecture model for filopodia. The filopodia from B5 and B19 neurons have exhibited different tapering mechanisms. The volumetric analysis has been used to estimate free Ca2+ concentration in the filopodium. The Phase Contrast Microscopy (PCM) images of the growth cones have been corrected to thickness provided by AFM in order to analyze the spatial refractive index variations in the growth cone. AFM experiments have been carried out on InN and InGaN epilayers. Ternary InGaN alloys are promising for device applications tunable from ultraviolet (Eg[GaN]=3.4 eV) to near-infrared (Eg [InN]=0.7 eV). The real-time optical characteristics and ex-situ material properties of InGaN epilayers have been analyzed and compared to the surface morphological properties in order to investigate the relation between the growth conditions and overall physical properties. The effects of composition, group V/III molar ratio and temperature on the InGaN material characteristics have been studied and the growth of high quality indium-rich InGaN epilayers are demonstrated.

Photoionization cross section calculations are performed for the ground ([Ne]3s23p63d 2D ) and the first two excited ([Ne]3s23p63d 2D and [Ne]3s23p64s 2S ) states of potassium-like transition metal ions (Sc+2, Ti+3, V+4, Cr+5, Mn+6, Fe+7), along with photoionization calculations for K-like Ca+ ions in the ground ([Ne]3s23p64s 2S ) state and the first two excited ([Ne]3s23p63d 2D and [Ne]3s23p63d 2D ) states. The discrete N-electron final state ion system orbitals are generated using the computer program AUTOSTRUCTURE; 24 configurations are included in the configuration-interaction (CI) calculation for transition metal ions, and 30 configurations for the case of Ca+ ions. The initial and final (N+1)-electron wavefunctions are generated using R-matrix along with photoionization cross sections. In addition to the non-relativistic (LS-coupling) R-matrix, we have used the relativistic (Breit-Pauli) R -matrix method to carry out these calculations to focus on relativistic effects. Relativistic and non-relativistic results are compared to demonstrate the influence of relativistic effects. The prominent 3p → 3d giant resonances are analyzed and identified, and our calculated positions and widths are compared with experimental results for K-like ions such as Ca+, Sc+2 and Ti+3. In the case of lower Z (22  Z  20) ions (Ca+, Sc+2 and Ti+3), the photoionization cross section spectra are dominated by the giant (3p  3d excitation) resonances, while in cases of higher Z (26  Z  23) ions (V+4, Cr+5, Mn+6 and Fe+7), the 3p  3d resonances lie below the ionization threshold, and the cross sections are dominated by 3p53d nd and 3p53d n’s Rydberg series of resonances. Comparison of the Ca+, Sc+2 and Ti3+ results with available theoretical and experimental data shows good agreement.

The fact that loosely bonded DNA bases could tolerate large structural fluctuations, form a dissipative environment for a charge traveling through the DNA. Nonlinear stochastic nature of structural fluctuations facilitates rich charge dynamics in DNA. We study the complex charge dynamics by solving a nonlinear, stochastic, coupled system of differential equations. Charge transfer between donor and acceptor in DNA occurs via different mechanisms depending on the distance between donor and acceptor. It changes from tunneling regime to a polaron assisted hopping regime depending on the donor-acceptor separation. Also we found that charge transport strongly depends on the feasibility of polaron formation. Hence it has complex dependence on temperature and charge-vibrations coupling strength. Mismatched base pairs, such as different conformations of the G・A mispair, cause only minor structural changes in the host DNA molecule, thereby making mispair recognition an arduous task. Electron transport in DNA that depends strongly on the hopping transfer integrals between the nearest base pairs, which in turn are affected by the presence of a mispair, might be an attractive approach in this regard. I report here on our investigations, via the I –V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I –V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-binding model, such as the transfer integrals and on-site energies, are determined from first-principles calculations. The changes in electrical current through the DNA chain due to the presence of a mispair depend on the conformation of the G・A mispair and are appreciable for DNA consisting of up to 90 base pairs. For homogeneous DNA sequences the current through DNA is suppressed and the strongest suppression is realized for the G(anti)・A(syn) conformation of the G・A mispair. For inhomogeneous (generic) DNA molecules, the mispair result can be either suppression or an enhancement of the current, depending on the type of mispairs and actual DNA sequence.

Multistability is a fundamental attribute of the dynamics of neuronal systems under normal and pathological conditions. The mechanism of bistability of bursting and silence is not well understood and to our knowledge has not been experimentally recorded in single neurons. We considered four models. Two of them described the dynamics of a leech heart interneuron: the canonical model and a low-dimensional model. The other two models described mammalian pacemakers from the respiratory center. 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, Ih, and the reduction of the fast Ca2+ current, ICaF, 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.

Fourier transform infrared (FTIR) microscopy has shown promise as an analytical tool for detecting changes in cells and tissues, such as those due to viral infection, apoptosis induction or malignancy. In many cases, diagnosis via FTIR microscopy can be undertaken on a timescale shorter than that required for other physical or histological techniques. 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.

The self-calibration method, a new interferometric technique using measurements in the K′-band (2.1 μm) at the CHARA Array, has been used to derive orbits for several spectroscopic binaries. This method uses the wide component of a hierarchical triple system to calibrate visibility measurements of the triple’s close binary system through quasi-simultaneous observations of the separated fringe packets of both. Prior to the onset of this project, the reduction of separated fringe packet data had never included the goal of deriving visibilities for both fringe packets, so new data reduction software has been written. Visibilities obtained with separated fringe packet data for the target close binary are run through both Monte Carlo simulations and grid search programs in order to determine the best-fit orbital elements of the close binary. Several targets, with spectral types ranging from O to G and luminosity classesfrom 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.

This is a spectroscopic and photometric study of suspected close binary systems among the massive stars. The stars studied here include stars with temperatures ranging from 45,000 Kelvin (K) to 15,000 K, corresponding to spectral types ranging from O3 V to B5 III, masses between 47 Solar Masses and 5 Solar Masses, and absolute V magnitudes from -6.28 to -2.0. I categorize 30 targets according to my spectroscopic observations into groups with no radial velocity variability, single-lined, and double-lined variability. My analysis of the 18 constant velocity stars results in estimates of stellar effective temperature, Teff, gravity, log g, projected rotational velocity, v sin i, and spectral classification. Analyzing single-lined systems, I find the same stellar parameters for five more systems, and also present the first orbits for these systems. I also explore the probable characteristics of the unseen companions in these systems. Three double-lined systems, two eclipsing and one with an ellipsoidal variation in the light curve, are fully analyzed, and I present important astrophysical parameters for each of these systems, including stellar masses, radii, ages, and distances to each system. The masses are accurate to 4.3% and 3.6% for the primary and secondary for LH 54-425, 2.1% and 1.6% for HI Mon, and 1.1% and 0.6% for HD 42401. Two more double-lined systems are studied, and preliminary results are presented. Photometric observations are analyzed for 56 targets from the All Sky Automated Survey in order to facilitate spectroscopic observations at key points in the binary orbit where spectral features of both components will be well separated. New spectroscopic observations of these eclipsing binaries with my computed ephemerides will allow us to obtain double-lined orbital elements and determine their masses, radii, ages, and distances. These computed parameters will then allow for comparison with theoretical stellar models, and a better understanding of the evolution of massive stars.