Networks that self-organize in response to information are one of the most central studies in complex systems theory. A new time series analysis tool for studying self-organizing systems is developed and demonstrated. This method is applied to interacting complex swarms to explore the connection between information transport and group size, providing evidence for Dunbar's numbers having a foundation in network dynamics. A complex network model of information spread is developed. This network infodemic model uses reinforcement learning to simulate connection and opinion adaptation resulting from interaction between units. The model is applied to study polarized populations and echo chamber formation, exploring strategies for network resilience and weakening. The model is straightforward to extend to multilayer networks and networks generated from real world data. By unifying explanation and prediction, the network infodemic model offers a timely step toward understanding global collective behavior.

Increasing ubiquity of computational resources has enabled simulation of complex electronic systems and modern materials. The PAOFLOW software package is a tool designed to construct and analyze tight binding Hamiltonians from the solutions of DFT calculations. PAOFLOW leverages localized basis sets to greatly reduce computational costs of post-processing QE simulation results, enabling efficient determination of properties such as electronic density, band structures in the presence of electric or magnetic fields, magnetic or spin circular dichroism, spin-texture, Fermi surfaces, spin or anomalous Hall conductivity (SHC or AHC), electronic transport, and more. PAOFLOW's broad functionality is detailed in this work, and several independent studies where PAOFLOW's capabilities directly enabled research on promising candidates for ferroelectric and spintronic based technologies are described. Today, Quantum computers are at the forefront of computational information science. Materials scientists and quantum chemists can use quantum computers to simulate interacting systems of fermions, without having to perform the iterative methods of classical computing. This dissertation also describes a study where the band structure for silicon is simulated for the first time on quantum hardware and broadens this concept for simulating band structures of generic crystalline structures on quantum machines.

The developments of nuclear medicine lead to an increasing demand for the production of radioisotopes with suitable nuclear and chemical properties. Furthermore, from the literature it is evident that the production of radioisotopes using charged-particle accelerators instead of nuclear reactors is gaining increasing popularity. The main advantages of producing medical isotopes with accelerators are carrier free radionuclides of short lived isotopes, improved handling, reduction of the radioactive waste, and lower cost of isotope fabrication. Proton-rich isotopes are the result of nuclear interactions between enriched stable isotopes and energetic protons. An interesting observation is that during the production of proton-rich isotopes, fast and intermediately fast neutrons from nuclear reactions such as (p,xn) are also produced as a by-product in the nuclear reactions. This observation suggests that it is perhaps possible to use these neutrons to activate secondary targets for the production of neutron-rich isotopes. The study of secondary radioisotope production with fast neutrons from (p,xn) reactions using a particle accelerator is the main goal of the research in this thesis.

Using multiple theoretical methods, comprehensive calculations are performed to create a new and more comprehensive data set for elastic scattering and related transport cross sections for collisions of (H$^+$ + H), (H + H) and (He$^{2+}$ + H) in the center-of-mass energy frame. In proton-atomic hydrogen collisions, we have significantly updated and extended previous work of elastic scattering, charge transfer and related transport integral and differential cross sections in the center-of-mass energy range $10^{-4} - 10^4$ eV where the multi-channel molecular orbital approach (MO3) is used. For atomic hydrogen-hydrogen collisions, similar updates have been made of elastic scattering and spin exchange differential and integral cross sections, also for the H + H collision the ionization and negative ion formation cross sections are provided in energy range (1-20 KeV) by use of the 'hidden crossing' theoretical framework. For collisions of alpha particles with atomic hydrogen we have computed the elastic scattering cross section in the center-of-mass energy range $10^{-4} - 10^8$ eV. In this case, at the lowest energies where elastic scattering greatly dominates other reaction channels, a single-channel quasi-molecular-orbital approach (MO1) is used. With the opening of inelastic channels at higher energies the multi-channel atomic-orbital, close-coupling method is applied, and …

In recent years, continuum models of solvation have had exceptional success in materials simulations as well as condensed matter physics. They can easily capture the effects of disordered systems, such as neutral liquids or electrolytes solutions, on material interfaces without the need for expensive statistical sampling. The Environ library (www.quantum-environ.org) implements different continuum models and correction schemes, which is the focus of this presentation. Recently refactored into a stand-alone library, many changes have been introduced in Environ, making it more flexible and computationally efficient. Introduction of a double-cell formalism allows for faster ab initio DFT calculations while reparameterization of soft-sphere continuum model allows for smaller density cutoffs. Furthermore, Environ's periodic boundary conditions correction schemes have been expanded by including the AFC90 library, which allows for faster DFT calculations of partially periodic systems, such as slabs, wires, and isolated molecules. Finally, stand-alone Environ can now provide atomic and molecular descriptors, which can be used to characterize solvated interfaces, e.g. in machine learning applications. The specific details of the implementations are reviewed as well as their efficiency and some choice applications for different calculation setups and systems.

This work explores a continuum representation for diffuse layer models, thereby endowing continuum embedding models the ability to capture electrostatic phenomena in the environment such as the existence of electrolyte ions, and the nature of ionic liquids. It introduces a new field-aware continuum model that adjusts the size of the quantum regime per atom based on the distribution of charge in a system. The model accounts for the asymmetric nature of solvent distribution when applied to cations versus anions; it also overcomes the need to parameterize continuum interface models for different charged systems. The continuum representation of cavitation in water does not account for the tendency for water to form a hydrogen bonding network that is broken due to the formation of cavities. This effect is a major contributor to hydrophobic solvation and is an important precondition to the investigation of solvated proteins with continuum embedding. A new model inspired by machine learning advances is trained on molecular dynamics simulations due to the difficulty of isolating the cavitation energy term in experiment. Thermodynamic integration is used to calculate the energy from a step-like repulsive potential from cavities in TIP4P water, cavities ranging from small organic molecules, to small proteins. Predictions …

This dissertation is a collection of papers on anomalous phenomena in physics, biology, and sociology. These phenomena are primarily analyzed in terms of their temporal and spatiotemporal statistical properties. The analysis is based on both numerical simulations and, in some cases, real-world physiological and sociological data. The primary methods of analysis are diffusion entropy analysis, power spectral analysis, multifractal analysis, and survival (or waiting-time) analysis.

This dissertation is devoted to study of complex systems in human physiology particularly heartbeats and brain dynamics. We have studied the dynamics of heartbeats that has been a subject of investigation of two independent groups. The first group emphasized the multifractal nature of the heartbeat dynamics of healthy subjects, whereas the second group had established a close connection between healthy subjects and the occurrence of crucial events. We have analyzed the same set of data and established that in fact the heartbeats are characterized by the occurrence of crucial and Poisson events. An increase in the percentage of crucial events makes the multifractal spectrum broader, thereby bridging the results of the former group with the results of the latter group. The crucial events are characterized by a power index that signals the occurrence of 1/f noise for complex systems in the best physiological condition. These results led us to focus our analysis on the statistical properties of crucial events. We have adopted the same statistical analysis to study the statistical properties of the heartbeat dynamics of subjects practicing meditation. The heartbeats of people doing meditation are known to produce coherent fluctuations. In addition to this effect, we made the surprising …

A resonant cavity operating in TE011 mode was used to study the adsorption response of single walled carbon nanotubes (SWCNTs) and other nanomaterials for different types of gas molecules. The range of the frequency signal as a probe was chosen as geometry dependent range between 9.1 -9.8 GHz. A highly specific range can be studied for further experiments dependent on the type of molecule being investigated. It was found that for different pressures of gases and for different types of nanomaterials, there was a different response in the shifts of the probe signal for each cycle of gassing and degassing of the cavity. This dissertation suggests that microwave spectroscopy of a complex medium of gases and carbon nanotubes can be used as a highly sensitive technique to determine the complex dielectric response of different polar as well as non-polar gases when subjected to intense electromagnetic fields within the cavity. Also, as part of the experimental work, a range of other micro-porous materials was tested using the residual gas analysis (RGA) technique to determine their intrinsic absorption/adsorption characteristics when under an ultra-high vacuum environment. The scientific results obtained from this investigation, led to the development of a chemical biological sensor prototype. …

Phononic crystals are structures composed of periodically arranged scatterers in a background medium that affect the transmission of elastic waves. They have garnered much interest in recent years for their macro-scale properties that can be modulated by the micro-scale components. The elastic properties of the composite materials, the contrast in the elastic properties of the composite materials, and the material arrangement all directly affect how an elastic wave will behave as it propagates through the sonic structure. The behavior of an elastic wave in a periodic structure is revealed in its transmission bandstructure, and modification of any the elastic parameters will result in tuning of the band structure. In this dissertation, a phononic crystal with properties that can be modulated using electromagnetic radiation, and more specifically, radio-frequency (RF) light will be presented.

The nonlinear refractive index (n2) of room temperature liquid CS2 in the wavelength range of 9 to 11 micrometers is measured. A line tunable hybrid C02 TEA laser and amplifier system is used for the experiments. In these measurements the well known photoacoustic method is utilized to observe the onset of whole beam self-focusing. The photoacoustic signal in a CS2 cell, much longer than the confocal parameter, is monitored. The departure of the acoustic signal from linear growth marks the critical power for the onset of nonlinearity. It is experimentally verified that the phenomenon is power dependent as expected from self-focusing theory. The value of n2 is then calculated from the theoretical model of self focusing. Measurements of the on-axis irradiance transmitted through the nonlinear material as well as the measurements of beam distortion are used to verify the validity of the photoacoustic method. In all the measurements the on-axis intensity was smaller than the calculated threshold intensity for stimulated Brillouin scattering. The back reflection was monitored to make sure that stimulated Brillouin scattering was not playing a role in the phenomenon.

This dissertation is an attempt at establishing a bridge between biology and physics leading naturally from the field of phase transitions in physics to the cooperative nature of living systems. We show that this aim can be realized by supplementing the current field of evolutionary game theory with a new form of self-organized temporal criticality. In the case of ordinary criticality, the units of a system choosing either cooperation or defection under the influence of the choices done by their nearest neighbors, undergo a significant change of behavior when the intensity of social influence has a critical value. At criticality, the behavior of the individual units is correlated with that of all other units, in addition to the behavior of the nearest neighbors. The spontaneous transition to criticality of this work is realized as follows: the units change their behavior (defection or cooperation) under the social influence of their nearest neighbors and update the intensity of their social influence spontaneously by the feedback they get from the payoffs of the game (environment). If units, which are selfish, get higher benefit with respect to their previous play, they increase their interest to interact with other units and vice versa. Doing this, …

Positronium-hydrogen (Ps-H) scattering is of interest, as it is a fundamental four-body Coulomb problem. We have investigated low-energy Ps-H scattering below the Ps(n=2) excitation threshold using the Kohn variational method and variants of the method with a trial wavefunction that includes highly correlated Hylleraas-type short-range terms. We give an elegant formalism that combines all Kohn-type variational methods into a single form. Along with this, we have also developed a general formalism for Kohn-type matrix elements that allows us to evaluate arbitrary partial waves with a single codebase. Computational strategies we have developed and use in this work will also be discussed.With these methods, we have computed phase shifts for the first six partial waves for both the singlet and triplet states. The 1S and 1P phase shifts are highly accurate results and could potentially be viewed as benchmark results. Resonance positions and widths for the 1S-, 1P-, 1D-, and 1F-waves have been calculated.We present elastic integrated, elastic differential, and momentum transfer cross sections using all six partial waves and note interesting features of each. We use multiple effective range theories, including several that explicitly take into account the long-range van der Waals interaction, to investigate scattering lengths for the 1,3S …

Structural and optical properties of ZnO nanostructures synthesized by low energy ion implantation technique were examined. ZnO molecular ions were implanted into Si/SiO2 substrates at room temperature and then furnace annealed under different temperatures and environments. In all as-implanted samples only Zn nanostructures with varying diameters distributed into the Si/SiO2 matrices were observed. No trace of ZnO was found. The distributions of Zn nanostructures in Si/SiO2 closely matched results from Stopping and Range of Ions in Matter (SRIM) simulations. During annealing at 750 oC, Zn diffused both toward and away from the surface of the substrate and combine with oxygen to form ZnO nanostructures. At higher annealing temperatures ZnO bonding started to break down and transfer to zinc silicate (Zn2SiO4), and at 900 oC the ZnO was completely converted into Zn2SiO4. The average sizes of Zn/ZnO nanostructures depended on the ion fluence. If the fluence increased the average sizes of nanostructures also increased and vice versa. For room temperature photoluminescence (RT-PL), band-edge emission in the ultraviolet (UV) region was observed from all samples annealed at 700 oC/750 oC and were slightly blue shifted as compare to bulk ZnO. Donor-bound exciton (D,X) and acceptor-bound exciton (A,X) transitions were observed in low …

This work explores two very different structural systems: n-type hydrogenated amorphous silicon (a-Si:H) and gold nanoparticles (AuNPs) suspended in a matrix of organic ligands. For a-Si:H, examination of the gas-phase concentration of dopant (1-6% PH3/SiH4) and argon diluent effects includes the temperature dependent conductivity, low-frequency electronic noise, and Raman spectroscopy to examine structure. It is found that a-Si:H samples grown with high dopant concentration or with argon dilution exhibit an anomalous hopping conduction mechanism with an exponent of p=0.75. An experimental approach is used to determine correlations between conduction parameters, such as the pre-exponential factor and the characteristic temperature, rather than an analysis of existing models to explain the anomalous conduction. From these results, the anomalous conduction is a result of a change in the shape of the density of states and not a shift of the Fermi level with dopant. Additionally, it is found that argon dilution increases the carrier mobility, reduces the doping efficiency, and causes a degradation of the short-range order. With AuNPs, a comparison of temperature dependent conductivity and low-frequency noise shows that the temperature coefficient of resistance (TCR) is independent of the length of interparticle distance while the noise magnitude decreases.

Various nanostructured materials display unique and interesting optical properties. Specific nanoscale objects discussed in an experimental perspective in this dissertation include optical metamaterials, surface plasmon sensors, and two-dimensional materials. These nanoscale objects were fabricated, investigated optically, and their applications are assessed. First, one-dimensional magnetic gratings were studied, followed by their two-dimensional analog, the so-called "fishnet." Both were fabricated, characterized, and their properties, such as waveguiding modes, are examined. Interestingly, these devices can exhibit optical magnetism and even negative refraction; however, their general characterization at oblique incidence is challenging due to diffraction. Here, a new method of optical characterization of metamaterials which takes into account diffraction is presented. Next, surface plasmon resonance (SPR) was experimentally used in two schemes, for the first time, to determine the transition layer characteristics between a metal and dielectric. The physics of interfaces, namely the singularity of electric permittivity and how it can be electrically shifted, becomes clearer owing to the extreme sensitivity of SPR detection mechanisms. Finally, ultra-thin two-dimensional semiconducting materials had their radiative lifetime analyzed. Their lifetimes are tuned both by number of atomic layers and applied voltage biasing across the surface, and the changes in lifetime are suspected to be due to quenching …

Strong coherence in quasi-resonant laser driven system interferes with effective relaxations, resulting in behaviors like, coherent population trapping and Electromagnetically induced transparency. The Raman system can optimize this utilizing excited coherence in the lambda system when exposed to counter- intuitive pump-stokes pulses. The phenomenon can result in complete population transfer between vibrational levels called Stimulated Raman adiabatic passage(STIRAP). STIRAP and CHIRAP have been studied with Gaussian and chirped pulses. The optical propagation effects in dense medium for these phenomenon is studied to calculate the limitations and induced coherences. Further, the effect of rotational levels has been investigated. The molecular vibrational coherence strongly depends on the effect of rotational levels. The change in coherence interaction for ro-vibrational levels are reported and explained. We have considered the effects on the phase of radiation related to rotational mechanical motion of quantum system by taking advantages in ultra strong dispersion medium provided by quantum coherence in lambda system. The enhanced Fizeau effect on a single atom is observed.

This thesis examines the properties of transmission and transport of light and charged particles in periodic or quasiperiodic systems of solid state and optics, especially the nonlinear and external field effects and the dynamic properties of these systems.

The existence of singly, doubly, and triply charged diatomic molecular ions was observed by using an Accelerator Mass Spectrometry (AMS) technique. The mean lifetimes of 3 MeV boron diatomic molecular ions were measured. No isotopic effects on the mean lifetimes of boron diatomic molecules were observed for charge state 3+. Also, the mean lifetime of SiF^3+ was measured.

This thesis examines the evolution of beams in synchrotrons. Following an introduction to accelerator physics in Chapter 1, in Chapter 2 I describe the Fermilab E778 'diffusion' experiment. Families of sextupoles were powered to drive the 2/5 resonance, and a beam was then kicked to populate a nonlinear region of the transverse phase space. The beam was then observed over periods of approximately 30 minutes for a variety of kick amplitudes and physical apertures. In Chapter 3 comments about the analytic treatment of such systems are discussed, including the assumptions inherent in the conventional treatment. I motivate my use of a simplified model in Chapter 4 after examining common computational methods. Deriving the model from the formalism of traditional accelerator physics, I discuss its implementation on a massively parallel computer, the Intel iPSC/860 hypercube, and examine the performance of this algorithm in detail. Using the simple model to perform the numerical experiment equivalent to E778 is the subject of Chapter 5. I derive the parameters needed for the simple model based upon the physical experiment. Both three dimensional cases and cases with reduced dimensionality are run. From power supply ripple data and an electrical model of the magnet string, I …