<p> This dissertation contains investigations based on Molecular Dynamics (MD) of a variety of systems, from small atomic clusters to polymers in solution and in their condensed phases. The overall research is divided in three parts. First, I tested a new thermostat in the literature on the thermal equilibration of a small cluster of Lennard-Jones (LJ) atoms. The proposed thermostat is a Hamiltonian thermostat based on a logarithmic oscillator with the outstanding property that the mean value of its kinetic energy is constant independent of the mass and energy. I inspected several weak-coupling interaction models between the LJ cluster and the logarithmic oscillator in 3D. In all cases I show that this coupling gives rise to a kinetic motion of the cluster center of mass without transferring kinetic energy to the interatomic vibrations. This is a failure of the published thermostat because the temperature of the cluster is mainly due to vibrations in small atomic clusters This logarithmic oscillator cannot be used to thermostat any atomic or molecular system, small or large. </p><p> The second part of the dissertation is the investigation of the inherent structure of the polymer polyethylene glycol (PEG) solvated in three different solvents: water, water with 4% ethanol, and ethyl acetate. PEG with molecular weight of 2000 Da (PEG₂₀₀₀) is a polymer with many applications from industrial manufacturing to medicine that in bulk is a paste. However, its structure in very dilute solutions deserved a thorough study, important for the onset of aggregation with other polymer chains. I introduced a modification to the GROMOS 54A7 force field parameters for modeling PEG₂₀₀₀ and ethyl acetate. Both force fields are new and have now been incorporated into the database of known residues in the molecular dynamics package Gromacs. This research required numerous high performance computing MD simulations in the ARGO cluster of GMU for systems with about 100,000 solvent molecules. My findings show that PEG₂₀₀₀ in water acquires a ball-like structure without encapsulating solvent molecules. In addition, no hydrogen bonds were formed. In water with 4% ethanol, PEG₂₀₀₀ acquires also a ball-like structure but the polymer ends fluctuate folding outward and onward, although the general shape is still a compact ball-like structure. </p><p> In contrast, PEG₂₀₀₀ in ethyl acetate is quite elongated, as a very flexible spaghetti that forms kinks that unfold to give rise to folds and kinks in other positions along the polymer length. The behavior resembles an ideal polymer in a &thetas; solvent. A Principal Component Analysis (PCA) of the minima composing the inherent structure evidences the presence of two distinct groups of ball-like structures of PEG₂₀₀₀ in water and water with 4% ethanol. These groups give a definite signature to the solvated structure of PEG₂₀₀₀ in these two solvents. In contrast, PCA reveals several groups of avoided states for PEG₂₀₀₀ in ethyl acetate that disqualify the possibility of being an ideal polymer in a &thetas; solvent. </p><p> The third part of the dissertation is a work in progress, where I investigate the condensed phase of PEG₂₀₀₀ and study the interface between the condensed phase and the three different solvents under study. With a strategy of combining NPT MD simulations at different temperatures and pressures, PEG₂₀₀₀ condensed phase displays the experimental density within a 1% discrepancy at 300 K and 1 atm. This is a very encouraging result on this ongoing project. </p><p>

<p> We show that a combination of different theoretical methods is a viable approach to calculate and explain the relative binding affinities of inhibitors of the human butyrylcholinesterase enzyme. We probe structural properties of the enzyme-inhibitor complex in the presence of dialkyl phenyl phosphates and derivatives that include changes to the aromatic group and alkane-to-cholinyl substitutions that help these inhibitors mimic physiological substrates. Monte Carlo docking allowed for the identification of three regions within the active site of the enzyme where substituents of the phosphate group could be structurally stabilized. Computational clustering was used to identify distinct binding modes and their relative stabilities. Molecular dynamics suggest an essential asparagine residue not previously characterized as strongly influencing inhibitor strength which may serve as a crucial component in catalytic and inhibitory activity. This study provides a framework for suggesting future inhibitors that we expect will be effective at sub-micromolar concentrations. </p><p>

<p> The nervous system encodes information about external stimuli through sophisticated computations performed by vast networks of sensory neurons. Since the space of all possible stimuli is much larger than the space of those that are ultimately meaningful, dimensionality reduction techniques were developed to identify the subspace of stimulus space relevant to neural activity. However, dimensionality reduction methods provide limited insight into the nonlinear functions that build the nervous system&rsquo;s internal model of the world. In Chapter 2, the <i>functional basis</i> is introduced that transforms the relevant subspace to a basis that describes the computational function of the subunits that make up the neural circuitry. This functional basis is used to uncover novel insights about the computations performed by neurons in low-level vision and, later on, high-level auditory circuitry. For the latter, significant barriers are found in the capability of current dimensionality reduction methods to recover the relevant subspaces of high-level sensory neurons. This barrier is caused by the relative difficulty of stimulating high-level sensory neurons, which are often unresponsive to noise stimuli, while still maintaining a thorough exploration of the stimulus distribution. In response, a new approach to dimensionality reduction is formulated in Chapter 3 called the <i>low-rank maximum noise entropy method</i> that makes it possible to overcome challenges presented by high-level sensory systems. In Chapter 4, functional bases derived from the relevant subspaces recovered by the low-rank maximum noise entropy method are employed to study the neural computations performed by high-level auditory neurons.</p><p>

This dissertation concerns the planning, implementation, and results from a highly sensitive, automated search for new pulsars. This research effort was begun with a study of the relevant signal detection theory, and the conclusions reached are presented. The general procedures developed were specifically tailored for use on a high speed minicomputer, and produced a search relatively free from observational selection effects. The actual computer coding of these procedures is also described, with emphasis on how the required speed and efficiency of these routines was obtained. The final system applied over half a million different matched digital filters to the data obtained from each successive telescope beam area. These filters correspond to a similar number of discrete combinations of possible pulsar parameters, within the approximate bounds: 0 ≤ DM ≤ 1280 cm-3 pc, 0.033< P <3.9 s, and 0.016< (w/P) <0.125. Here DM is the dispersion measure to the pulsar (the column density of free electrons), P is the pulsation period, and (w/P) is the ratio of pulse width to period, or duty cycle. Use of this search system at the 1000 foot telescope of the Arecibo Observatory resulted in the detection of 50 pulsars, 40 of which were not previously known. Parameters are presented for these new pulsars. The relatively limited range in dispersion measure exhibited by this pulsar sample is used, along with other evidence, to infer a reduced number density of pulsars at distances beyond approximately 10 kpc from the galactic center.

2025 / Type-II superlattices (T2SLs) have emerged as promising alternatives to the more established bulk material systems for infrared (IR) photodetection. This is due to predicted fundamental advantages, such as the tunability of the band gap and theoretically reduced Auger recombination rates. However, the superiority of these materials has not been experimentally realized, prompting the need for further investigation. A bottleneck in the development of improved superlattice (SL) structures and devices is the cost in time and resources required to prototype and characterize these materials as well as incomplete knowledge of the material properties and physical phenomena that characterize these structures. Therefore, the field would greatly benefit from simulation methodologies that enable the development of advanced T2SL materials. In this work, the field of IR photodetection is reviewed highlighting the most common T2SLs structures currently being experimentally implemented. A quantum transport model that includes the necessary physical mechanisms to model carrier transport in these structures will be presented. The results of an investigation on the extraction of vertical carrier mobility, a property important for carrier collection, from quantum transport simulations is presented for an example T2SL. It is demonstrated thatcarrier transport in these structures can be highly coherent. In this case, the apparent mo-bility is suppressed due to ballistic resistance, requiring care when predicting the intrinsic mobility of these materials. The best method of mobility extraction is one that considers the dependence of the resistance on device length. This method was applied to predict the quantum efficiency (QE) in curved focal-plane arrays composed of n-type mid-wave InAs/InAsSb and InAs/GaSb structures subjected to the effects of superlattice disorder and external strain imposed by the curving procedure. It is demonstrated that the external strain has a minimal impact on the QE relative to disorder in both structures suggesting the device design could be viable. Additionally, it was found that large magnitudes of positive axisymmetric strain could result in enhanced hole transport. Finally, a comprehensive investigation is presented that probed for optimized n-type long-wave InAsSb/InAsSb SL structures, a material known to result in low QE devices, for various substrate lattice constants. Several structures were found demonstrating hole mobilities with greater resilience to SL disorder providing potential candidates for future prototyping.

<p>There are many different codes available for making molecular dynamic simulation. Most of these are focused on high performance mainly. We have moved that focus towards modularity, flexibility and user friendliness. Our goal has been to design a software that is easy to use, can handle many different kind of simulations and is easily extendable to meet new requirements.</p><p>In the report we present you with the theory that is needed to understand the principles of a molecular dynamics simulation. The four different potentials we have used in the software are presented. Further we give a detailed description of the design and the different design choices we have made while constructing the software.</p><p>We show some examples of how the software can be used and discuss some aspects of the performance of the implementation. Finally we give our thoughts on the future of the software.</p>

There are many different codes available for making molecular dynamic simulation. Most of these are focused on high performance mainly. We have moved that focus towards modularity, flexibility and user friendliness. Our goal has been to design a software that is easy to use, can handle many different kind of simulations and is easily extendable to meet new requirements. In the report we present you with the theory that is needed to understand the principles of a molecular dynamics simulation. The four different potentials we have used in the software are presented. Further we give a detailed description of the design and the different design choices we have made while constructing the software. We show some examples of how the software can be used and discuss some aspects of the performance of the implementation. Finally we give our thoughts on the future of the software.

<p>The Short Time Fourier transform and the S-transform are among the most used methods of spectral decomposition to localize spectra in time and frequency. The S-transform utilizes a frequency-dependent Gaussian analysis window that is normalized for energy conservation purposes. The STFT, on the other hand, has a selected fixed time window that does not depend on frequency. In previous literature, it has been demonstrated that the S-transform distorts the Fourier spectra, shifting frequency peaks, and could result in misleading frequency attributes. Therefore, one way of making the S-transform more appropriate for quantitative seismic signal analysis is to ignore the conservation of energy over time requirement. This suggests a hybrid approach between the Short Time Fourier transform and the S-transform for seismic interpretation purposes. In this work, we introduce the Multi-Scale Boxcar transform that has temporal resolution comparable to the S-transform while giving correct Fourier peak frequencies. The Multi-Scale Boxcar transform includes a special analysis window that focusses the analysis on the highest amplitude portion of the Gaussian window, giving a more accurate time-frequency representation of the spectra in comparison with the S-transform. Post-stack seismic data with a strong well logs control was used to demonstrate the differences of the Multi-Scale Boxcar transform and the S-transform. The analysis area in this work is the Pennsylvanian and Lower Permian Horseshoe Atoll Carbonate play in the Midland Basin, a sub-basin in the larger Permian Basin. The Multi-Scale Boxcar transform spectral decomposition method improved the seismic interpretation of the study area, showing better temporal resolution for resolving the layered reservoirs? heterogeneity. The time and depth scale values on the figures are shifted according to the sponsor request, but the relative scale is correct.

Extensive information can be obtained on wave-particle interactions and wave fields by direct measurement of perturbed ion distribution functions using laser-induced fluorescence (LIF). For practical purposes, LIF is frequently performed on metastable states that are produced from neutral gas particles and ions in other electronic states. If the laser intensity is increased to obtain a better LIF signal, then optical pumping can produce systematic effects depending on the collision rates which control metastable population and lifetime. We numerically simulate the ion velocity distribution measurement and wave-detection process using a Lagrangian model for the LIF signal. The simulations show that optical pumping broadening affects the ion velocity distribution function (IVDF) $f_0(v)$ and its first-order perturbation $f_1(v,t)$ when laser intensity is increased above a certain level. The results also suggest that ion temperature measurements are only accurate when the metastable ions can live longer than the ion-ion collision mean free time. For the purposes of wave detection, the wave period has to be significantly shorter than the lifetime of metastable ions for a direct interpretation. Experiments are carried out to study the optical pumping broadening and metastable lifetime effects, and the results are compared with the simulation in order to validate the Lagrangian model for LIF. It is more generally true that metastable ions may be viewed as test-particles. As long as an appropriate model is available, LIF can be extended to a range of environments.

<p> We introduce an elastic constitutive model of gravity that enables the interpretation of cosmological observations in terms of established ideas from Solid Mechanics and multi-scale modeling. The behavior of physical space is identified with that of a material-like medium called "cosmic fabric," which exhibits constitutive behavior. This cosmic fabric is a solid hyperplate that is broad in the three ordinary spatial dimensions and thin in a fourth hyperspatial dimension. Matter in space is treated as fabric inclusions that prescribe in-plane (three-dimensional) strain causing the transverse bending of the fabric into the fourth hyperspatial dimension. The linearized Einstein-Hilbert action, which governs the dynamics of physical space, is derived from postulating Hooke's Law for the fabric, and the Schwarzschild metric is recovered from investigating matter-fabric interactions. At the continuum length scale, the Principle of Relativity is shown to apply for both moving and stationary observers alike, so that the fabric's rest reference frame remains observationally indistinguishable at such a length scale. Within the Cosmic Fabric paradigm, the structural properties of space at different hierarchical length scales can be investigated using theoretical notions and computational tools from solid mechanics to address outstanding problems in cosmology and fundamental physics. For example, we propose and offer theoretical support for the "Inherent Structure Hypothesis", which states that the gravitational anomalies currently attributed to dark matter may in fact be manifestations of the inherent (undeformed) curvature of space. In addition, we develop a numerical framework wherein one can perform numerical "experiments" to investigate the implications of said hypothesis. </p><p>