Molecular dynamics simulations of the liquid crystal phases of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine (2PhP) and 5-(4-butyloxyphenyl)-2-octyloxy-pyrimidine (5PhP) are the focus of this thesis. The 2PhP and 5PhP mesogens display different liquid crystalline phase sequences, despite having very similar molecular structures. Specifically, both mesogens consist of aromatic phenyl and pyrimidine cores in between two flexible alkoxy tails, but they differ in the preferred core conformation. A multi-site coarse-grained model, in which the aromatic rings are represented by soft quadrupolar ellipsoids and the alkoxy chains are given a united atom representation, is proposed in this thesis. A parameterization route for the intra- and intermolecular potentials appropriate for liquid crystal simulations is developed. The ab initio based derivation of suitable molecular models for the two mesogens is discussed in detail, with particular emphasis on capturing proper phenyl-pyrimidine interactions which proved to be essential to correctly represent core-core interactions between neighboring molecules. A systematic determination of suitable Gay-Berne (GB) parameters has been adopted for the aromatic rings of 2PhP and 5PhP. To account for the pi-electron cloud below and above the ring plane, a quadrupole was added perpendicular to the ring. In the end, four parameterizations for aromatic rings have been selected for the simulations. Model characterization via pair interactions proved to be valuable in identifying and analyzing the short range structure in the phases. Extensive molecular dynamics simulations of these fluids at various temperatures are performed. Intermolecular structure and order, in aromatic core and the flexible tail regions, are analyzed. Intermolecular structure is divided into contributions parallel and perpendicular to the layers, as indicated by a layer normal or by a director, to differentiate smectic A (SmA) from smectic C (SmC). The presence of a ring quadrupole in the molecular model is shown to be essential to the correct reproduction of the experimentally observed phases. Simulations correctly indicate phases in agreement with experiment: SmC and SmA phases for 2PhP, and only a SmA phase for 5PhP. / Thesis (Ph.D, Chemistry) -- Queen's University, 2009-10-27 20:23:37.89

This dissertation investigated the impact of the Surficial Fine-Grained Laminae (SFGL) upon stream biogeochemical cycles to constrain stream C and N budgets. Collection and analysis of 8 years of transported sediment elemental and isotopic signatures, weekly, from a SFGL dominated stream, a novel dissolved C and N dataset, statistical and time-series analysis of sediment and dissolved data, and development of a comprehensive modeling framework that couples hydrodynamics, sediment, C and N biogeochemistry, and stable isotope sub-models to simulate fluvial C and N budgets was used. SFGL C modeling suggests benthic particulate C stocks and transport vary seasonally and annually but are in a state of long-term equilibrium which is governed by negative feedback mechanisms whereby high POC export due to extreme hydrologic events and high frequency hydrologic events reduces benthic particulate C stocks and inhibits benthic particulate C growth. Model distribution fitting suggests transported particulate C in SFGL streams is Gamma distributed; in which statistical moments are governed by variability of the SFGL. Stable isotope un-mixing of the bed source suggests that the SFGL has varying levels of carbon quality seasonally and annually, in which non-equilibrium conditions stem from extreme depositional events. Coupling stable isotope mass balance and SFGL fractionation processes into water quality modeling frameworks, reduced uncertainty of the C budget by nearly 60%, suggesting algal sloughing constitutes nearly 40% of the total organic C budget, shifting the balance from dissolved C to particulate C dominated. Time series analysis of the eight year dataset suggest nitrogen dynamics in the SFGL dominated stream were consistent with existing conceptual models when algal biomass is the prominent organic matter source in the SFGL, but contradicts conventional wisdom in winter through late spring when abiotic sorption appears prominent. The development of a new numerical model to simulate the fluvial N budget couples this new conceptual model of SFGL stream N dynamics to isotope mass-balances and C dynamics in order to provide a comprehensive management tool for restoration engineers. Meta-analysis and upscaling of results for regional to global scales will enable researchers to place the role of the SFGL in a broader context.

Small lowland agricultural systems promote conditions where benthic biological communities can thrive. These biogeochemical processes have significant impacts on terrestrial ecosystem processes including POC flux and fate, nutrient balances, water quality budges, and aquatic biological functioning. Limited information is available on coupled biological and hydrologic processes in fluvial systems. This study investigates the mixture of biological and hydrologic processes in the benthic layer in order to understand POC cycling in the South Elkhorn system. Further, comprehensive modeling of POC flux in lowland systems has not been performed previously and the behavior of potentially controlling variables, such as hydrologic forcing and seasonal temperature regimes, is not well understood. Conceptual hydraulic and sediment transport models were simulated for the South Elkhorn. Based on data and model results it was concluded that during a hydrologic event, upland and bank sources produce high variability of POC sources. Likewise, over time, the density of hydrologic events influenced accrual of benthic algal biomass in the POC pool. Environmental variables such as temperature and light availability drove seasonal variations of POC in the streambed. Based on model estimates, around 0.29 metric tCkm-2yr-1 of POC is flushed from the system annually with 13 % coming from autochthonous algae.

In this study, the behavior of partially saturated coarse-grained soil packings was studied as a function of solid surface composition and aqueous salt concentration. The substrates tested were PTFE and soda lime glass, while the aqueous electrolytes consisted of NaCl and CaCl2 in differing concentrations. In order to gain a fundamental understanding of the unsaturated soils system, the two phase intersections of gas-liquid and solid-liquid were studied. The effect of varying aqueous electrolytes on the gas-liquid interface was analyzed by testing the surface tension while systematically varying the electrolyte concentration, while the effect on the solid/liquid/gas interface was studied by altering the surface hydrophobicity and aqueous solution concentration. In order to extend the analysis to soil fabrics, four ideal coarse gained packings were subdivided into their smallest repeating units. These repeating units, along with the measured dependence of the contact angles and surface tension on salt types, allowed an estimation of the equilibrium behavior of the capillary rise and tensile strength within a uniform coarse-grained fabric.

The modeling of transport behavior of charged particles carried out in our laboratory is based on classical continuum electro kinetic theory. It is applied to a variety of systems from small electrolyte ions to macromolecules including peptides, DNA and nanoparticles. Systems range from weakly charged particles to highly charged ones. Transport properties studied include conductance, electrophoresis, and diffusion. In this dissertation, the conductance of polyvalent electrolytes ions is studied both by a “small ion” model [R.M. Fuoss, L. Onsager, J. Phys. Chem. 61 (1957) 668] and “large ion” model [R.W. O’Brien, L.R. White, J. Chem. Soc. Faraday Trans. 2 (74) (1978) 1607)]. Also, the coarse-grained continuum primitive model is developed and used to characterize the titration and electrical conductance behavior of aqueous solutions of fullerene hexa-malonic acid, which is a highly charged electrolyte with an absolute valence charge as high as 12. Free solution electrophoresis is closely related to conductance and a coarse-grained bead modeling methodology, BMM, developed in the Allison’s laboratory starting in 2006, is generalized to characterize peptide systems with respect to the charge, conformation, and possibly specific interactions with components of the BGE. For weakly charged peptides, the electrostatic potential is treated at the level of linear Poisson-Boltzmann equation, which predicts the electrophoretic mobility with considerable accuracy [S. Allison, H. Pei, U. Twahir, H. Wu, J. Sep. Sci., 2010, 33(16):2430-2438], but fails for highly charged systems. A new nonlinear Poisson-Boltzmann, NLPB-BM procedure is developed and applied to the free solution electrophoretic mobility of low molecular mass oligolysines. The difficulty of highly charged systems is twofold: more complex handeling of electrostatics and accounting for the relaxation effect. Both issues are addressed in this dissertation. A related problem we investigated deals with the retarding influence of a gel on the rotational motion of a macromolecule. This is investigated within the framework of the Effective Medium (EM) model and is applied to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. Modeling is also compared with experiment.

Background: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text. Methods: We annotated 5397 disorder mentions from the ShARe corpus to SNOMED CT that were previously normalized as "CUI-less" in the "SemEval-2015 Task 14" shared task because they lacked a pre-coordinated mapping. Unlike the previous normalization method, we do not restrict concept mappings to a particular set of the Unified Medical Language System (UMLS) semantic types and allow normalization to occur to multiple UMLS Concept Unique Identifiers (CUIs). We computed annotator agreement and assessed semantic coverage with this method. Results: We generated the largest clinical text normalization corpus to date with mappings to multiple identifiers and made it freely available. All but 8 of the 5397 disorder mentions were normalized using this methodology. Annotator agreement ranged from 52.4% using the strictest metric (exact matching) to 78.2% using a hierarchical agreement that measures the overlap of shared ancestral nodes. Conclusion: Our results provide evidence that compositional concepts can increase semantic coverage in clinical text. To our knowledge we provide the first freely available corpus of compositional concept annotation in clinical text.

Single wall carbon nanotubes (SWCNTs) show a variety of unparalleled properties such as high electrical and thermal conductivity, high specific surface area (SSA) and a large stiffness under axial loads. One of the major challenges in tapping the vast potential of SWCNTs is to fabricate nanotube based macrostructures that retain the unique properties of nanotubes. Pristine SWCNT aerogels are highly porous, isotropic structures of nanotubes mediated via van der Waals (VDW) interactions at junctions. The mechanical behavior of such aerogels is examined in several experimental studies. However, it is necessary to supplement these studies with insights from simulations in order to develop a fundamental understanding of deformation behavior of SWCNT aerogels. In this study, the mechanical behavior of SWCNT networks is studied using a multi-scale modeling approach. The mechanics of an individual nanotube and interactions between few nanotubes are modeled using molecular dynamics (MD) simulations. The results from atomistic simulations are used to inform meso-scale and continuum scale finite element (FE) models. The deformation mechanism of pristine SWCNT networks under large compressive strain is deduced from insights offered by meso-scale simulations. It is found that the elasticity of such networks is governed by the bending deformation of nanotubes while the plastic deformation is governed by the VDW interactions between nanotubes. The stress response of the material in the elastic regime is dictated by the VDW stresses on nanotubes while in the plastic regime, both the VDW and axial deformation stresses on nanotubes drive the overall stress response. In this study, the elastic behavior of a random SWCNT network with any set of junction stiffness and network density is also investigated using FE simulations. It is found that the elastic deformation of such networks can be governed either by the deformation of the nanotubes (bending, axial compression) or deformation of the junctions. The junction stiffness and the network density determine the network deformation mode. The results of the FE study are also applicable to any stiff fiber network.

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