Physical Sciences and Mathematics Commons^™

A New Insight Into Fungal Cell Wall Architecture By Functional Genomics And Solid-State Nmr Along With Recent Advancements In Dynamic Nuclear Polarization For Analyzing Biomolecules, Arnab Chakraborty

LSU Master's Theses

This dissertation summarizes the findings related to the way by which supramolecular architecture of fungal cell wall changes with genetic mutation, dispensing genes responsible for biosynthesis of cell wall polysaccharides. This is necessary because without perfect picture of how supramolecular assembly changes with genetic mutation it is hard to assess new anti-fungal targets. Alongside this we have highlighted how recent advancement into Dynamic Nuclear Polarization (DNP) methods improved characterization of biomolecules both in case of labeled and unlabeled samples.

First study utilized Solid-state NMR (SSNMR) which is a non-destructive technique hence enabled us for the first time to deduce how …

Infrared Investigation Of Lithium Ion Electrolytes: Characterization Of Structure And Dynamics Via Linear And Nonlinear Spectroscopy, Jeramie Christopher Rushing

LSU Doctoral Dissertations

Lithium ion batteries are widely employed in energy storage, but the connection between the molecular interactions in their electrolytes and the macroscopic properties remains elusive. Across three vastly different electrolytes, speciation and dynamics were studied via linear and nonlinear infrared spectroscopy to shed light on this relationship. The impact of mixed solvation on ionic speciation was studied from the perspective of the anion, which revealed a significant energetic favorability for the formation of contact ion pairs in linear carbonate solvents over cyclic carbonates. Infrared spectroscopy and density functional theory calculations described a complete inversion of the speciation due to solvent …

Functional Structure Of Biomacromolecules In Plant Biomass Using Solid-State Nmr And Dynamic Nuclear Polarization, Alex Kipchirchir Kirui

LSU Doctoral Dissertations

This dissertation summarizes the recent findings on complex biomacromolecules in cell wall of plants and fungi which perform important roles in cell recognition, structural build up, and energy storage. Because of the technical difficulty in characterizing these biomacromolecules, which are often polymorphic and disordered in structure, the functional structure of these biomacromolecules remains elusive. In this dissertation, I present two solid-state nuclear magnetic resonance (ssNMR) and dynamic nuclear polarization (DNP) studies of carbohydrate-rich biosystems: the energy-rich plant biomass and disease-relevant, pathogenic fungi.

First, we have investigated the secondary cell wall of plant biomass which is a carbohydrate-rich biosystem using solid …

Non-Adiabatic Excited State Molecular Dynamics Using Ehrenfest And Modulated X-Ray Absorption In Titania, Alexander Matthew Meyer

LSU Doctoral Dissertations

This dissertation contains two separate sections aside from an introduction (Chapter 1): theory and methods (Chapter 2), time dependent density functional theory with Ehrenfest for excited state lifetimes in materials (Chapter 3), and simulated field modulated X-ray absorption in titania (Chapter 4).

Excited state lifetime in insulators and semiconductors can be difficult to compute using quantum chemistry due to their dense excited states. Non-radiative decay in these materials requires the use of non-adiabatic effects to dissipate energy through the means of electron-nuclear coupling such as coherent phonon generation. One method of approaching this challenge in these materials is using Ehrenfest …

Investigation On The Structure And Dynamics Of Lithium Ion Solvation Shell By Linear And Non-Linear Infrared Spectroscopy, Xiaobing Chen

LSU Doctoral Dissertations

Lithium ion battery (LIB) is a lightweight, rechargeable and powerful battery that is used widely from mobile phones to laptops to electric cars. It has many exceptional advantages such as high energy density, high output power, relatively low self-discharge, etc. However, it has some disadvantages such as safety issues, capacity loss, and expensive manufacture. LIB is composed of three main components: electrolytes, positive and negative electrodes. Researchers have been working on improving the performance of LIB for the past decade, but only a few have focused on investigating the electrolytes at the molecular level. In addition, the molecular mechanisms behind …

Adsorption And Transport Of Colloids At Interface And In Bulk, Jingyun Lee

LSU Doctoral Dissertations

Colloids are suspensions of microscopic insoluble particles dispersed in a continuum phase such as liquid or gas. Colloids are found in our everyday life from food and cosmetic industries to pharmaceutical and biomedical applications. Depending on a global minimum of the free-energy landscape, colloidal suspensions can be classified as two major classes: equilibrium or active colloidal system. This Ph.D dissertation presents strategies to engineer equilibrium self-assembled structures and out-of-equilibrium active matter using various interparticle forces.

First, we introduce the means to promote the equilibrium self-assembled structures driven by adsorption of colloids at interface. Typically, adsorption of colloids at interface is …

Investigation Of The Structure And Dynamics Of Novel Battery Electrolytes By Utilizing Multidimensional Infrared Spectroscopic Techniques, Susith Rajitha Abeythunga Galle Kankanamge

LSU Doctoral Dissertations

Novel battery technologies are being developed due to the high global demand for energy in many fields where different specifications are required. The battery electrolyte provides a medium for ions to diffuse between electrodes and its composition determines the compatibility with the electrode pair. While many works focus on characterizing novel electrolyte systems to advance new batteries, the understanding of the microscopic structure and dynamics of speciations present in these electrolytes is limited. Many experiment methods have obtained incomplete time-averaged structure information due to lack of instrumental time resolution compared to the molecular intrinsic time sales of electrolytes that range …

Structure And Dynamics Of Phospholipid Vesicles And The Dependence On Nanoscale Interactions With Molecules Of Varying Complexity, Lakshapathy Widanelage Judith Upeka De Mel

LSU Doctoral Dissertations

In this dissertation, molecular interactions and changes imposed by nano-scale structures on phospholipid vesicles were investigated. 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) large unilamellar vesicles (LUVs) were used as the model system. Understanding changes of the bilayer structure, interfacial properties, lipid dynamics, and self-assembly, allows bridging relationships between biological cell membrane structure and dynamics to cellular functionalities. For example, membrane curvature changes are linked to membrane protein functions, although the exact mechanisms of control are not yet understood. Moreover, the knowledge gained from vesicle models allows exploring novel strategies for drug delivery applications. To achieve this, DOPC LUVs were synthesized and characterized by a …

Computational Investigations Of Battery Electrolytes, Ke Li

LSU Doctoral Dissertations

In this dissertation, the structure and dynamics of battery electrolytes were investigated using atomistic molecular dynamics (MD) simulations. Battery electrolytes play a key role in transporting ions between the cathode and anode. The chemical stability and ionic conductivity of electrolytes influence battery performance. In order to design better electrolytes, one needs an understanding of the relationship between electrolyte structure, dynamics, and bulk properties. To bridge the gap between the macroscopic phenomenon and the hidden molecular physics, in the first project we focused on probing an ether-based electrolyte, chosen for its relevance in sodium-based batteries. Through studying the impact of concentration …

Adsorption And Reconfiguration Of Amphiphiles At Silica-Water Interfaces: Role Of Electrostatic Interactions, Van Der Waals Forces And Hydrogen Bonds, Yao Wu

LSU Doctoral Dissertations

The ability to explore and predict metastable structures of hybrid self-assemblies is of central importance for the next generation of advanced materials with novel properties. As compared to their thermodynamically stable forms, the kinetically stabilized materials show improved functionality potentially over their stable counterparts. The self-assembly processes usually originate from weak intermolecular interactions, involving a dynamic competition between attractive and repulsive interactions. These weak forces, including van der Waals (vdW), electrostatic interaction and the hydrogen bonding (H-bonding), can be tuned by external stimuli, e.g., confinement, temperature and ionization, and consequently driving hybrid materials into different configurations. It is challenging to …

Effect Of Oxidation Level On The Interfacial Water At The Graphene Oxide-Water Interface: From Spectroscopic Signatures To Hydrogen-Bonding Environment, Rolf David, Aashish Tuladhar, Le Zhang, Christopher Arges, Revati Kumar

Faculty Publications

The interfacial region of the graphene oxide (GO)-water system is nonhomogenous due to the presence of two distinct domains: an oxygen-rich surface and a graphene-like region. The experimental vibrational sum-frequency generation (vSFG) spectra are distinctly different for the fully oxidized GO-water interface as compared to the reduced GO-water case. Computational investigations using ab initio molecular dynamics were performed to determine the molecular origins of the different spectroscopic features. The simulations were first validated by comparing the simulated vSFG spectra to those from the experiment, and the contributions to the spectra from different hydrogen bonding environments and interfacial water orientations were …

Second Harmonic Generation Spectroscopy And Microscopy Of Liposomes, Nanoparticles, And Cells, Prakash Hamal

LSU Doctoral Dissertations

Second harmonic generation (SHG) is used to investigate the factors that impact nanoparticle-based drug-delivery applications. In the first study, molecular adsorption and transport kinetics of a positively-charged dye, malachite green isothiocyanate (MGITC), is characterized at the surface of different colloidal liposomes in water using SHG spectroscopy. The molecular interactions of MGITC is compared to our previous investigations with malachite green (MG). In comparison to MG, MGITC demonstrates stronger adsorption and faster transport through lipid membranes. Correspondingly, the SHG experimental results are in excellent agreement with the molecular dynamics (MD) simulations results. A key finding illustrates the importance of functional groups, …

Probing The Surface Acidity Of Supported Aluminum Bromide Catalysts, Md Ashraful Abedin, Swarom Kanitkar, Nitin Kumar, Zi Wang, Kunlun Ding, Graham Hutchings, James J. Spivey

Faculty Publications

Solid acid catalysis is an important class of reactions. The principal advantages of solid acid catalysts as compared to their corresponding fluid acids include minimal waste and ease of product separation. One type of these catalysts is based on aluminum bromide (Al2Br6), which is a stronger Lewis acid than Al2Cl6. In this report, Al(2)Br(6)is grafted on commercial mesoporous silica (CMS), SBA-15 and silica gel to create a solid catalyst similar to the silica-supported Al(2)Cl(6)superacid. These supported Al(2)Br(6)catalysts were characterized by NH3-Temperature Programmed Desorption (TPD), pyridine Diffuse Reflectance for Infrared Fourier Transform Spectroscopy (DRIFTS) and Magic Angle Spinning Nuclear Magnetic Resonance …

Solvation Structures And Dynamics Of Small Molecules: Experimental And Computational Studies Using Carbonyl Vibrational Modes As Probe, Xiaoliu Zhang

LSU Doctoral Dissertations

Solutions are ubiquitous in both the global environment and the human body, and play a significant role in scientific research and industrial production. The structures and dynamics of solutions have been studied for centuries. However, conventional experimental methods, whose intrinsic measuring time is on the order of nanoseconds to microseconds, could not detect the fast dynamics taking place in the solution on the timescale of femto- and pico-second. In this dissertation, the ultrafast two-dimensional infrared (2DIR) spectroscopy was applied to characterize the structure and dynamics in three different types of solutions on the sub-picosecond timescale. Linear Fourier transform infrared spectroscopy …

Behavior Of Iron Species And Free Radicals In Ambient Pm2.5 And Pm Surrogates, Cholena Russo Ren

LSU Doctoral Dissertations

Air pollution, consisting of ambient particulate matter (PM), has been a rising health concern to the public. PM contains free radicals and have been known to damage human cells; however, their free radical chemistry is not well understood. This study utilized various vacuum and/or heat treatments to study free radical behavior in PM_2.5 (particulate matter with an aerodynamic diameter of 2.5 mm or less) and PM surrogates and simulated sunlight effects on PM_2.5. To mimic PM, iron-silica catalysts (i.e. PM surrogates) were synthesized and real-world ambient PM_2.5 was selected. The free radicals in PM_{2.5 …}

Modeling And Simulations Of Peptoids, Pu Du

LSU Doctoral Dissertations

Polypeptoids, or poly-N-substituted glycines, are a class of sequence defined polymers that are structural mimics of polypeptides. Polypeptoids currently have received a growing interest due to their improved thermal stability, larger chemical diversity, and easier synthetic pathways as compared to peptides. Their lack of backbone hydrogen bonding and stereochemistry coupled with their easily tunability make them an ideal prototypical model system to study the effect of secondary/non-covalent interactions on self-assembly in solution. In order to develop a molecular level understanding of the effect of secondary interactions on polypeptoid self-assembly, systematic studies were carried out using molecular dynamics simulations on several …

Ultrafast And Real-Time Dynamics Of Nanomaterials Studied By Advanced Spectroscopic Techniques, Jeewan Chaminda Ranasinghe

LSU Doctoral Dissertations

Ultrafast and nonlinear spectroscopies are used to study excited-state dynamics and monitor real-time growth dynamics of different types of nanomaterials. In the first study, the growth dynamics of colloidal gold-silver core-shell nanoparticles are studied using in situ second harmonic generation and extinction spectroscopy. The growth lifetimes are studied under different reaction conditions, resulting in different silver shell thicknesses, with spectral comparisons to finite-difference time-domain calculations. The results are consistent with a three-step growth process. During the first step of the nanoparticle growth reaction, rough and uneven surfaces are formed rapidly giving rise to plasmonic hot spots with corresponding broad, red-shifted …

Modeling Chemical Reactivity In Aqueous And Organic Systems: From Electronic Structure Methods To Force Field Development, Caitlin Gibson Bresnahan

LSU Doctoral Dissertations

Modeling reactivity in chemical systems has evolved dramatically in line with the capabilities of modern computing. Despite the advances in computational ability, the level in which one can model a system depends on a number of factors including the region of reactivity, size of the system, level of sophistication required in the molecular description, and so on. Electronic structure methods allow for a detailed description of the potential energy surface and inherently include all essential physics required for reactivity to occur, however these methods are limited by their computational expense. On the other hand, force fields allow for an atomistic …

Calculation Guided Rational Design And Synthesis Of Novel Cationic Fluorescent Meso–Pyridinium Bodipys For Bio-Imaging, Daniel J. Lamaster

LSU Doctoral Dissertations

Chapter 1 contains a brief overview of the history, synthesis, and properties of BODIPY dyes as well as that of the biomedical applications of bio-imaging and photodynamic therapy. Additionally, an overview of the theoretical framework of density functional theory and its time-dependent variant are provided. In Chapter 2, the effects of structural modification on the electronic structure and electron dynamics of cationic meso-(4-pyridyl)-BODIPYs were investigated. A library of 2,6-difunctionalized meso-(4-pyridyl)-BODIPYs bearing various electron-withdrawing substituents was designed and DFT calculations were used to model the redox properties, while TDDFT was used to determine the effects of functionalization on the excited …

Ultrafast And Nonlinear Spectroscopy Of Nanomaterials, Rami Anthony Khoury

LSU Doctoral Dissertations

Ultrafast and nonlinear spectroscopies are implemented in the investigation of excited-state dynamics and structural properties of materials and nanomaterials. In the first study, the excited-state dynamics of size-dependent colloidal TiO₂-Au nanocomposites are investigated using ultrafast transient absorption spectroscopy. The dynamics corresponding to the plasmon depletion band are characterized by electron-phonon and phonon-phonon coupling lifetimes that are observed to be independent of the gold nanocluster shell thickness. The excited-state dynamics corresponding to the interband transition of gold is also spectrally overlapped with the interfacial electron transfer lifetime, which is shown to decrease as the nanocluster shell thickness increases. In …

Accelerated Broadband Spectra And Attosecond Charge Migration Simulations Using Real-Time Time-Dependent Density Functional Theory, Adam S. Bruner

LSU Doctoral Dissertations

In this dissertation, the calculations of light-matter interactions offer insight into the structure and dynamical response of electrons in molecular systems. Such information is useful for characterizing molecules, electronic structure, photochemistry, photomaterials, and a host of other applications. In the first part of this work, simulations of broadband absorption spectra are accelerated by the use of Pad´e approximanants of Fourier Transforms and dipole decomposition. Electronic absorption spectra from valence and core levels are obtained using time-dependent methods and compared to results from established perturbative techniques. In addition, core level absorption spectra are calculated for a nickel porphyrin and shown to …

Investigation Of Structure And Dynamics Of Deep Eutectic Solvent Using Infrared Spectroscopy, Yaowen Cui

LSU Doctoral Dissertations

Deep Eutectic Solvents (DES) are liquid mixtures prepared from solids. As a new class of green solvents, DES not only share many properties with ionic liquids, such as low volatility, conductivity, tailorable constituents, but also have some advantages over ionic liquids, like easier preparation, safe and inexpensive materials, biodegradability, low toxicity, and excellent solubility. Because of those attractive properties, DES has been studied in many scientific and engineering fields. However, compared with the great number of studies of the application, many questions about structure and dynamics of DES are unanswered. To shed light on the mystery of solvent or solvation …

Innovative Monte Carlo Methods For Sampling Molecular Conformations, Aliasghar Sepehri

LSU Doctoral Dissertations

Sampling molecular conformations is an important step in evaluating physical, mechanical, hydrodynamic, and optical properties of flexible molecules especially polymers. One powerful method for this purpose is configurational-bias Monte Carlo in which one random segment of a molecule is chosen, all segments toward one random end are removed, and then regrown segment by segment to produce a new geometry to be accepted/rejected according to probability laws. The advantage of this method is the ability to generate acceptable conformations that are favorable for intra- and intermolecular energies to save computational costs. However, when there are several interdependent energetic terms, trial generation …

Coupled Plasmon/Molecule Dynamics Near Core-Shell Nanoparticles: Synthesis, Ultrafast Characterization, And Quantum/Classical Modeling, Holden Tyler Smith

LSU Doctoral Dissertations

In this dissertation, the resonance coupling of chromaphoric dyes adsorbed on the surface of plasmonic nanoparticles (NPs) are investigated using a combined theoretical and experi- mental approach. Colloidal gold, gold-silver core-shell, silver-gold core-shell, and gold-silver- gold core-shell-shell NPs are considered. These NPs are thiolated with mercaptosuccinic acid, and malachite green dyes are adsorbed to the surface of the nanoparticle (NP) via elec- trostatic interactions. Second harmonic generation is used to determine the surface to the isotherm of the molecular dyes to the colloidal nanoparticle surface. Adsorption isotherms show that the SHG intensity increases as the concentration of dye increases, reaching …

Nanoparticle-Based Drug-Delivery Systems Studied By Second Harmonic Generation, Raju Ram Kumal

LSU Doctoral Dissertations

Second harmonic generation (SHG) is used to study different types of colloidal nanoparticle drug-delivery systems. The surface charge density, electrostatic surface potentials, and ion adsorptions of 50 nm colloidal gold nanoparticle samples coated with mercaptosuccinic acid are determined using SHG measurements under varying NaCl and MgCl₂ concentrations in water. Numerical solutions to the spherical Poisson-Boltzmann equation are fit to the SHG results to account for the nanoparticle surface curvature and ion adsorption to the Stern layer interface, showing excellent agreement with electrophoretic mobility measurements. In another study, nanoparticles of gold, silver and polystyrene are functionalized with microRNA using a …

Characteristic Length Scales Of The Secondary Relaxations In Glass-Forming Glycerol, Sudipta Gupta, Eugene Mamontov, Niina Jalarvo, Laura Stingaciu, Michael Ohl

Faculty Publications

We investigate the secondary relaxations and their link to the main structural relaxation in glass-forming liquids using glycerol as a model system. We analyze the incoherent neutron scattering signal dependence on the scattering momentum transfer, Q , in order to obtain the characteristic length scale for different secondary relaxations. Such a capability of neutron scattering makes it somewhat unique and highly complementary to the traditional techniques of glass physics, such as light scattering and broadband dielectric spectroscopy, which provide information on the time scale, but not the length scales, of relaxation processes. The choice of suitable neutron scattering techniques depends …