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Title: DERIVING THE DENSITY OF STATES FOR GRANULAR CONTACT FORCES.
Creator: Metzger, Philip, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: The density of single grain states in static granular packings is derived from first principles for an idealized yet fundamental case. This produces the distribution of contact forces P_f(f) in the packing. Because there has been some controversy in the published literature over the exact form of the distribution, this dissertation begins by reviewing the existing empirical observations to resolve those controversies. A method is then developed to analyze Edwards' granular contact force...
Show moreThe density of single grain states in static granular packings is derived from first principles for an idealized yet fundamental case. This produces the distribution of contact forces P_f(f) in the packing. Because there has been some controversy in the published literature over the exact form of the distribution, this dissertation begins by reviewing the existing empirical observations to resolve those controversies. A method is then developed to analyze Edwards' granular contact force probability functional from first principles. The derivation assumes Edwards' flat measure -- a density of states (DOS) that is uniform within the metastable regions of phase space. A further assumption, supported by physical arguments and empirical evidence, is that contact force correlations arising through the closure of loops of grains may be neglected. Then, maximizing a state-counting entropy results in a transport equation that can be solved numerically. For the present it has been solved using the "Mean Structure Approximation," projecting the DOS across all angular coordinates to more clearly identify its predominant features in the remaining stress coordinates. These features are: (1) the Grain Factor related to grain stability and strong correlation between the contact forces on the same grain, and (2) the Structure Factor related to Newton's third law and strong correlation between neighboring grains. Numerical simulations were then performed for idealized granular packings to permit a direct comparison with the theory, and the data including P_f(f) were found to be in excellent agreement. Where the simulations and theory disagree, it is primarily due to the coordination number Z because the theory assumes Z to be a constant whereas in disordered packings it is not. The form of the empirical DOS is discovered to have an elegant, underlying pattern related to Z. This pattern consists entirely of the functional forms correctly predicted by the theory, but with only slight parameter changes as a function of Z. This produces significant physical insight and suggests how the theory may be generalized in the future.
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Date Issued: 2005
Identifier: CFE0000381, ucf:46325
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000381

Title: SIMULATION STUDIES OF SELF-ASSEMBLY AND PHASE DIAGRAMOF AMPHIPHILIC MOLECULES.
Creator: Bourov, Geuorgui, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: The aim of this dissertation is to investigate self-assembled structures and the phase diagram of amphiphilic molecules of diverse geometric shapes using a number of different computer simulation methods. The semi-realistic coarse-grained model, used extensively for simulation of polymers and surfactant molecules, is adopted in an off-lattice approach to study how the geometric structure of amphiphiles affects the aggregation properties. The results of simulations show that the model system...
Show moreThe aim of this dissertation is to investigate self-assembled structures and the phase diagram of amphiphilic molecules of diverse geometric shapes using a number of different computer simulation methods. The semi-realistic coarse-grained model, used extensively for simulation of polymers and surfactant molecules, is adopted in an off-lattice approach to study how the geometric structure of amphiphiles affects the aggregation properties. The results of simulations show that the model system behavior is consistent with theoretical predictions, experiments and lattice simulation models. We demonstrate that by modifying the geometry of the molecules, self-assembled aggregates are altered in a way close to theoretical predictions. In several two and three dimensional off-lattice Brownian Dynamics simulations, the influence of the shape of the amphiphilic molecules on the size and form of the aggregates is studied systematically. Model phospholipid molecules, with two hydrophobic chains connected to one hydrophilic head group, are simulated and the formation of stable bilayers is observed. In addition, (practically very important) mixtures of amphiphiles with diverse structures are studied under different mixing ratios and molecular structures. We find that in several systems, with Poisson distributed chain lengths, the effect on the aggregation distribution is negligible compared to that of the pure amphiphilic system with the mean length of the Poisson distribution. The phase diagrams of different amphiphilic molecular structures are investigated in separate simulations by employing the Gibbs Ensemble Monte Carlo method with an implemented configurational-bias technique. The computer simulations of the above mentioned amphiphilic systems are done in an area where physics, biology and chemistry are closely connected and advances in applications require the use of new theoretical, experimental and simulation methods for a better understanding of their self-assembling properties. Obtained simulation results demonstrate the connection between the structure of amphiphilic molecules and the properties of their thermodynamically stable aggregates and thus build a foundation for many applications of the remarkable phenomena of amphiphilic self-assembly in the area of nanotechnology.
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Date Issued: 2005
Identifier: CFE0000695, ucf:46491
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0000695

Title: The safe removal of frozen air from the annulus of a liquid hydrogen storage tank.
Creator: Krenn, Angela, Bhattacharya, Aniket, Youngquist, Robert, Vasu Sumathi, Subith, University of Central Florida
Abstract / Description: Large Liquid Hydrogen (LH2) storage tanks are vital infrastructure for NASA. Eventually, air may leak into the evacuated and perlite filled annular region of these tanks. Although the vacuum level is monitored in this region, the extremely cold temperature causes all but the helium and neon constituents of air to freeze. A small, often unnoticeable pressure rise is the result. As the leak persists, the quantity of frozen air increases, as does the thermal conductivity of the insulation system...
Show moreLarge Liquid Hydrogen (LH2) storage tanks are vital infrastructure for NASA. Eventually, air may leak into the evacuated and perlite filled annular region of these tanks. Although the vacuum level is monitored in this region, the extremely cold temperature causes all but the helium and neon constituents of air to freeze. A small, often unnoticeable pressure rise is the result. As the leak persists, the quantity of frozen air increases, as does the thermal conductivity of the insulation system. Consequently, a notable increase in commodity boiloff is often the first indicator of an air leak. Severe damage can then result from normal draining of the tank. The warming air will sublimate which will cause a pressure rise in the annulus. When the pressure increases above the triple point, the frozen air will begin to melt and migrate downward. Collection of liquid air on the carbon steel outer shell may chill it below its ductility range, resulting in fracture. In order to avoid a structural failure, as described above, a method for the safe removal of frozen air is needed. Two potential methods for air removal are evaluated here. The first method discussed is the connection of a vacuum pump to the annulus which provides pumping in parallel with drainage of LH2. The goal is to keep the annular pressure below the triple point so that the air continues to sublimate, thus eliminating the threat that liquefaction poses. The second method discussed is the application of heat to the bottom of the outer tank during tank drain. Though liquefaction in the annular space will occur, the goal of the heater design is to keep the outer shell above the embrittlement temperature, so that cracking will not occur.In order to evaluate these methods, it is first necessary to characterize some the physical properties and changes that take place in the system. A thermal model of the storage tank was created in SINDA/FLUINT (C(&)R Technologies, 2014) to identify locations where air can freeze. This model shows the volume that is capable of freezing air under varying conditions. It is also necessary to characterize the changes in thermal conductivity of perlite which has nitrogen frozen into its interstitial spaces. The details and results of an experiment designed for that purpose is outlined. All data, including operational data from existing LH2 tanks, is compiled and a physics-based evaluation of the two proposed air removal techniques is performed.Due to small pumping capacities at low pressure and the large quantity of air inside the annulus, the pumping option is not deemed feasible. It would take many years to remove a significant amount of air by pumping while maintaining the annular pressure below the necessary triple point. Application of heating devices is a feasible option. For a specific case, it is shown that approximately 105 kilowatts of power would be required to vaporize the air in the annulus and keep the temperature of the outer tank wall above the freezing point of water. Several engineering solutions to accomplish this are also discussed. There are many unknowns and complexities in addressing the problem of safely removing frozen air from the annulus of an LH2 storage sphere. The work that follows utilized: research, modeling, experimentation, analysis, and data from existing tanks to arrive at possible solutions to the problem. Heating solutions may be implemented immediately and could result in significant savings to the user.
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Date Issued: 2015
Identifier: CFE0005969, ucf:50766
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005969

Title: Translocation of a semiflexible polymer through a nanopore.
Creator: Adhikari, Ramesh, Bhattacharya, Aniket, Chen, Bo, Kokoouline, Viatcheslav, Hernandez, Florencio, University of Central Florida
Abstract / Description: The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology....
Show moreThe transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length and rigidity of the chain, viscosity of the solvent, and diameter of the nanopore, we provide a detailed description of the translocation process. Our studies are relevant for fundamental understanding of the translocation process which is essential for making accurate nano-pore based devices.
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Date Issued: 2015
Identifier: CFE0005915, ucf:50830
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005915

Title: Conformations and Dynamics of Semi-Flexible Polymers.
Creator: Huang, Aiqun, Bhattacharya, Aniket, Kokoouline, Viatcheslav, Tatulian, Suren, Campiglia, Andres, University of Central Florida
Abstract / Description: In this dissertation, we investigate the conformations, transverse fluctuations and dynamics of two-dimensional (2D) semi-flexible polymers both in the bulk and under channel confinement. We present unified scaling relations in regard to various quantities of interest for a broad range of combinations of chain length and chain stiffness using Langevin dynamics simulation. We also present a three-dimensional (3D) heterogeneous semi-flexible chain model for a double stranded DNA (dsDNA). Our...
Show moreIn this dissertation, we investigate the conformations, transverse fluctuations and dynamics of two-dimensional (2D) semi-flexible polymers both in the bulk and under channel confinement. We present unified scaling relations in regard to various quantities of interest for a broad range of combinations of chain length and chain stiffness using Langevin dynamics simulation. We also present a three-dimensional (3D) heterogeneous semi-flexible chain model for a double stranded DNA (dsDNA). Our model not only confirms the established findings for homogeneous dsDNA, but also predicts new physical phenomenon for heterogeneous dsDNA. The problems studied in this dissertation are relevant to analysis of the conformations and dynamics of biopolymers (such as DNA) in living organisms, and also offer insights for developing devices which operate on the single-molecule level.In particular, we present a unified description for the dynamics of building-blocks (monomers) of a semi-flexible chain. We consider the full range of flexibility from the case where the chain is fully flexible (no stiffness at all) to the case where the chain behaves like a rod (infinite stiffness). Our theory predicts qualitatively different sub-diffusive regimes for the monomer dynamics originating from the chain stiffness by studying the mean square displacement (MSD) of the monomers before the chain dynamics become purely diffusive.For the conformations in the bulk, we present results confirmed and agreed by two completely different models of semi-flexible polymers, with one of which is the bead-spring model (studied by Langevin dynamics) in the continuum space, the other (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles are possible. We point out the universal features of chain conformations and fluctuations which are independent of the models.For the conformations under channel confinement, we discover qualitatively different conformations and dynamics of the chain as a function of the channel width and chain stiffness, and show how globule like shapes ((")de Gennes blobs(")) for more flexible chains continuously go over to shapes in the form of deflections from the wall ((")Odijk limit(")) for more stiff chains. We provide theoretical arguments how these regimes occur and interpolate among each other as one varies different parameters of the model. We also demonstrate the effect of physical dimensions (either 2D or 3D) on these regimes and argue that since in 2D the excluded volume (EV) effect is more severe compared to 3D, certain regimes do not exist in 2D.Finally, we study a model of a dsDNA , where both base-pairing and base-stacking interactions are accounted for albeit at a low computational cost compared to the other existing models. Our model correctly recovers the stiffness for dsDNA and ssDNA at different temperatures. Under most conditions of interest, a dsDNA can locally denature and form bubbles due to thermal fluctuations. At a critical temperature, a dsDNA undergoes a phase transition, in which the two strands of dsDNA completely melt to two single strands (two ssDNA). By considering EV interactions and calculating the bubble size distribution, recent studies have shown that this denaturation process is a first order transition. We show that for a homogeneous dsDNA made of only AT or GC pairs, our simulation results agree with the previous conclusion of first order transition, however, for sequences of periodic AT and GC regions, when the periodic size is relatively large compared to the sequence length, we show that the bubble size distribution exhibits peaks expressing the sequence pattern, and more importantly, the denaturation is no longer a first order transition.All these studies reported in the dissertation are relevant to the physics of living systems.
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Date Issued: 2016
Identifier: CFE0006464, ucf:51429
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006464

Title: Spin and Charge Transport in Graphene Based Devices.
Creator: Anguera Antonana, Marta, Del Barco, Enrique, Peale, Robert, Bhattacharya, Aniket, Schoenfeld, Winston, University of Central Florida
Abstract / Description: The present dissertation is comprehended in two main parts. The first part is focused on understanding the mechanisms behind spin current to charge current interconversion (i.e. the spin Hall angle), where the spin current is generated by means of spin pumping. The measurement of a positive spin Hall angle of magnitude 0.004 in Uranium is reported in Chapter 2. These results support the idea that the electronic configuration may be at least as important as the atomic number in governing spin...
Show moreThe present dissertation is comprehended in two main parts. The first part is focused on understanding the mechanisms behind spin current to charge current interconversion (i.e. the spin Hall angle), where the spin current is generated by means of spin pumping. The measurement of a positive spin Hall angle of magnitude 0.004 in Uranium is reported in Chapter 2. These results support the idea that the electronic configuration may be at least as important as the atomic number in governing spin Hall effects. In Chapter 3, the design of a spintronics device designed to interconvert charge and spin currents in CVD graphene is presented. The second part of the thesis is centered in the study of transport through single molecules with the use of three-terminal devices. The first evidence of a molecular double quantum dot is detailed in Chapter 5. The conclusions are supported by self-assembled monolayers (SAMs) and single-electron transistors (SETs) measurements. Using gold electrodes for SETs measurements has its disadvantages, two of the main ones being: the junctions are not stable at room temperature and it does not allow for transport measurements in the presence of light. Graphene electrodes, on the other hand, have been reported to be stable at temperatures above room temperature and have no absorption in the visible range. Along those lines, the development of a multilayer graphene-based SET is reported in Chapter 6. Finally, a new technique, based on CVD graphene transistors, that will allow three-terminal measurements on an STM is described in Chapter 7.
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Date Issued: 2017
Identifier: CFE0006715, ucf:51897
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006715

Title: Nanoscale Characterization and Mechanism of Electroless Deposition of Silver Metal.
Creator: Grabill, Christopher, Kuebler, Stephen, Beazley, Melanie, Zou, Shengli, Frazer, Andrew, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: This dissertation is an investigation of the nanoscale characteristics and mechanism of electrolessly deposited silver metal seeded by gold nanoparticles. The process of growing seed-nanoparticles on a polymer surface was studied. Several bifunctional amines and organic reducing agents were used to explore how these chemical factors affect the size and distribution of gold nanoparticles formed at the interface. The nanoparticles were characterized by transmission electron microscopy (TEM) and...
Show moreThis dissertation is an investigation of the nanoscale characteristics and mechanism of electrolessly deposited silver metal seeded by gold nanoparticles. The process of growing seed-nanoparticles on a polymer surface was studied. Several bifunctional amines and organic reducing agents were used to explore how these chemical factors affect the size and distribution of gold nanoparticles formed at the interface. The nanoparticles were characterized by transmission electron microscopy (TEM) and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). An electroless deposition (ED) bath developed by Danscher was selected to study electroless deposition of silver in detail. The chemical species in the bath were varied to determine how concentration, nature of the carboxylate buffering species, and the presence and absence of gum arabic affect the morphology of silver metal formed by ED and the overall rate of deposition at the surface. The kinetics of deposition using the Danscher bath was studied in detail to elucidate the mechanism of ED. Knowledge generated from this investigation can be used to expand applications of silver ED where strict control over the nanoscale morphology of the deposited metal is required to obtain specific chemical and physical properties.
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Date Issued: 2018
Identifier: CFE0007009, ucf:52051
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007009

Title: Detection of Mercury Through Surface Plasmon Resonance of Immobilized Gold Nanorods.
Creator: Trieu, Khang, Campiglia, Andres, Rex, Matthew, Heider, Emily, Frazer, Andrew, Harper, James, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: Mercury is a known environmental pollutant that can damage the brain, heart, kidney and lungs upon exposure. Emissions from fossil fuel plants can release mercury into the air, where it can settle into the water supply and be exposed to human and aquatic life. The use of gold nanorods functionalized on solid substrates as a mercury sensor in tap water samples is investigated herein. The functionalization of the substrates involves the physical immobilization of the nanorods onto the solid...
Show moreMercury is a known environmental pollutant that can damage the brain, heart, kidney and lungs upon exposure. Emissions from fossil fuel plants can release mercury into the air, where it can settle into the water supply and be exposed to human and aquatic life. The use of gold nanorods functionalized on solid substrates as a mercury sensor in tap water samples is investigated herein. The functionalization of the substrates involves the physical immobilization of the nanorods onto the solid surface through the use of (3-mercaptopropyl)trimethoxysilane (MPTMS). The immobilization of the nanorods drastically increases their stability, allowing for use in complicated sample matrices. When gold nanorods are exposed to mercury in aqueous samples, their amalgamation to mercury metal causes a reduction of the effective aspect ratio of the nanoparticles and a blue shift of their maximum longitudinal surface plasmon resonance (SPR) absorption wavelength. Quantitative analysis is made possible due to the linear correlation that exists between the concentration of mercury and the wavelength shift of the maximum SPR absorption wavelength. In order to achieve the quantitative amalgamation of Hg (II) with the nanorods, it is necessary to reduce the mercury ions to mercury metal, which is accomplished herein via chemical or electrochemical processes. Chemical reduction of mercury was been carried out with a strong reducing agent, specifically sodium borohydride. Electrochemical reduction has been accomplished with gold nanorods immobilized on Indium Tin Oxide (ITO) substrates. Mercury determination in tap water using the immobilized gold nanorods was successfully conducted, with further experiments on improving selectivity with potential control, and improving sensitivity through flow injection analysis.
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Date Issued: 2019
Identifier: CFE0007544, ucf:52604
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007544

Title: Transient CFD analysis of autorotation using hybrid LES and adaptive mesh morphing techniques.
Creator: Coronado Domenge, Patricia, Das, Tuhin, Kassab, Alain, Kumar, Ranganathan, Leishman, J., Bhattacharya, Aniket, University of Central Florida
Abstract / Description: Large-Eddy Simulation (LES) based turbulence modeling is a developing area of research in Fluid-Structure Interaction (FSI). There is considerable scope for further scientific research in this field and this dissertation aims to extend it to the study of flow-induced motion. The emphasis of this work is on autorotation, an important category of flow-induced motion that is commonly seen in energy applications such as wind turbines and in aviation applications such as the autogyro. In contrast...
Show moreLarge-Eddy Simulation (LES) based turbulence modeling is a developing area of research in Fluid-Structure Interaction (FSI). There is considerable scope for further scientific research in this field and this dissertation aims to extend it to the study of flow-induced motion. The emphasis of this work is on autorotation, an important category of flow-induced motion that is commonly seen in energy applications such as wind turbines and in aviation applications such as the autogyro. In contrast to existing works on FSI that typically assume prescribed motion of structures in a flow field, this research develops LES based FSI studies for large-scale flow-induced motions as seen in autorotation. The uniqueness of the formulation and modeling approach lies in the development of a numerically stable computational scheme that incorporates a moving and morphing mesh structure. The method is first demonstrated for the autorotation of a square flat plate and then extended to a rotor structure similar to that of a helicopter.In order to simulate an autorotating square flat plate, a coupled Computational Fluid Dynamics (CFD) - Rigid Body Dynamics (RBD) model is proposed, employing the delayed-detached-eddy simulation (DDES) and the Smagorinsky turbulence models to resolve subgrid-scale stresses (SGS). The plate is allowed to spin freely about its center of mass. Computational results are compared to experimental measurements and Reynolds Average Navier-Stokes (RANS) simulations found in the literature. When compared to RANS, the results from the LES models provide better predictions of the pressure coefficient. Moreover, LES accurately captures the transient behavior of the plate, and close correspondence is found between the predicted and measured moment coefficients. The qualitative prediction of vortex structures and the quantitative computation of pressure coefficients are in good agreement with experimental results. Hybrid models, such as improved Delayed-Detached-Eddy Simulation (iDDES), are shown to provide very similar results to those of pure LES. Therefore hybrid models are found to be a good alternative to use for the simulation of FSI in autorotation, saving valuable computational time . The iDDES method combines both RANS and LES, dividing the flow domain into LES far away from a solid wall and RANS near a solid wall, overcoming the computational costs of pure LES.Encouraging results from this effort prompted the extension to a realistic scenario, namely the autorotation of a flapping-blade rotor in a prevailing wind field. A coupled CFD - Multi Body Dynamics (MBD) model is developed to study the complex FSI of an autorotating 3-blade rotor, similar to that of a helicopter, employing the iDDES turbulence model. In addition to the rotor being allowed to spin freely about its axis, each of the individual blades is free to rotate about hinges at the root. This adds degrees of freedom to the kinematics of the rotor and necessitates localized mesh morphing around the blades to capture the FSI with accuracy. The model is validated against experimental data and shows excellent agreement. The experimental apparatus consists of a flapping blade rotor and a fixture used to mount it at different angles of incidence with respect to the wind field. The rotor is instrumented with a DC motor that is operated in generator mode. The setup is dual-purpose, providing speed measurement using the motor's back-emf and regenerative braking by varying the current draw. Overall, the presented research can help obtain accurate values of aerodynamic parameters at a high spatial resolution that would be otherwise difficult to acquire in experiments. Ultimately this approach can be a cost effective means of aerodynamic modeling in applications involving large scale FSI.
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Date Issued: 2016
Identifier: CFE0006088, ucf:50952
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006088

Title: Fluorescence Off-On Sensors for F-, K+, Fe3+, and Ca2+ Ions.
Creator: Sui, Binglin, Belfield, Kevin, Miles, Delbert, Zou, Shengli, Frazer, Andrew, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: Fluorescence spectroscopy has been considered to be one of the most important research techniques in modern analytical chemistry, biochemistry, and biophysics. At present, fluorescence is a dominant methodology widely used in a great number of research domains, including biotechnology, medical diagnostics, genetic analysis, DNA sequencing, flow cytometry, and forensic analysis, to name just a few. In the past decade, with the rapid development of fluorescence microscopy, there has been a...
Show moreFluorescence spectroscopy has been considered to be one of the most important research techniques in modern analytical chemistry, biochemistry, and biophysics. At present, fluorescence is a dominant methodology widely used in a great number of research domains, including biotechnology, medical diagnostics, genetic analysis, DNA sequencing, flow cytometry, and forensic analysis, to name just a few. In the past decade, with the rapid development of fluorescence microscopy, there has been a considerable growth in applying fluorescence technique to cellular imaging. The distinguished merits of fluorescence techniques, such as high sensitivity, non-invasiveness, low cytotoxicity, low cost, and convenience, make it a promising tool to replace radioactive tracers for most biochemical measurements, avoiding the high expense and difficulties of handling radioactive tracers.Among the wide range of applications of fluorescence technique, fluorescent sensing of various cations and anions is one of the most important and active areas. This dissertation is all about developing fluorescent sensors for physiologically significant ions, including F-, K+, Fe3+, and Ca2+. All of these sensors demonstrate fluorescence (")turn-on(") response upon interacting with their respective ions, which makes them much more appealing than those based on fluorescence quenching mechanisms.In Chapter II, a novel highly selective fluorescence turn-on F- sensor (FS), comprised of a fluorene platform serving as the chromophore, and two 1,2,3-triazolium groups functioning as the signaling moieties, is described. The function of FS is established on the basis of deprotonation of the C-H bonds of 1,2,3-triazolium groups, which makes FS the first reported anion sensor based on the deprotonation of a C-H bond. Easy-to-prepare test strips were prepared for determining F- in aqueous media, providing an inexpensive and convenient approach to estimate whether the concentration of F- contained in drinking water is at a safe level.Chapter III contains an optimized synthesis of a reported K+-selective group (TAC), and the development of two TAC-based fluorescence turn-on K+ sensors (KS1 and KS2). The synthetic route of TAC is shortened and its overall yield is enhanced from 3.6% to 19.5%. Both KS1 and KS2 exhibited excellent selectivity toward K+ over other physiological metal cations, high sensitivity for K+ sensing, and pH insensitivity in the physiological pH range. Confocal fluorescence microscopy experiments demonstrate that they are capable of sensing K+ within living cells. 2PA determination reveals that KS2 has a desirable 2PA cross section of 500 GM at 940 nm, which makes it a two-photon red-emitting fluorescent sensor for K+.Chapter IV describes the development of a novel BODIPY-based fluorescence turn-on Fe3+ sensor (FeS). FeS is a conjugate of two moieties, a BODIPY platform serving as the fluorophore and a 1,10-diaza-18-crown-6 based cryptand acting as the Fe3+ recognition moiety. FeS displays good selectivity, high sensitivity, reversibility, and pH insensitivity toward Fe3+ sensing. Based on its excellent performance in determining Fe3+ and very low cytotoxicity, FeS was effectively applied to sensing Fe3+ in living cells.In Chapter V, a new BODIPY-based fluorescence turn-on sensor (CaS) was designed and synthesized for selectively and sensitively determining Ca2+. CaS is comprised of two moieties, a BODIPY fluorophore and a Ca2+ complexing unit. CaS demonstrated selective fluorescence turn-on response towards Ca2+ over other biological metal cations. Moreover, CaS exhibited desirable sensitivity for Ca2+ detection, which makes it more suitable for extracellular Ca2+ determination. In addition, CaS was insensitive to the pH of the physiological environment, especially in the pH range of blood and serum. Therefore, CaS has potential to be applied to sensing Ca2+ ions in extracellular environments.Chapter VI discusses potential future work of KS2 and CaS, following the results achieved in this dissertation. Based on the desirable performances of both sensors in sensing their respective ions, future work could largely be focused on their applications in cellular imaging.
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Date Issued: 2014
Identifier: CFE0005888, ucf:50883
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005888

Title: On the Capillary Electrophoresis of Monohydroxy Metabolites of Polycyclic Aromatic Hydrocarbons and its Application to the Analysis of Biological Matrices.
Creator: Knobel, Gaston, Campiglia, Andres, Clausen, Christian, Belfield, Kevin, Liao, Yi, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: Polycyclic aromatic hydrocarbons (PAH) are a class of environmental pollutants consisting of a minimum of two fused aromatics rings originating from the incomplete combustion of organic matter and/or anthropogenic sources. Numerous possible anthropogenic and natural sources make the presence of PAH ubiquitous in the environment. The carcinogenic nature of some PAH and their ubiquitous presence makes their chemical analysis a topic of environmental and toxicological importance. Although...
Show morePolycyclic aromatic hydrocarbons (PAH) are a class of environmental pollutants consisting of a minimum of two fused aromatics rings originating from the incomplete combustion of organic matter and/or anthropogenic sources. Numerous possible anthropogenic and natural sources make the presence of PAH ubiquitous in the environment. The carcinogenic nature of some PAH and their ubiquitous presence makes their chemical analysis a topic of environmental and toxicological importance. Although environmental monitoring of PAH is an important step to prevent exposure to contaminated sites, it provides little information on the actual uptake and subsequent risks. Parent PAH are relatively inert and need metabolic activation to express their carcinogenicity. Covalent binding to DNA appears to be the first critical step in the initiation of the tumor formation process.To this end, the determination of short term biomarkers (-) such as monohydroxy-PAH metabolites (OH-PAH) - fills an important niche to interpret actual PAH exposure levels, prevent extreme body burdens and minimize cancer risk. One would certainly prefer an early warning parameter over a toxicological endpoint (-) such as DNA-adducts (-) indicating that extensive damage has already been done. Several methods have been developed to determine OH-PAH in specific tissue or excreta and food samples. The general trend for the analysis of OH-PAH follows the pattern of sample collection, sample clean-up and pre-concentration, chromatographic separation and quantification. Popular approaches for sample clean-up and pre-concentration include liquid-liquid extraction (LLE) and solid-phase extraction (SPE). Chromatographic separation and quantification has been based on high-performance liquid chromatography-room temperature fluorescence detection (HPLC) and gas chromatography-mass spectrometry (GC-MS).Although chromatographic techniques provide reliable results in the analysis of OH-PAH, their experimental procedures are time consuming and expensive. Elution times of 30-60 minutes are typical and standards must be run periodically to verify retention times. If the concentrations of target species are found to lie outside the detector's response range, the sample must be diluted and the process repeated. On the other end of the concentration range, many samples are (")zeroes,(") i.e. the concentrations are below detection limits. Additional problems arise when laboratory procedures are scaled up to handle thousands of samples under mass screening conditions. Under the prospective of a sustainable environment, the large usage of organic solvents is one of the main limitations of the current chromatographic methodology.This dissertation focuses on the development of a screening methodology for the analysis of OH-PAH in urine and milk samples. Screening techniques capable of providing a (")yes or no(") answer to OH-PAH contamination prevent unnecessary scrutiny of un-contaminated samples via conventional methods, reduce analysis cost and expedite the turnaround time for decision making purposes. The proposed methodology is based on capillary zone electrophoresis (CZE) and synchronous fluorescence spectroscopy (SFS). Metabolites extraction and pre-concentration is achieved with optimized SPE, LLE and/or QuEChERS (quick, easy, cheap, effective, rugged and safe) procedures. The small sample and extracting solvent volumes facilitate the simultaneous extraction of numerous samples via an environmentally friendly procedure, which is well-suited for routine monitoring of numerous samples. Sample stacking is successfully implemented to improve CZE limits of detection by two orders of magnitude. The unique electrophoretic pattern of positional isomers of OH-PAH demonstrates the potential of CZE for the unambiguous determination of metabolites with similar chromatographic behaviors and virtually similar fragmentation patterns. The direct determination of OH-PAH without chromatographic separation is demonstrated via SFS. The non-destructive nature of SFS provides ample opportunity for further metabolite confirmation via chromatographic techniques.
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Date Issued: 2013
Identifier: CFE0005102, ucf:50761
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005102

Title: Novel Photodynamic Cancer Therapy Agent and Biochemical Phosphate Sensor Based on Nanomaterials.
Creator: Fadhel, Alaa, Campiglia, Andres, Belfield, Kevin, Harper, James, Koculi, Eda, Bhattacharya, Aniket, University of Central Florida
Abstract / Description: Biochemical research and clinical studies have revolutionized the field of medicine in both diagnosis and therapy. Researchers in the field of biochemistry and biotechnology are using nanomaterials in different applications to develop devices and materials that offer benefits to both patients and the health care industry. These include biochemical sensors, enzyme encapsulation, biomarkers, and drug delivery improvements for the treatment of cancer. This dissertation focuses on investigating...
Show moreBiochemical research and clinical studies have revolutionized the field of medicine in both diagnosis and therapy. Researchers in the field of biochemistry and biotechnology are using nanomaterials in different applications to develop devices and materials that offer benefits to both patients and the health care industry. These include biochemical sensors, enzyme encapsulation, biomarkers, and drug delivery improvements for the treatment of cancer. This dissertation focuses on investigating two biochemical aspects using nanomaterials; namely therapy and clinical diagnosis.For therapy purposes, Silica nanoparticles were used as drug delivery system to develop a new photodynamic cancer therapy agent photo-acid generator (PAG) that selectively induces necrotic cell death of cancer cells. The developed PAG is oxygen-independent and - when excited at specific wavelengths - drops the pH within the lysosome of cancer cells to produce apoptosis/necrosis. It was specifically designed for in vivo applications and conjugated with synthesized, highly monodispersed silica nanoparticles (Si NPs) functionalized with amine groups via amid links (SiN-NH-PAG). Additional Features include high photo-acid quantum yield, high one-photon (1PA) and two-photon absorption (2PA) with low fluorescence quantum yield. In vivo, confocal microscope studies with HCT-116 (Human colorectal carcinoma) cancer cells showed that photodynamic processes in the presence of PAG were completed under one- photon absorption (1PA) conditions. In these experiments, cells were imaged at 1 min intervals for a total of 4 hours with the aid of Differential Interference Contrast (DIC). Among the photodynamic therapy agents tested via cytotoxicity experiments with the MTS assay, (SiN-NH- PAG) showed the best efficiency to induce cell death. The increased effectiveness of the new agent is probably due to the large number of PAG groups present on the surface of Si NPs.iiLysosome colocalization indicates that PAGs are mainly built in lysosomes. The increase of acidic content inside the lysosome was demonstrated with the aid of the LysoSensor Green probe. The drop in the intralysosomal pH was approximately 0.3 units. This is a desirable outcome as most cells underwent necrosis at pH ? 4.4. For clinical diagnosis purposes, a biochemical sensor was developed for the analysis of phosphate ions in urine samples. Abnormal levels of inorganic phosphate in human urine samples are related to the development of certain types of cancers affecting several organs of the human body, including breast, pancreas, lung and thyroid. The new biochemical sensor is based on the fluorescence energy transfer between a lanthanide luminescent probe [Tb-EDTA]-1 and gold nanoparticles (Au NPs) capped with a Cetyltrimethylammonium bromide (CTAB) micelle. With this approach, it was possible to selectively determine inorganic phosphate (Pi) in urine samples at the micro-molar concentration level. Urine samples collected from healthy, non-smoking individuals showed no interference from concomitants usually found in human urine samples. The simplicity of analysis provides an approach well-suited for (")real-time(") monitoring of phosphate ions. Analysis time is made possible within approximately 10 min per sample.
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Date Issued: 2016
Identifier: CFE0006528, ucf:51384
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006528

Title: Aggregation of Squaraine Dye Derivatives in Solid State Spin-coated Thin Films.
Creator: Daoudi, Mohammed, Belfield, Kevin, Miles, Delbert, Campiglia, Andres, Bhattacharya, Aniket, Rex, Matthew, University of Central Florida
Abstract / Description: Squaraine dyes have been the subject of intensive studies due their unusual electronic properties that make them good candidates for a wide range of applications in various technological fields. They are particularly promising in nonlinear optics, bioimaging for labeling and sensing of biomolecules, as sensitizers for solar energy harvesting in solar cells and organic photovoltaics, two-photon absorbing materials, near-infrared (NIR) emitting fluorescent probes, second harmonic generation...
Show moreSquaraine dyes have been the subject of intensive studies due their unusual electronic properties that make them good candidates for a wide range of applications in various technological fields. They are particularly promising in nonlinear optics, bioimaging for labeling and sensing of biomolecules, as sensitizers for solar energy harvesting in solar cells and organic photovoltaics, two-photon absorbing materials, near-infrared (NIR) emitting fluorescent probes, second harmonic generation organic dyes, and sensitizers for photodynamic therapy among others. In this dissertation, the aggregation behaviors and features of several squaraine dye derivatives in solid state thin films were studied and reported.In the first chapter of the dissertation, three squaraine dye derivatives with two and four hydroxy groups and with different N-alkyl amino donor substituents were synthesized and used as models to study aggregation behavior. Their UV-vis absorption, thermal properties, and photoluminescence properties were determined. The models with four hydroxy substituents exhibited higher thermal stability and melt at higher temperature compared to the dye with only two hydroxy substituents due to increased hydrogen bonding. The UV-vis absorption and photoluminescence properties in liquid solution at room temperature were found to be similar.In the second chapter, the squaraine dyes, 2,4-bis [4-(N,N-di-n-pentylamino)-2-hydroxyphenyl] squaraine [SQC5(OH)2], 2,4-bis [4-(N,N-di-n-pentylamino)-2,4-hydroxyphenyl] squaraine [SQC5(OH)4 n], and 2,4-bis [4-(N,N-di-isopentylamino)-2,4-hydroxyphenyl] squaraine [SQC5(OH)4 b], where (")n(") and (")b(") stand for normal or linear and branched alkyl groups, respectively, were investigated to study their aggregation in solid state thin film form using UV-vis absorption spectroscopy. The investigation revealed significant differences in aggregation behaviors and features. The dye SQC5(OH)2 mainly exhibited J-type aggregation with an intense absorption band in the NIR region. In contrast, the SQC5(OH)4 n and SQC5(OH)4 b compounds mainly exhibited H-type aggregation, characterized by less intense and blue shifted absorption bands. The third chapter presents the kinetic study conducted on the squaraine dye derivative 2,4-bis [4-(N,N-di-n-pentylamino)-2-hydroxyphenyl] squaraine [SQC5(OH)2] in solid state spin-coated thin films. The study revealed the formation of J-aggregates with bands at 767 nm at room temperature. This aggregate was temperature dependent. It was transformed into H-aggregates as the temperature increased. The activation energy of the decay (transformation) process was found to be 91.2 kJ. The values of ?H and ?S are 88.4 kJ/mol and 48.2 J/K.mol, respectively, indicating the J-aggregate of SQC5(OH)2 was a kinetic product while the H-aggregate was thermondynamically more stable.
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Date Issued: 2015
Identifier: CFE0005778, ucf:50064
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005778

Aggreagtion in solid state (1)	+ -
Autorotation (1)	+ -
Biophysics (1)	+ -
Brownian Dynamics (1)	+ -
Brownian dynamics simulation (1)	+ -

CFD (1)	+ -
DDES (1)	+ -
DNA (1)	+ -
Edwards (1)	+ -
Electroless deposition (1)	+ -
Fluid Structure Interaction (1)	+ -
Frozen air (1)	+ -
Gibbs ensemble (1)	+ -
Gold Nanorods (1)	+ -
J-aggregation (1)	+ -
LES (1)	+ -
Langevin dynamics (1)	+ -
Lysosomal pH drop (1)	+ -
MD simulation (1)	+ -
Mercury (1)	+ -
Molecular Dynamics (1)	+ -
OH-PAH (1)	+ -
Polymer Sequencing (1)	+ -
SET (1)	+ -
STM (1)	+ -
Sensors (1)	+ -
Soft Matter Physics (1)	+ -
Squaraine dyes (1)	+ -
Translocation (1)	+ -
UV-Vis Spectroscopy (1)	+ -

Bhattacharya, Aniket (13)	+ -
University of Central Florida (13)	+ -
Campiglia, Andres (5)	+ -
Belfield, Kevin (4)	+ -
Frazer, Andrew (3)	+ -

Harper, James (2)	+ -
Kokoouline, Viatcheslav (2)	+ -
Miles, Delbert (2)	+ -
Rex, Matthew (2)	+ -
Zou, Shengli (2)	+ -
Adhikari, Ramesh (1)	+ -
Anguera Antonana, Marta (1)	+ -
Beazley, Melanie (1)	+ -
Bourov, Geuorgui (1)	+ -
Chen, Bo (1)	+ -
Clausen, Christian (1)	+ -
Coronado Domenge, Patricia (1)	+ -
Daoudi, Mohammed (1)	+ -
Das, Tuhin (1)	+ -
Del Barco, Enrique (1)	+ -
Fadhel, Alaa (1)	+ -
Grabill, Christopher (1)	+ -
Heider, Emily (1)	+ -
Hernandez, Florencio (1)	+ -
Huang, Aiqun (1)	+ -
Kassab, Alain (1)	+ -
Knobel, Gaston (1)	+ -
Koculi, Eda (1)	+ -
Krenn, Angela (1)	+ -
Kuebler, Stephen (1)	+ -

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