Matching Items (37)

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The Focusing of Proteins Using Dielectrophoresis in an Improved Microfluidic Device

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Dielectrophoresis is a separations strategy that has the potential to separate small amounts of different proteins from each other. The forces at play in the channel used for dielectrophoresis are

Dielectrophoresis is a separations strategy that has the potential to separate small amounts of different proteins from each other. The forces at play in the channel used for dielectrophoresis are electroosmotic flow (EOF), electrophoresis (EP), and dielectrophoresis (DEP). EOF is the force exerted on liquid from an applied potential (1). EP is the force exerted on charged particles in a uniform electric field (2). DEP is the force exerted on particles (charged and uncharged) in a non-uniform electric field (3). This experiment was focused on the testing of a new microfluidic device to see if it could improve the focusing of proteins in dielectrophoresis. It was predicted that the addition of a salt bridge would improve focusing by preventing the ions created by the electrolysis of water around the electrodes from interacting with the proteins and causing aggregation, among other problems. Control trials using the old device showed that electrolysis was likely occurring and was the causal agent for poor outcomes. After applying the electric potential for some time a pH front traveled through the channel causing aggregation of proteins and the current in the channel decreased rapidly, even while the voltage was held constant. The resistance in the channels of the control trials also slightly decreased over time, until the pH shift occurred, at which time it increased rapidly. Experimental trials with a new device that included salt bridges eliminated this pH front and had a roughly linear increase of current in the channel with the voltage applied. This device can now be used in future research with protein dielectrophoresis, including in the potential differentiation of different proteins. References: 1) Electroosmosis. Oxford Dictionary of Biochemistry and Molecular Biology. 2. Oxford University Press: Oxford, England. 2006. 2) Electrophoresis. Oxford Dictionary of Biochemistry and Molecular Biology. 2. Oxford University Press: Oxford, England. 2006. 3) Dielectrophoresis. Oxford Dictionary of Biochemistry and Molecular Biology. 2. Oxford University Press: Oxford, England. 2006.

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  • 2016-05

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Investigation of Cu(II) Binding Sites in de Novo Proteins by Electron Paramagnetic Resonance Spectroscopy

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Circular Dichroism (CD) and electron paramagnetic resonance (EPR) were used to investigate the metal-binding sites of five different four-helix bundles, which have slight differences in the population of their side

Circular Dichroism (CD) and electron paramagnetic resonance (EPR) were used to investigate the metal-binding sites of five different four-helix bundles, which have slight differences in the population of their side chains. Of the four-helix bundles, three have central dinuclear metal binding sites; two of these three also have outer dinuclear metal binding sites. The other two peptides have two identical, non-central, dinuclear metal binding sites. The CD spectra showed changes in the secondary structure of the peptides, and X-band EPR spectra of these peptides revealed the unique four peak signal of Cu(II). These findings improve our understanding of the metal binding environments of these peptides.

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  • 2016-05

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Multifunctional Soft Materials: Design, Development and Applications

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Soft materials are matters that can easily deform from their original shapes and structures under thermal or mechanical stresses, and they range across various groups of materials including liquids, foams,

Soft materials are matters that can easily deform from their original shapes and structures under thermal or mechanical stresses, and they range across various groups of materials including liquids, foams, gels, colloids, polymers, and biological substances. Although soft materials already have numerous applications with each of their unique characteristics, integrating materials to achieve complementary functionalities is still a growing need for designing advanced applications of complex requirements. This dissertation explores a unique approach of utilizing intermolecular interactions to accomplish not only the multifunctionality from combined materials but also their tailored properties designed for specific tasks. In this work, multifunctional soft materials are explored in two particular directions, ionic liquids (ILs)-based mixtures and interpenetrating polymer network (IPN).

First, ILs-based mixtures were studied to develop liquid electrolytes for molecular electronic transducers (MET) in planetary exploration. For space missions, it is challenging to operate any liquid electrolytes in an extremely low-temperature environment. By tuning intermolecular interactions, the results demonstrated a facile method that has successfully overcome the thermal and transport barriers of ILs-based mixtures at extremely low temperatures. Incorporation of both aqueous and organic solvents in ILs-based electrolyte systems with varying types of intermolecular interactions are investigated, respectively, to yield optimized material properties supporting not only MET sensors but also other electrochemical devices with iodide/triiodide redox couple targeting low temperatures.

Second, an environmentally responsive hydrogel was synthesized via interpenetrating two crosslinked polymer networks. The intermolecular interactions facilitated by such an IPN structure enables not only an upper critical solution temperature (UCST) transition but also a mechanical enhancement of the hydrogel. The incorporation of functional units validates a positive swelling response to visible light and also further improves the mechanical properties. This studied IPN system can serve as a promising route in developing “smart” hydrogels utilizing visible light as a simple, inexpensive, and remotely controllable stimulus.

Over two directions across from ILs to polymeric networks, this work demonstrates an effective strategy of utilizing intermolecular interactions to not only develop multifunctional soft materials for advanced applications but also discover new properties beyond their original boundaries.

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Date Created
  • 2020

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Passivation and Dissolution of Alloys

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The passivity of metals is a phenomenon of vast importance as it prevents many materials in important applications from rapid deterioration by corrosion. Alloying with a sufficient quantity of passivating

The passivity of metals is a phenomenon of vast importance as it prevents many materials in important applications from rapid deterioration by corrosion. Alloying with a sufficient quantity of passivating elements (Cr, Al, Si), typically in the range of 10% - 20%, is commonly employed to improve the corrosion resistance of elemental metals. However, the compositional criteria for enhanced corrosion resistance have been a long-standing unanswered question for alloys design. With the emerging interest in multi-principal element alloy design, a percolation model is developed herein for the initial stage of passive film formation, termed primary passivation. The successful validation of the assumptions and predictions of the model in three corrosion-resistant binary alloys, Fe-Cr, Ni-Cr, and Cu-Rh supports that the model which can be used to provide a quantitative design strategy for designing corrosion-resistant alloys. To date, this is the only model that can provide such criteria for alloy design.The model relates alloy passivation to site percolation of the passivating elements in the alloy matrix. In the initial passivation stage, Fe (Ni in Ni-Cr or Cu in Cu-Rh) is selectively dissolved, destroying the passive network built up by Cr (or Rh) oxides and undercutting isolated incipient Cr (Rh) oxide nuclei. The only way to prevent undercutting and form a stable protective passive film is if the concentration of Cr (Rh) is high enough to realize site percolation within the thickness of the passive film or the dissolution depth. This 2D-3D percolation cross-over transition explains the compositional dependent passivation of these alloys. The theoretical description of the transition and its assumptions is examined via experiments and kinetic Monte Carlo simulations. The initial passivation scenario of the dissolution selectivity is validated by the inductively coupled plasma mass spectrum (ICP-MS). The electronic effect not considered in the kinetic Monte Carlo simulations is addressed by density functional theory (DFT). Additionally, the impact of the atomic configuration parameter on alloy passivation is experimentally measured, which turns out to agree well with the model predictions developed using Monte Carlo renormalization group (MC-RNG) methods.

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  • 2020

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Contact and length dependent effects in single-molecule electronics

Description

Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure

Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition voltage for molecules with between two and six repeat units. While the molecule with only one repeat unit shows temperature invariant behavior. Density functional theory calculations show that at higher temperatures the oligomers with multiple repeat units assume a more planar conformation, which increases the conjugation length and decreases the effective energy barrier of the junction.

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Date Created
  • 2013

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A computational and theoretical study of conductance in hydrogen-bonded molecular junctions

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This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport

This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano- junctions between molecular electronic devices and biological systems.

This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction.

In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions.

A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.

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Date Created
  • 2017

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Nonlinear dielectric effects and modification of supramolecular structures in monohydroxy alcohols

Description

A driving force for studies of water, alcohols, and amides is the determination of the role of hydrogen bonding. Hydrogen bonds can break and reform, consequently creating supramolecular structures. Understanding

A driving force for studies of water, alcohols, and amides is the determination of the role of hydrogen bonding. Hydrogen bonds can break and reform, consequently creating supramolecular structures. Understanding the role supramolecular structures play in the dynamics of monohydroxyl alcohols is important to understanding hydrogen bonding in more complex systems such as proteins. Since many monohydroxyl alcohols are good glass formers, dielectric spectroscopy in the supercooled regime is used to gather information about the dynamics of these liquids. Application of high external fields will reversibly alter the polarization responses of the material from the linear response. This results in nonlinear dielectric effects (NDE) such as field induced suppression (saturation) and enhancement of amplitudes (chemical effects) as well as shifts in the time constants toward slower (entropy) and faster (energy absorption) dynamics.

The first part of this thesis describes the nonlinear dielectric experiments on monohydroxyl alcohols, with an emphasis on the time dependence of NDEs. For the first time, time-dependent experiments on monoalcohols were done, the results showed that NDEs occur on the Debye time scale. Furthermore, physical vapor deposition (PVD) is used to modify the supramolecular structure of 4-methyl-3-heptanol. Upon deposition the film cannot form the ring like structures, which are preferred in the bulk material. The as deposited film shows an enhancement of the dielectric peak by a factor of approximately 11 when compared to the bulk material. The conversion from the as deposited material back to the near bulk material was found to occur on the Debye timescale.

The second part of this thesis focuses on the question of what is governing the field induced changes seen in the liquids studied. Here a complete set of high field experiments on highly polar propylene carbonate derivatives were performed. It was demonstrated that these materials exhibit a Debye-like peak and using a combination of Adam-Gibbs and Fröhlich’s definition of entropy, proposed by Johari [G.P. Johari, J. Chem. Phys 138, 154503 (2013)], cannot solely be used to describe a frustration of dynamics. It is important to note that although these material exhibit a Debye like peak, the behavior is much different than monoalcohols.

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Date Created
  • 2019

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Measurement of molecular conductance

Description

This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule

This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two section, the first one involving the characterization of the Dyad monolayers and conductance measurement in the dark. The Dyads are designed to form charge separated states on illumination. The lifetime of the charged states have been measured efficiently but the single-molecule conductance through the molecules have yet to be characterized. The second part of the project describes the set-up of a novel sample stage which enables the study of molecular conductance under illumination. This part also describes the subsequent study of the molecule under illumination and the observation of a unique charge-separated state. It also contains the verification of the presence of this charge-separated using other characterization techniques like transient absorption spectroscopy. The second project described in the dissertation was studying and comparing the predicted rectifying nature of two molecules, identical in every way except for one stereocenter. This project describes the formation of monolayers of the molecule on gold and then studying and analyzing the current-voltage characteristics of the molecules and looking for rectification. Both the molecules proved to be rectifying, one more than the other as predicted by theoretical calculations.

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Date Created
  • 2011

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Assessing the Impact of H2O and CH4 Opacity Data in Exoplanetary Atmospheres: Laboratory Measurements and Radiative Transfer Modeling Approaches

Description

One strategic objective of the National Aeronautics and Space Administration (NASA) is to find life on distant worlds. Current and

One strategic objective of the National Aeronautics and Space Administration (NASA) is to find life on distant worlds. Current and future missions either space telescopes or Earth-based observatories are frequently used to collect information through the detection of photons from exoplanet atmospheres. The primary challenge is to fully understand the nature of these exo-atmospheres. To this end, atmospheric modeling and sophisticated data analysis techniques are playing a key role in understanding the emission and transmission spectra of exoplanet atmospheres. Of critical importance to the interpretation of such data are the opacities (or absorption cross-sections) of key molecules and atoms. During my Doctor of Philosophy years, the central focus of my projects was assessing and leveraging these opacity data. I executed this task with three separate projects: 1) laboratory spectroscopic measurement of the infrared spectra of CH4 in H2 perturbing gas in order to extract pressure-broadening and pressure-shifts that are required to accurately model the chemical composition of exoplanet atmospheres; 2) computing the H2O opacity data using ab initio line list for pressure and temperature ranges of 10^-6–300 bar and 400–1500 K, and then utilizing these H2O data in radiative transfer models to generate transmission and emission exoplanetary spectra; and 3) assessing the impact of line positions in different H2O opacities on the interpretation of ground-based observational exoplanetary data through the cross-correlation technique.

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Date Created
  • 2019

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Charge transport in single molecules

Description

Studying charge transport through single molecules is of great importance for unravelling charge transport mechanisms, investigating fundamentals of chemistry, and developing functional building blocks in molecular electronics.

First, a study of

Studying charge transport through single molecules is of great importance for unravelling charge transport mechanisms, investigating fundamentals of chemistry, and developing functional building blocks in molecular electronics.

First, a study of the thermoelectric effect in single DNA molecules is reported. By varying the molecular length and sequence, the charge transport in DNA was tuned to either a hopping- or tunneling-dominated regimes. In the hopping regime, the thermoelectric effect is small and insensitive to the molecular length. Meanwhile, in the tunneling regime, the thermoelectric effect is large and sensitive to the length. These findings indicate that by varying its sequence and length, the thermoelectric effect in DNA can be controlled. The experimental results are then described in terms of hopping and tunneling charge transport models.

Then, I showed that the electron transfer reaction of a single ferrocene molecule can be controlled with a mechanical force. I monitor the redox state of the molecule from its characteristic conductance, detect the switching events of the molecule from reduced to oxidized states with the force, and determine a negative shift of ~34 mV in the redox potential under force. The theoretical modeling is in good agreement with the observations, and reveals the role of the coupling between the electronic states and structure of the molecule.

Finally, conclusions and perspectives were discussed to point out the implications of the above works and future studies that can be performed based on the findings.

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Date Created
  • 2017