Parametric Analysis for Monitoring 2D Kinetics of Receptor-Ligand binding

Thermal fluctuation approach is widely used to monitor association kinetics of surface-bound receptor-ligand interactions. Various protocols such as sliding standard deviation (SD) analysis (SSA) and Page's test analysis (PTA) have been used to estimate two-dimensional (2D) kinetic rates from the time course of displacement of molecular carrier. In the current work, we compared the estimations from both SSA and modified PTA using measured data from an optical trap assay and simulated data from a random number generator. Our results indicated that both SSA and PTA were reliable in estimating 2D kinetic rates. Parametric analysis also demonstrated that such the estimations were sensitive to parameters such as sampling rate, sliding window size, and threshold. These results furthered the understandings in quantifying the biophysics of receptor-ligand interactions.

IL-8-induced L-selectin shedding regulates its binding kinetics to PSGL-1

L-selectin plays a crucial role in inflammation cascade by initiating the tethering and rolling of leukocytes on endothelium wall. While many L-selectin molecules are rapidly shed from the cell surface upon activation, the remaining membrane-anchored L-selectin may still play an important role in regulating leukocyte rolling and adhesion with different binding kinetics. Here we developed an in vitro model to activate Jurkat cells via interlukin-8 (IL-8) and quantified the two-dimensional (2D) binding kinetics, using a micropipette aspiration assay, of membrane-anchored L-selectin to P-selectin glycoprotein ligand 1 (PSGL-1) ligand coupled onto human red blood cells (RBCs). The data indicated that L-selectin shedding reduced the amount of membrane-anchored L-selectin and lowered both its reverse and forward rates. These results suggested that the rolling dynamics of activated leukocytes was determined by two opposite impacts: reducing the surface presentation would enhance the rolling but lowering the kinetic rates would decrease the rolling. This finding provides a new insight into understanding how L-selectin shedding regulates leukocyte rolling and adhesion.

The adsorption of protein molecules at a crystal/solution interface observed by an improved TIRFM

We have improved the ordinary total internal reflection fluorescence microscopy (TIRFM). Two improvements have been achieved, one is the interface between opaque material and solution can be observed, another is the interface far away (usually several ten micro meters) the objective lens can be observed. By this improved TIRFM, the adsorption of protein molecules at a crystal/solution interface had been successfully observed. We have obtained the results of relationship between the amount of adsorbed protein molecules on bunched steps and the height of bunched steps of a protein crystal.

On-chip integrated label-free optical biosensing

This thesis investigates the design and implementation of a label-free optical biosensing system utilizing a robust on-chip integrated platform. The goal has been to transition optical micro-resonator based label-free biosensing from a laborious and delicate laboratory demonstration to a tool for the analytical life scientist. This has been pursued along four avenues: (1) the design and fabrication of high-$Q$ integrated planar microdisk optical resonators in silicon nitride on silica, (2) the demonstration of a high speed optoelectronic swept frequency laser source, (3) the development and integration of a microfluidic analyte delivery system, and (4) the introduction of a novel differential measurement technique for the reduction of environmental noise.

The optical part of this system combines the results of two major recent developments in the field of optical and laser physics: the high-$Q$ optical resonator and the phase-locked electronically controlled swept-frequency semiconductor laser. The laser operates at a wavelength relevant for aqueous sensing, and replaces expensive and fragile mechanically-tuned laser sources whose frequency sweeps have limited speed, accuracy and reliability. The high-$Q$ optical resonator is part of a monolithic unit with an integrated optical waveguide, and is fabricated using standard semiconductor lithography methods. Monolithic integration makes the system significantly more robust and flexible compared to current, fragile embodiments that rely on the precarious coupling of fragile optical fibers to resonators. The silicon nitride on silica material system allows for future manifestations at shorter wavelengths. The sensor also includes an integrated microfluidic flow cell for precise and low volume delivery of analytes to the resonator surface. We demonstrate the refractive index sensing action of the system as well as the specific and nonspecific adsorption of proteins onto the resonator surface with high sensitivity. Measurement challenges due to environmental noise that hamper system performance are discussed and a differential sensing measurement is proposed, implemented, and demonstrated resulting in the restoration of a high performance sensing measurement.

The instrument developed in this work represents an adaptable and cost-effective platform capable of various sensitive, label-free measurements relevant to the study of biophysics, biomolecular interactions, cell signaling, and a wide range of other life science fields. Further development is necessary for it to be capable of binding assays, or thermodynamic and kinetics measurements; however, this work has laid the foundation for the demonstration of these applications.

Adsorption of Pb(II) and Cu(II) on α-quartz from aqueous solutions: influence of pH, ionic strength, and complexing ligands

Adsorption of aqueous Pb(II) and Cu(II) on α-quartz was studied as a function of time, system surface area, and chemical speciation. Experimental systems contained sodium as a major cation, hydroxide, carbonate, and chloride as major anions, and covered the pH range 4 to 8. In some cases citrate and EDTA were added as representative organic complexing agents. The adsorption equilibria were reached quickly, regardless of the system surface area. The positions of the adsorption equilibria were found to be strongly dependent on pH, ionic strength and concentration of citrate and EDTA. The addition of these non-adsorbing ligands resulted in a competition between chelation and adsorption. The experimental work also included the examination of the adsorption behavior of the doubly charged major cations Ca(II) and Mg(II) as a function of pH.

The theoretical description of the experimental systems was obtained by means of chemical equilibrium-plus-adsorption computations using two adsorption models: one mainly electrostatic (the James-Healy Model), and the other mainly chemical (the Ion Exchange-Surface Complex Formation Model). Comparisons were made between these two models.

The main difficulty in the theoretical predictions of the adsorption behavior of Cu(II) was the lack of the reliable data for the second hydrolysis constant(*β_2) The choice of the constant was made on the basis of potentiometric titratlons of Cu^(2+)

The experimental data obtained and the resulting theoretical observations were applied in models of the chemical behavior of trace metals in fresh oxic waters, with emphasis on Pb(II) and Cu(II).

Biossorção de tório e urânio pela macroalga marinha sargassum filipendula

Por ser um material de baixo custo e apresentar propriedades ligantes, a macroalga marinha Sargassum filipendula vem sendo utilizada como material biossorvente no processo de biossorção de metais. No presente trabalho a alga marrom foi utilizada no estudo cinético e de equilíbrio dos íons de tório e urânio individuais e os resultados comparados à biossorção desses metais em sistema binário. Os testes foram realizados nas concentrações 1 e 10 mg/L e pH= 1,0 e 4,0 na temperatura de 25 1C. A melhor condição para biossorção de tório foi encontrada para 1 mg/L e pH= 1,0, enquanto que para urânio foi em 1 mg/L e pH= 4,0. O estudo cinético de biossorção de tório mostrou que o modelo de segunda ordem descreve melhor os dados experimentais em 1 mg/L (R2= 0,9987) e 10 mg/L (R2= 0,9919) em pH= 1,0 e 1 mg/L (R2= 0,9976) em pH= 4,0, enquanto em 10 mg/L (R2= 0,9787) pH= 4,0 a curva encontrada representou uma cinética de primeira ordem. Para a cinética de urânio os dois modelos se adequaram bem aos dados em ambas as condições experimentais. O estudo de equilíbrio mostrou um perfil crescente de captação de tório, com uma remoção de 96% e 54% do metal em pH= 1,0 e 4,0, respectivamente, a partir da Co= 1 mg/L. A melhor eficiência de captação dos íons de urânio foi de 33% para Co= 100 mg/L em pH= 1,0 e 71% para Co= 1 mg/L em pH= 4,0. Os dados experimentais da isoterma de tório mostraram-se mais adequados ao modelo de Freundlich para pH= 1,0, enquanto que para o pH= 4,0 esses foram melhor representados pelo modelo de Langmuir, com valores de coeficiente de determinação superiores. Em relação à isoterma do urânio, o modelo de Freundlich representou bem os dados experimentais. Os parâmetros de equilíbrio calculados a partir do modelo de Langmuir (kL, qmax ) e Freundlich (kF, n) indicaram uma maior afinidade da biomassa pelos íons de tório em ambas as condições experimentais. O estudo de equilíbrio do sistema binário mostrou que a biossorção dos íons de tório não é afetada pela presença do urânio em solução. Por outro lado, a sorção do urânio foi fortemente afetada pela coexistência com os íons de tório.

Descoloração e Mineralização de Corantes Reativos por Processo Fotocatalítico Utilizando ZnO e Radiação UV

As indústrias consomem volumes elevados de água e outras substâncias químicas na síntese dos seus produtos e geram grande quantidade de rejeitos. Entre os mais importantes poluentes encontrados nos efluentes dessas indústrias estão os corantes sintéticos que representam um problema, pois não são facilmente destruídos por tratamentos convencionais. A fotocatálise heterogênea tem sido considerada como uma alternativa efetiva no tratamento de efluentes contendo esses corantes. Neste trabalho, estudou-se a cinética de descoloração e o grau de mineralização dos corantes sintéticos reativos Yellow 145, Black 5, Red 4 e Blue 21 através da fotocatálise utilizando ZnO puro e impregnado com íons Fe2+ e Co2+. Testes preliminares foram realizados para otimizar a concentração dos corantes e a massa mínima de catalisador a ser utilizado nos experimentos fotocatalíticos. Além da fotocatálise, experimentos individuais de fotólise e adsorção também foram realizados, porém se mostraram poucos eficientes. Através da espectrofotometria UV-Vis, verificou-se o total descoramento individual dos corantes em aproximadamente 30 minutos de irradiação com ZnO. O grau de mineralização de cada corante foi determinado através de análise de carbono orgânico total (COT), atingindo-se cerca de 70 a 80% de mineralização após 240 minutos de tratamento fotocatalítico. Foram comparadas, ainda, as eficiências de cada fotocatalisador ZnO, Fe/ZnO e Co/ZnO na mineralização de uma solução contendo a mistura dos quatro corantes já mencionados após 240 minutos de reação. A eficiência na mineralização da mistura dos corantes seguiu a seguinte ordem: Co/ZnO (32%), ZnO (78%) e Fe/ZnO (87%). A reação de degradação fotocatalítica do corante Black 5 seguiu uma cinética de primeira ordem, enquanto que os corantes Yellow 145, Red 4 e Blue 21 seguiram uma cinética de ordem zero.

Studies in nuclear reactor dynamics : I. The accuracy of point kinetics. II. The effect of delayed neutrons on the spectrum of the group-diffusion operator

This thesis is a theoretical work on the space-time dynamic behavior of a nuclear reactor without feedback. Diffusion theory with G-energy groups is used.

In the first part the accuracy of the point kinetics (lumped-parameter description) model is examined. The fundamental approximation of this model is the splitting of the neutron density into a product of a known function of space and an unknown function of time; then the properties of the system can be averaged in space through the use of appropriate weighting functions; as a result a set of ordinary differential equations is obtained for the description of time behavior. It is clear that changes of the shape of the neutron-density distribution due to space-dependent perturbations are neglected. This results to an error in the eigenvalues and it is to this error that bounds are derived. This is done by using the method of weighted residuals to reduce the original eigenvalue problem to that of a real asymmetric matrix. Then Gershgorin-type theorems .are used to find discs in the complex plane in which the eigenvalues are contained. The radii of the discs depend on the perturbation in a simple manner.

In the second part the effect of delayed neutrons on the eigenvalues of the group-diffusion operator is examined. The delayed neutrons cause a shifting of the prompt-neutron eigenvalue s and the appearance of the delayed eigenvalues. Using a simple perturbation method this shifting is calculated and the delayed eigenvalues are predicted with good accuracy.

Part I. Kinetics of coarsening of the gamma-prime precipitate in nickel-silicon alloys. Part II. Rate of crystallization of an amorphous Fe-P-C alloy

The coarsening kinetics of Ni₃ Si(γ') precipitate in a binary Ni-Si alloy containing 6.5 wt. % silicon was studied by magnetic techniques and transmission electronmicroscopy. A calibration curve was established to determine the concentration of silicon in the matrix. The variation of the Si content of the Ni-rich matrix as a function of time follows Lifshitz and Wagner theory for diffusion controlled coarsening phenomena. The estimated values of equilibrium solubility of silicon in the matrix represent the true coherent equilibrium solubilities.

The experimental particle-size distributions and average particle size were determined from dark field electron micrographs. The average particle size varies linearly with t^-1/3 as suggested by Lifshitz and Wagner. The experimental distributions of particle sizes differ slightly from the theoretical curve at the early stages of aging, but the agreement is satisfactory at the later stages. The values of diffusion coefficient of silicon, interfacial free energy and activation energy were calculated from the results of coarsening kinetics. The experimental value of effective diffusion coefficient is in satisfactory agreement with the value predicted by the application of irreversible the rmodynamics to the process of volume constrained growth of coherent precipitate during coarsening. The coherent γ' particles in Ni-Sialloy unlike those in Ni-Al and Ni-Ti seem to lose coherency at high temperature. A mechanism for the formation of semi-coherent precipitate is suggested.

Chemical studies of viral entry mechanisms: I. Hydrophobic protein-lipid interactions during sendai virus membrane fusion. II. Kinetics of bacteriophage λ DNA injection.

Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage λ DNA injection.

Sendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125 )I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.

Examination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.

The kinetics of DNA injection by bacteriophage λ. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.

It is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.

Kinetic investigations of heterogeneously catalyzed reactions on the Ru(001) and Pt(110)-(1x2) surfaces

The initial probabilities of activated, dissociative chemisorption of methane and ethane on Pt(110)-(1 x 2) have been measured. The surface temperature was varied from 450 to 900 K with the reactant gas temperature constant at 300 K. Under these conditions, we probe the kinetics of dissociation via trapping-mediated (as opposed to 'direct') mechanism. It was found that the probabilities of dissociation of both methane and ethane were strong functions of the surface temperature with an apparent activation energies of 14.4 kcal/mol for methane and 2.8 kcal/mol for ethane, which implys that the methane and ethane molecules have fully accommodated to the surface temperature. Kinetic isotope effects were observed for both reactions, indicating that the C-H bond cleavage was involved in the rate-limiting step. A mechanistic model based on the trapping-mediated mechanism is used to explain the observed kinetic behavior. The activation energies for C-H bond dissociation of the thermally accommodated methane and ethane on the surface extracted from the model are 18.4 and 10.3 kcal/mol, respectively.

The studies of the catalytic decomposition of formic acid on the Ru(001) surface with thermal desorption mass spectrometry following the adsorption of DCOOH and HCOOH on the surface at 130 and 310 K are described. Formic acid (DCOOH) chemisorbs dissociatively on the surface via both the cleavage of its O-H bond to form a formate and a hydrogen adatom, and the cleavage of its C-O bond to form a carbon monoxide, a deuterium adatom and an hydroxyl (OH). The former is the predominant reaction. The rate of desorption of carbon dioxide is a direct measure of the kinetics of decomposition of the surface formate. It is characterized by a kinetic isotope effect, an increasingly narrow FWHM, and an upward shift in peak temperature with Ɵ_T, the coverage of the dissociatively adsorbed formic acid. The FWHM and the peak temperature change from 18 K and 326 K at Ɵ_T = 0.04 to 8 K and 395 K at Ɵ_T = 0.89. The increase in the apparent activation energy of the C-D bond cleavage is largely a result of self-poisoning by the formate, the presence of which on the surface alters the electronic properties of the surface such that the activation energy of the decomposition of formate is increased. The variation of the activation energy for carbon dioxide formation with Ɵ_T accounts for the observed sharp carbon dioxide peak. The coverage of surface formate can be adjusted over a relatively wide range so that the activation energy for C-D bond cleavage in the case of DCOOH can be adjusted to be below, approximately equal to, or well above the activation energy for the recombinative desorption of the deuterium adatoms. Accordingly, the desorption of deuterium was observed to be governed completely by the desorption kinetics of the deuterium adatoms at low Ɵ_T, jointly by the kinetics of deuterium desorption and C-D bond cleavage at intermediate Ɵ_T, and solely by the kinetics of C-D bond cleavage at high Ɵ_T. The overall branching ratio of the formate to carbon dioxide and carbon monoxide is approximately unity, regardless the initial coverage Ɵ_T, even though the activation energy for the production of carbon dioxide varies with Ɵ_T. The desorption of water, which implies C-O bond cleavage of the formate, appears at approximately the same temperature as that of carbon dioxide. These observations suggest that the cleavage of the C-D bond and that of the C-O bond of two surface formates are coupled, possibly via the formation of a short-lived surface complex that is the precursor to to the decomposition.

The measurement of steady-state rate is demonstrated here to be valuable in determining kinetics associated with short-lived, molecularly adsorbed precursor to further reactions on the surface, by determining the kinetic parameters of the molecular precursor of formaldehyde to its dissociation on the Pt(110)-(1 x 2) surface.

Overlayers of nitrogen adatoms on Ru(001) have been characterized both by thermal desorption mass spectrometry and low-energy electron diffraction, as well as chemically via the postadsorption and desorption of ammonia and carbon monoxide.

The nitrogen-adatom overlayer was prepared by decomposing ammonia thermally on the surface at a pressure of 2.8 x 10^(-6) Torr and a temperature of 480 K. The saturated overlayer prepared under these conditions has associated with it a (√247/10 x √247/10)R22.7° LEED pattern, has two peaks in its thermal desorption spectrum, and has a fractional surface coverage of 0.40. Annealing the overlayer to approximately 535 K results in a rather sharp (√3 x √3)R30° LEED pattern with an associated fractional surface coverage of one-third. Annealing the overlayer further to 620 K results in the disappearance of the low-temperature thermal desorption peak and the appearance of a rather fuzzy p(2x2) LEED pattern with an associated fractional surface coverage of approximately one-fourth. In the low coverage limit, the presence of the (√3 x √3)R30° N overlayer alters the surface in such a way that the binding energy of ammonia is increased by 20% relative to the clean surface, whereas that of carbon monoxide is reduced by 15%.

A general methodology for the indirect relative determination of the absolute fractional surface coverages has been developed and was utilized to determine the saturation fractional coverage of hydrogen on Ru(001). Formaldehyde was employed as a bridge to lead us from the known reference point of the saturation fractional coverage of carbon monoxide to unknown reference point of the fractional coverage of hydrogen on Ru(001), which is then used to determine accurately the saturation fractional coverage of hydrogen. We find that ƟSAT/H = 1.02 (±0.05), i.e., the surface stoichiometry is Ru : H = 1 : 1. The relative nature of the method, which cancels systematic errors, together with the utilization of a glass envelope around the mass spectrometer, which reduces spurious contributions in the thermal desorption spectra, results in high accuracy in the determination of absolute fractional coverages.

Exploring the Kinetics of Domain Switching in Ferroelectrics for Structural Applications

The complex domain structure in ferroelectrics gives rise to electromechanical coupling, and its evolution (via domain switching) results in a time-dependent (i.e. viscoelastic) response. Although ferroelectrics are used in many technological applications, most do not attempt to exploit the viscoelastic response of ferroelectrics, mainly due to a lack of understanding and accurate models for their description and prediction. Thus, the aim of this thesis research is to gain better understanding of the influence of domain evolution in ferroelectrics on their dynamic mechanical response. There have been few studies on the viscoelastic properties of ferroelectrics, mainly due to a lack of experimental methods. Therefore, an apparatus and method called Broadband Electromechanical Spectroscopy (BES) was designed and built. BES allows for the simultaneous application of dynamic mechanical and electrical loading in a vacuum environment. Using BES, the dynamic stiffness and loss tangent in bending and torsion of a particular ferroelectric, viz. lead zirconate titanate (PZT), was characterized for different combinations of electrical and mechanical loading frequencies throughout the entire electric displacement hysteresis. Experimental results showed significant increases in loss tangent (by nearly an order of magnitude) and compliance during domain switching, which shows promise as a new approach to structural damping. A continuum model of the viscoelasticity of ferroelectrics was developed, which incorporates microstructural evolution via internal variables and associated kinetic relations. For the first time, through a new linearization process, the incremental dynamic stiffness and loss tangent of materials were computed throughout the entire electric displacement hysteresis for different combinations of mechanical and electrical loading frequencies. The model accurately captured experimental results. Using the understanding gained from the characterization and modeling of PZT, two applications of domain switching kinetics were explored by using Micro Fiber Composites (MFCs). Proofs of concept of set-and-hold actuation and structural damping using MFCs were demonstrated.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Cavity-enhanced spectroscopies for applications of remote sensing, chemical kinetics and detection of radical species

This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O₂ and CO₂ for obtaining laboratory reference data in support of NASA’s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and ¹³C/¹²C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(¹D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado.

I. Thermochemistry and reaction kinetics of disolvated protons by ion cyclotron resonance spectroscopy. II. Thermochemical studies of small fluorocarbons by photoionization mass spectrometry

The disolvated proton, H(OH₂)₂⁺ is employed as a chemical reagent in low pressure (˂ 10^-5 torr) investigations by ion cyclotron resonance spectroscopy. Since termolecular reactions are absent at low pressure, disolvated protons are not generally observed. However H(OH₂)₂⁺ is produced in a sequence of bimolecular reactions in mixtures containing H₂O and one of a small number of organohalide precursors. Then a series of hydrated Lewis bases is produced by H₃O⁺ transfer from H(OH₂)₂⁺. In Chapter II, the relative stability of hydrated bases containing heteroatoms of both first and second row elements is determined from the preferred direction of H₃O⁺ transfer between BH(OH₂)⁺ complexes. S and P containing bases are shown to bind H₃O⁺ more weakly than O and N bases with comparable proton affinities. A simple model of hydrogen bonding is proposed to account for these observations.

H⁺ transfer from H(OH₂)₂⁺ to several Lewis bases also occurs at low pressure. In Chapter III the relative importance of H₃O⁺ transfer and H⁺ transfer from H(OH₂)₂⁺ to a series of bases is observed to be a function of base strength. Beginning with CH₃COOH, the weakest base for which H⁺ transfer is observed, the importance of H⁺ transfer increases with increasing proton affinity of the acceptor base. The nature of neutral products formed from H(OH₂)₂⁺ by loss of H⁺ is also considered.

Chapters IV and V deal with thermochemistry of small fluorocarbons determined by photoionization mass spectrometry. The enthalpy of formation of CF₂ is considered in Chapter IV. Photoionization of perfluoropropylene, perfluorocyclopropane, and trifluoromethyl benzene yield onsets for ions formed by loss of a CF₂ neutral fragment. Earlier determinations of ΔH^°_f298 (CF₂) are reinterpreted using updated thermochemical values and compared with results of this study. The heat of formation of neutral perfluorocyclopropane is also derived. Finally, the energetics of interconversion of perfluoropropylene and perfluorocyclopropane are considered for both the neutrals and their molecular ions.

In Chapter V the heats of formation of CF₃⁺ and CF₃I⁺are derived from photoionization of CF₃I. These are considered with respect to ion-molecule reactions observed in CF₃I monitored by the techniques of ion cyclotron resonance spectroscopy. Results obtained in previous experiments are also compared.