Molecular dynamics simulations of the adsorption and diffusion behavior of pure and mixed alkanes in silicalite

The adsorption and diffusion of mixed hydrocarbon components in silicalite have been studied using molecular dynamic simulation methods. We have investigated the effect of molecular loadings and temperature on the diffusional behavior of both pure and mixed alkane components. For binary mixtures with components of similar sizes, molecular diffusional behavior in the channels was noticed to be reversed as loading is increased. This behavior was noticeably absent for components of different sizes in the mixture. Methane molecules in the methane/propane mixture have the highest diffusion coefficients across the entire loading range. Binary mixtures containing ethane molecules prove more difficult to separate compared to other binary components. In the ternary mixture, however, ethane molecules diffuse much faster at 400 K in the channel with a tendency to separate out quickly from other components. © 2005 Elsevier Inc. All rights reserved.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Development of computer application for determination of chemical diffusion properties in biological tissues

The main objective of this work was to develop an application capable of determining the diffusion times and diffusion coefficients of optical clearing agents and water inside a known type of muscle. Different types of chemical agents can also be used with the method implemented, such as medications or metabolic products. Since the diffusion times can be calculated, it is possible to describe the dehydration mechanism that occurs in the muscle. The calculation of the diffusion time of an optical clearing agent allows to characterize the refractive index matching mechanism of optical clearing. By using both the diffusion times and diffusion of water and clearing agents not only the optical clearing mechanisms are characterized, but also information about optical clearing effect duration and magnitude is obtained. Such information is crucial to plan a clinical intervention in cooperation with optical clearing. The experimental method and equations implemented in the developed application are described in throughout this document, demonstrating its effectiveness. The application was developed in MATLAB code, but the method was personalized so it better fits the application needs. This process significantly improved the processing efficiency, reduced the time to obtain he results, multiple validations prevents common errors and some extra functionalities were added such as saving application progress or export information in different formats. Tests were made using glucose measurements in muscle. Some of the data, for testing purposes, was also intentionally changed in order to obtain different simulations and results from the application. The entire project was validated by comparing the calculated results with the ones found in literature, which are also described in this document.

Comparing charge transport predictions for a ternary electrolyte using the Maxwell–Stefan and Nernst–Planck equations

In this work, we investigate and compare the Maxwell–Stefan and Nernst–Planck equations for modeling multicomponent charge transport in liquid electrolytes. Specifically, we consider charge transport in the Li+/I−/I3−/ACN ternary electrolyte originally found in dye-sensitized solar cells. We employ molecular dynamics simulations to obtain the Maxwell–Stefan diffusivities for this electrolyte. These simulated diffusion coefficients are used in a multicomponent charge transport model based on the Maxwell– Stefan equations, and this is compared to a Nernst–Planck based model which employs binary diffusion coefficients sourced from the literature. We show that significant differences between the electrolyte concentrations at electrode interfaces, as predicted by the Maxwell–Stefan and Nernst–Planck models, can occur. We find that these differences are driven by a pressure term that appears in the Maxwell–Stefan equations. We also investigate what effects the Maxwell–Stefan diffusivities have on the simulated charge transport. By incorporating binary diffusivities found in the literature into the Maxwell–Stefan framework, we show that the simulated transient concentration profiles depend on the diffusivities; however, the simulated equilibrium profiles remain unaffected.

A cell migration device that maintains a defined surface with no cellular damage during wound edge generation

Studying the rate of cell migration provides insight into fundamental cell biology as well as a tool to assess the functionality of synthetic surfaces and soluble environments used in tissue engineering. The traditional tools used to study cell migration include the fence and wound healing assays. In this paper we describe the development of a microchannel based device for the study of cell migration on defined surfaces. We demonstrate that this device provides a superior tool, relative to the previously mentioned assays, for assessing the propagation rate of cell wave fronts. The significant advantage provided by this technology is the ability to maintain a virgin surface prior to the commencement of the cell migration assay. Here, the device is used to assess rates of mouse fibroblasts (NIH 3T3) and human osteosarcoma (SaOS2) cell migration on surfaces functionalized with various extracellular matrix proteins as a demonstration that confining cell migration within a microchannel produces consistent and robust data. The device design enables rapid and simplistic assessment of multiple repeats on a single chip, where surfaces have not been previously exposed to cells or cellular secretions.

Dynamic Micromapping of CO2 Sorption in Coal

We have applied X-ray and neutron small-angle scattering techniques (SAXS, SANS, and USANS) to study the interaction between fluids and porous media in the particular case of subcritical CO2 sorption in coal. These techniques are demonstrated to give unique, pore-size-specific insights into the kinetics of CO2 sorption in a wide range of coal pores (nano to meso) and to provide data that may be used to determine the density of the sorbed CO2. We observed densification of the adsorbed CO2 by a factor up to five compared to the free fluid at the same (p, T) conditions. Our results indicate that details of CO2 sorption into coal pores differ greatly between different coals and depend on the amount of mineral matter dispersed in the coal matrix: a purely organic matrix absorbs more CO2 per unit volume than one containing mineral matter, but mineral matter markedly accelerates the sorption kinetics. Small pores are filled preferentially by the invading CO2 fluid and the apparent diffusion coefficients have been estimated to vary in the range from 5 × 10-7 cm2/min to more than 10-4 cm2/min, depending on the CO2 pressure and location on the sample.

Dendritic structures produced on solidification of multicomponent aqueous solutions

Dendrite structures of ice produced on undirectional solidification of ternary and quaternary aqueous solutions have been studied. Upon freezing, solutions containing more than one solute produce plate-shaped dendrites of ice. The spacing between dendrites increase linearly with the distance from the chill surface and the square root of local solidification time (or square root of inverse freezing rate) for any fixed composition. For fixed freezing conditions, the dendrite spacings from multicomponent aqueous solutions were a function of the concentrations and diffusion coefficients of the individual solutes. The dendrite spacing produced by freezing of a solution was changed by the addition of a solute different from those already present. If the main diffusion coefficient of the added solute is higher than that of solutes already present, the dendrite spacing is increased and vice versa. The dendrite spacing in multi-component systems increases with the total solute concentration if the constituent solutes are present in equal amounts. The dendrite spacing obtained on freezing of these dilute multicomponent solutions can be expressed by regression equations of the type Image Full-size image (2K) where L is the dendrite spacing in microns, C1, C2 and C3 are concentrations of individual solutes, Θf is the total freezing time and A1 −A8 are constants. A Yates analysis of the dendrite spacings in a factorial design of quaternary solutions indicates that there are strong interactions between individual solutes in regard to their effect on the dendrite spacings. A mass transport analysis has been used to calculate the interdendritic supersaturation ΔC of the individual solutes, the supercooling in the interdendritic liquid ΔT, and the transverse growth velocity of the dendrites, VT. In ternary solutions if two solutes are present in equal amount the supersaturation of the solute with higher main diffusion coefficient is lower, and vice versa. If a solute with higher main diffusion coefficient is added to a binary solution, the interface growth velocity, the interdendritic supersaturation of the base solute and the interdendritic supercooling increase with the quantity of solute added.

Molecular Interactions Chlorin Assemblies and NMR Separations

Photosynthesis is a chemical process in which the energy of the light quanta is transformed into chemical energy. Chlorophyll (Chl) molecules play a key role in photosynthesis; they function in the antennae systems and in the photosynthetic reaction center where the primary charge separation (CS) takes place. Bio-inspired mimicry of the CS is an essential unit in dye-sensitized solar cells. Aim of this study was to design and develop electron donor-acceptor (EDA) pairs from Chls and fullerenes (C60) or carbon nanotubes (CNT). The supramolecular approach was chosen, as long synthetic sequences required by the covalent approach lead to long reaction schemes and low yields. Here, a π-interaction between soluble CNTs and Chl was used in EDA construction. Also, a beta-face selective two-point bound Chl-C60 EDA was introduced. In addition, the photophysical properties of the supramolecular EDA dyads were analyzed. In organic chemistry, nuclear magnetic resonance (NMR) spectroscopy is the most vital analytical technique in use. Multi-dimensional NMR experiments have enabled a structural analysis of complex natural products and proteins. However, in mixture analysis NMR is still facing difficulties. In many cases overlapping signals can t be resolved even with the help of multi-dimensional experiments. In this work, an NMR tool based on simple host-guest chemistry between analytes and macromolecules was developed. Diffusion ordered NMR spectroscopy (DOSY) measures the mobilities of compounds in an NMR sample. In a liquid state NMR sample, each of the analytes has a characteristic diffusion coefficient, which is proportional to the size of the analyte. With normal DOSY experiment, provided that the diffusion coefficients of the analytes differ enough, individual spectra of analytes can be extracted. When similar sized analytes differ chemically, an additive can be introduced into the sample. Since macromolecules in a liquid state NMR sample can be considered practically stationary, even faint supramolecular interaction can change the diffusion coefficient of the analyte sufficiently for a successful resolution in DOSY. In this thesis, polyvinylpyrrolidone and polyethyleneglycol enhanced DOSY NMR techniques, which enable mixture analysis of similar in size but chemically differing natural products, are introduced.

Light and heat induced interdiffusion in Sb/As2S3 nano-multilayered film

The light and heat induced changes in the optical band gap of Sb/As2S3 nanomultilayered chalcogenide film has been studied. Even though the changes in optical bandgap are attributed to the light and heat induced interdiffusion, the diffusional intermixing between the layers is rather different with light and heat. The observed difference in the light and heat induced interdiffusion is due to unequal diffusion coefficients of light and heat predicted by thermal spike model.

The fully implicit stochastic-alpha method for stiff stochastic differential equations

A fully implicit integration method for stochastic differential equations with significant multiplicative noise and stiffness in both the drift and diffusion coefficients has been constructed, analyzed and illustrated with numerical examples in this work. The method has strong order 1.0 consistency and has user-selectable parameters that allow the user to expand the stability region of the method to cover almost the entire drift-diffusion stability plane. The large stability region enables the method to take computationally efficient time steps. A system of chemical Langevin equations simulated with the method illustrates its computational efficiency.

Studies of the polarographic and coulometric behaviour of aromatic nitro-compounds: I. Nitrobenzene in ethanol

A detailed polarographic (a.c. and d.c.) and coulometric investigation of nitrobenzene has been made at various pH values in the presence of different concentrations of ethanol. Below pH 4.7, two waves are apparent but above this pH, the second wave does not appear. Coulometric evidence indicates that the first and second waves correspond to the four-and two-electron processes, respectively. The coulometric method was not applicable in sodium hydroxide and sodium acetate solutions. When the diffusion coefficients (from the diaphragm cell) are used in the Ilkovic equation, no reliable conclusions can be reached for the number of electrons involved in the reduction process in alkaline solutions. The a.c. polarographic method gives evidence for the formation of species such as: C6H5NO2H22+, C6H5NO2− and C6H5NO22−. Analysis of d.c. polarographic data by Delahay's treatment of irreversible waves, indicates that the number of electrons involved in the rate-determining step is 2. In sodium hydroxide solutions, however, the first main wave is split indicating more than one rate-determining step. The results presented in this paper indicate that the first wave in the reduction of nitrobenzene is a four-electron process at all pH values. The second wave, which appears below pH 4.7, corresponds to a two-electron process irrespective of wave heights. The difference in the a.c. polarographic behaviour in acid and alkaline solutions has given evidence for the formation of species like C6H5NO2H2, C6H5NO2−, and C6H5NO22.

Distribution of products around a burning droplet: an analytical approach

A knowledge of the concentration distribution around a burning droplet is essential if accurate estimates are to be made of the transport coefficients in that region which influence the burning rate. There are two aspects of this paper; (1) determination of the concentration profiles, using the simple assumption of constant binary diffusion coefficients for all species, and comparison with experiments; and (2) postulation of a new relation for the therinal conductivity, which takes into account the variations of both temperature and concentrations of various species. First, the theoretical concentration profiles are evaluated and compared with experimental results reported elsewhere [5]. It is found that the agreement between the theory and experiment is fairly satisfactory. Then, by the use of these profiles and the relations proposed in the literature for the thermal conductivity of a mixture of nonpolar gases, a new relation for thermal conductivity: K = (A1 + B1 T) + (A2 + B2 T) xr (21). is suggested for analytical solutions of droplet combustion problems. Equations are presented to evaluate A1, A2, B1, and B2, and values of these terms for a few hydrocarbons are tabulated.

The Influence of Titania on Creep in Superplastic Zirconia

Detailed high-temperature compression creep experiments on a pure 3 mol% yttria-stabilized tetragonal zirconia (3YTZ) and 3YTZ doped with 4.8 wt% TiO2 revealed that both materials exhibit a similar transition in stress exponents from n similar to 1 to n similar to 2 with a decrease in stress. The stress exponent of 1 and the inverse grain size dependence p of similar to 3 are consistent with the Coble diffusion creep at high stresses; the increase in stress exponent at low stresses is attributed to an interface-controlled diffusion creep process. Measurements revealed that grain-boundary sliding contributes to >similar to 50% of the total strain in both regions with n similar to 1 and n similar to 2, indicating the operation of the same fundamental deformation process in both regions. The creep data indicate that doping with TiO2 leads to an increase in the grain-boundary diffusion coefficients. The increase observed in the dihedral angle with doping is also consistent with the increase in grain boundary diffusion coefficient and the reported enhanced ductility in such materials.

Polarization relaxation, dielectric dispersion, and solvation dynamics in dense dipolar liquid

A unified treatment of polarization relaxation, dielectric dispersion and solvation dynamics in a dense, dipolar liquid is presented. It is shown that the information of solvent polarization relaxation that is obtained by macroscopic dielectric dispersion experiments is not sufficient to understand dynamics of solvation of a newly created ion or dipole. In solvation, a significant contribution comes from intermediate wave vector processes which depend critically on the short range (nearest‐neighbor) spatial and orientational order that are present in a dense, dipolar liquid. An analytic expression is obtained for the time dependent solvation energy that depends, in addition to the translational and rotational diffusion coefficients of the liquid, on the ratio of solute–solvent molecular sizes and on the microscopic structure of the polar liquid. Mean spherical approximation (MSA) theory is used to obtain numerical results for polarization relaxation, for wave vector and frequency dependent dielectric function and for time dependent solvation energy. We find that in the absence of translational contribution, the solvation of an ion is, in general, nonexponential. In this case, the short time decay is dominated by the longitudinal relaxation time but the long time decay is dominated by much slower large wave vector processes involving nearest‐neighbor molecules. The presence of a significant translational contribution drastically alters the decay behavior. Now, the long‐time behavior is given by the longitudinal relaxation time constant and the short time dynamics is controlled by the large wave vector processes. Thus, although the continuum model itself is conceptually wrong, a continuum model like result is recovered in the presence of a sizeable translational contribution. The continuum model result is also recovered in the limit of large solute to solvent size ratio. In the opposite limit of small solute size, the decay is markedly nonexponential (if the translational contribution is not very large) and a complete breakdown of the continuum model takes place. The significance of these results is discussed.

Use of metastable equilibria for determination of Gibbs energy of solids

Attempts are made to measure activities of both components of a binary alloy (A�B) at 650 K using a solid-state galvanic cell incorporating a new composite solid electrolyte. Since the ionic conductivity of the composite solid electrolyte is three orders of magnitude higher than that of pure CaF2, the cell can be operated at lower temperatures. The alloy phase is equilibrated in separate experiments with flourides of each component and fluorine potential is measured. The mixture of the alloy (A�B) and the fluoride of the more reactive component (BF2) is stable, while (A�B) + AF2 mixture is metastable, Factors governing the possible use of metastable equilibria have been elucidated in this study. In the Co�Ni system, where the difference in Gibbs energies of formation of the fluorides is 21.4 kJ/mol, emf of the cell with metastable phases at the electrode is constant for periods ranging from 90 to 160 ks depending on alloy composition. Subsequently, the emf decreases because of the onset of the displacement reaction. In the Ni�Mn system, measurement of the activity of Ni using metastable equilibria is not fully successful at 650 K because of the large driving force for the displacement reaction (208.8 kJ/mol). Critical factors in the application of metastable equilibria are the driving force for displacement reaction and diffusion coefficients in both the alloy and fluoride solid solution.