Considerable jump and slip phenomena are observed at the non-equilibrium phase interface in microflows. Hence, accurate modelling of the liquid-vapour interface transport mechanisms that matches the observations is required, e.g. in applications such as micro/nanotechnology and micro fuel cells. In the sharp interface model, the classical Navier-Stokes-Fourier (NSF) equations can be used in the liquid and vapour phases, while the interface resistivities describe the jump and slip phenomena at the interface. However, resistivities are challenging to find from the measurements, and most of the classical kinetic theories consider them as constants. One possible approach is to determine them from a model that resolves the phase interface. In order to resolve the interface and the transport processes at and in front of the interface in high resolutions, there are two ways in general, microscopic or macroscopic. The microscopic studies are based either on molecular dynamics (MD) or kinetic models, such as the Enskog-Vlasov (EV) equation. The EV equation modifies the Boltzmann equation by considering dense gas effects, such as the interaction forces between the particles and their finite size. It can be solved by the Direct Simulation Monte Carlo (DSMC) method, which considers sample particles that stand in for thousands to hundred thousands of particles and determine most likely collisions based on interaction probabilities, but it is time-consuming and costly. Here, a closed set of 26-moment equations is numerically solved to resolve the liquid-vapour interface macroscopically while considering the dense gas and phase change effects. The 26-moment set of equations is derived by Struchtrup & Frezzotti as an approximation of the EV equation using Grad's moment method. The macroscopic moment equations resolve the phase interface in a high resolution competitive to the microscopic studies. The resolved interface visualizes the interface structure and the changes of the system variables between the two phases at the interface. The 26-moment equations are solved for a one-dimensional steady-state system for non-equilibrium evaporation/condensation process. Then, solutions are used to find the jump and slip conditions at the interface, which leads to determining the interface resistivities at different interface temperatures and non-equilibrium strengths from the Linear Irreversible Thermodynamics (LIT). The interface resistivities show their dependence on the temperature of the liquid at the interface as well as the strength of the non-equilibrium process. As a result, in further studies, similar systems can be modelled using the sharp interface method with the appropriate jump conditions at the phase interface that can be found from the determined EV interface resistivities. / Graduate

[pt] Na Termodinâmica estocástica, o calor é uma variável aleatória que flutua estatisticamente e, portanto, precisa ser investigada por meio de métodos estatísticos. Para compreender essa quantidade, a investigamos em diversos sistemas, como superamortecidos, subamortecidos, não-lineares, isotérmicos e não-isotérmicos. Os resultados aqui obtidos podem ser divididos em duas contribuições: a caracterização das distribuições de calor e dos momentos para diferentes sistemas, e a correção da fórmula do calor para sistemas superamortecidos, onde descobrimos a necessidade de incluir a energia cinética, que era previamente ignorada na literatura. Esta tese tem como foco a compreensão do calor, quantidade fundamental na termodinâmica estocástica. / [en] In Stochastic Thermodynamics, heat is a random variable that statistically fluctuates and therefore needs to be investigated using statistical methods. To understand this quantity, we investigated it for various systems, overdamped, underdamped, nonlinear, isothermal, and non-isothermal. The resultsobtained here can be divided into two contributions, the characterization ofthe distributions of heat and the moments in these different systems, and thecorrection of the formula of heat for overdamped systems, where we discoveredthe need to include the kinetic energy that was previously ignored in the literature. This thesis focuses on understanding heat, a quantity that is fundamentalin stochastic thermodynamics.

Thesis: B.S., Massachusetts Institute of Technology, Department of Mechanical Engineering, 1976 / Includes bibliographical references. / by A. Ken Yasuda. / B.S. / B.S. Massachusetts Institute of Technology, Department of Mechanical Engineering

No description available.

Master of Science / Department of Biochemistry / Paul E. Smith / We are developing a force field (FF) for molecular dynamics (MD) simulations of peptides and small proteins that is grounded in the Kirkwood-Buff theory of solutions. Here we present the Kirkwood-Buff Force Field (KBFF) parameters for the aromatic amino acids, based upon simulations of binary mixtures of small molecules representative of these amino acids over their entire composition ranges (excluding Histidine). Many aromatics are not fully soluble in water, so they have instead been studied in solvents of methanol or toluene. The parameters were developed by studying the following binary solutions: Phenylalanine − benzene + methanol, toluene + methanol, and toluene + benzene; Tyrosine − toluene + phenol and toluene + p-Cresol; Tryptophan − pyrrole + methanol and indole + methanol; Histidine − pyrrole + methanol, pyridine + methanol, pyridine + water, histidine + water (at 0.25 molal), and histidine monohydrochloride + water (at 0.3 molal and 0.6 molal). Our simulations reproduce the Kirkwood-Buff integrals, which guarantees that the KBFF provides an adequate balance of solute-solvent, solute-solute, and solvent-solvent interactions. Additionally, we show that the KBFF does not sacrifice reproduction of other solution properties in order to achieve this improved description of intermolecular interactions. We present these results as validating evidence for the future use of the KBFF in simulations of peptides and small proteins.

<p>Virtually all biologically relevant functions and processes are mediated by non-covalent, molecular recognition events, demonstrating astonishingly diverse affinities and specificities. Despite extensive research, the origin of affinity and specificity in aqueous solution - specifically the relationship between ligand binding thermodynamics and structure - remains remarkably obscure and is further complicated in the context of multivalent interactions. Multivalency describes the combinatorial interaction of multiple discrete epitopes across multiple binding surfaces where the association is considered as the sum of contributions from each epitope and the consequences of multivalent ligand assembly. Gaining the insight necessary to predictably influence biological processes with novel therapeutics begins with an understanding of the molecular basis of solution-phase interactions, and the thermodynamic parameters that follow from those interactions. Here we continue our efforts to understand the basis of aqueous affinity and the nature of multivalent additivity.</p><p>Multivalent additivity is the foundation of fragment-based drug discovery, where small, low affinity ligands are covalently assembled into a single high affinity inhibitor. Such systems are ideally suited for investigating the thermodynamic consequences of multivalent ligand assembly. In the first part of this work, we report the design and synthesis of a fragment-based ligand series for the Grb2-SH2 protein and thermodynamic evaluation of the low affinity ligand fragments compared to the intact, high affinity inhibitor by single and double displacement isothermal titration calorimetry (ITC). Interestingly, our investigations reveal positively cooperative multivalent additivity - a binding free energy of the full ligand greater than the sum of its constituent fragments - that is largely enthalpic in origin. These results contradict the most common theory of multivalent affinity enhancement arising from a "savings" in translational and rotational entropy. The Grb2-SH2 system reported here is the third distinct molecular system in which we have observed enthalpically driven multivalent enhancement of affinity.</p><p>Previous research by our group into similar multivalent affinity enhancements in protein-carbohydrate systems - the so-called "cluster glycoside effect" - revealed that evaluation of multivalent interactions in the solution-phase is not straightforward due to the accessibility of two disparate binding motifs: intramolecular, chelate-type binding and intermolecular, aggregative binding. Although a number of powerful techniques for evaluation of solution-phase multivalent interactions have been reported, these bulk techniques are often unable to differentiate between binding modes, obscuring thermodynamic interpretation. In the second part of this work, we report a competitive equilibrium approach to Molecular Recognition Force Microscopy (MRFM) for evaluation of ligand binding at the single-molecule level with potential to preclude aggregative associations. We have optimized surface functionalization strategies and MRFM experimental protocols to evaluate the binding constant of surface- and tip-immobilized single stranded DNA epitopes. Surprisingly, the monovalent affinity of an immobilized species is in remarkable agreement with the solution-phase affinity, suggesting the competitive equilibrium MRFM approach presents a unique opportunity to investigate the nature of multivalent additivity at the single molecule level.</p> / Dissertation

This research addresses the manufacturing problems of the fuel cell in an applied industrial approach with the aim of investigating the technology of manufacturing of Proton Exchange Membrane (PEM) fuel cells, and using this technology in reducing the cost of manufacturing through simplifying the design and using less exotic materials. The first chapter of this thesis briefly discusses possible energy alternatives to fossil fuels, arriving at the importance of hydrogen energy and fuel cells. The chapter is concluded with the main aims of this study. A review of the relevant literature is presented in chapter 2 aiming to learn from the experience of previous researchers, and to avoid the duplication in the current work. Understanding the proper working principles and the mechanisms causing performance losses in fuel cells is very important in order to devise techniques for reducing these losses and their cost. This is covered in the third chapter of this thesis which discusses the theoretical background of the fuel cell science. The design of the fuel cell module is detailed in chapter 4, supported with detailed engineering drawings and a full description of the design methodology. So as to operate the fuel cell; the reactant gases had to be prepared and the performance and operating conditions of the fuel cell tested, this required a test facility and gas conditioning unit which has been designed and built for this research. The details of this unit are presented in chapter 5. In addition to the experimental testing of the fuel cell under various geometric arrangements, a three dimensional 3D fully coupled numerical model was used to model the performances of the fuel cell. A full analysis of the experimental and computational results is presented in chapter 6. Finally, the conclusions of this work and recommendations for further investigations are presented in chapter 7 of this thesis. In this work, an understanding of voltage loss mechanism in the fuel cell based on thermodynamic irreversibility is introduced for the first time and a comprehensive formula for efficiency based on the actual operating temperature is presented. Furthermore, a novel design of a 100W (PEMFC) module which is apt to reduce the cost of manufacturing and improve water and thermal management of the fuel cell is presented. The work also included the design and manufacturing of a test facility and gas conditioning unit for PEM fuel cells which will be useful in performing further experiments on fuel cells in future research work. Taking into consideration that fuel cell technology is not properly revealed in the open literature, where most of the work on fuel cells does not offer sufficient information on the design details and calculations, this thesis is expected to be useful in the manifestation of fuel cell technology. It is also hoped that the work achieved in this study is useful for the advancement of fuel cell science and technology.

The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles, but has been limited by particle instability. Previously, it was found the three-way junction (3WJ) of the Phi29 DNA packaging motor pRNA was found to be ultra-stable and assemble in solution without the presence of metal ions. The three-way junction is composed of three short oligo RNA strands and proven to be thermodynamically stable. Here the assembly mechanism, thermodynamic and enzymatic stabilities, and kinetics are examined in order to understand the stability behind this unique motif. Thermodynamic and kinetics studies found that the pRNA 3WJ formed out of three components at a rapid rate creating a single-step three component collision with a lack of dimer intermediate formation while being governed by entropy, instead of the commonly seen enthalpy. Furthermore, the pRNA 3WJ proved to be stable at temperatures above 50 °C, concentrations below 100 pM, and produced a free energy of formation well below other studied RNA structures and motifs. With the high stability and folding efficiency of the pRNA 3WJ, it serves as an ideal platform for multi-branched RNA nanoparticles constructed through bottom-up techniques. RNA nanoparticles were constructed for the specific targeting of prostate cancer cells expressing Prostate Specific Membrane Antigen (PSMA) by receptor mediated endocytosis through the addition of an RNA aptamer; and the delivery of anti-miRNA sequences for gene regulation. The resulting nanoparticles remained stable while showing highly specific binding and entry in PSMA positive cells through cell surface receptor endocytosis. Furthermore, the entry of the nanoparticles allowed for the knockdown of against onco-miRNAs. Nanoparticles harboring antimiRNAs led to the upregulation of tumor suppressor genes, and signaling of apoptotic pathways. These findings display RNA nanotechnology can result in the production of stable nanoparticles and result in the specific treatment of cancers, specifically prostate cancer.

Thesis (MSc (Chemistry and Polymer Science))--Stellenbosch University, 2008. / Please refer to full text to view abstract.

Various techniques of fabricating surface patterns of small scales have been widely studied due to the potential applications of surface patterns in a variety of areas. It is a challenge to fabricate well-ordered surface area efficiently and economically. Evaporation-induced surface patterning is a promising approach to fabricate well-ordered surface patterns over a large area at low cost. In this study, the evaporation-induced surface patterns with controllable geometrical characteristics have been constructed. The dewetting kinetics on deformable substrate is also investigated. Using simple templates to control the geometry and the evaporation behavior of a droplet of volatile solvent, various gradient surface patterns, such as concentric rings, multiple straight stripes formed with a straight copper wire, etc. have been constructed on PMMA films. The wavelength and amplitude are found to decreases with the decrease of the distance to the objects used in templates. There is also a nearly linear relation between the amplitude and wavelength. The effects of several experimental parameters on the geometrical characteristics of the surface structures are studied, i.e. dimensions of the template, film thickness (solution concentration), substrate temperature, etc. The wavelength and amplitude increase with the increase of the film thickness (solution concentration), with the increase of the dimension of the template. However with the increase of the substrate temperature, the wavelength increases, while the amplitude decrease. Hexagonal network in pre-cast PMMA film have been fabricated by a “breath figure” approach at low humidity and low substrate temperature. The dimensions of the hexagonal holes are dependent on the template size and film thickness. The kinetics of the evaporative dewetting of a liquid (toluene) film on a deformable substrate (PMMA film) with the confinement of a circular copper ring is also studied. The liquid film first dewets from the outside towards the copper ring. When a critical volume is reached, an internal contact line appears, which dewets from the center to the copper ring smoothly with a constant velocity, then switches to a “stick-slip” motion. The average velocity of the smooth motion increases with the increase of the copper ring size and film thickness.