Eicosapentaenoic acid (EPA, C20:5, n-3) is a long chain crucial unsaturated fatty acid, essential for the regulation of critical biological functions in humans. Its benefits include the therapeutic treatment of cardiovascular disease, schizophrenia and Alzheimer's disease. The fungus Pythium irregulare (ATCC 10951) has great potential as a natural EPA producer. In this study, the electroporation conditions for P. irregulare were determined. The auxotrophic selectable genes ura, trp and his were respectively cloned into the plasmid pESC to construct shuttle vectors. Electroporation with 2.0kV and a 0.2cm cuvette was applied as the most effective condition for heterogeneous genes transformation. The yield and content of EPA and other components of total fatty acids (TFA) were further determined by the FAME approach with GC, as well as the analysis of biomass. The EPA content in P. irregulare with heterologous pESC-TRP vector reached 16.68 mg/g if cultured in auxotrophic medium, which showed a 52.33% increase compared to the wild-type P. irregulare. The maximum of EPA yield was 98.52 mg/L from P. irregulare containing the pESC-URA plasmid, a 32.28% increase over the wild-type. However, the maximum cell dried weight of these two organisms were respectively 6.13g/L and 5.3g/L, significantly less than the 6.80g/L of the wild-type. Not only was a feasible approach detected to electro-transform and increase the EPA yield of P. irregulare, this study also inferred that Ï -6 route was mainly involved in the EPA biosynthesis in this organism. An antisense RNA (asRNA) thermodynamic model was developed to design new asRNA constructs capable of fine-tuning gene expression knockdown. The asRNA technology is now identified as an effective and specific method for regulating microbial gene expression at the posttranscriptional level. This is done by targeting mRNA molecules. Although the study of regulation by small RNAs is advanced in eukaryotes, the regulation of expression through artificially introducing antisense oligodeoxynucleotides into host is still being developed in prokaryotes. To study the thermodynamics of asRNA and mRNA binding, (i) the fluorescence protein genes GFP and mCherry were separately cloned into the common pUC19 vector and (ii) antisense GFP and antisense mCherry DNA fragments were randomly amplified and inserted into the constructed plasmid under the control of an additional plac promoter and terminator. The expression level of fluorescence reporter proteins was determined by plate reader in this combinatorial study. A thermodynamic model to describe the relationship between asRNA binding and observed expression level was created. The study indicates two factors that minimum binding energy of the asRNA-mRNA complex and the percentage of asRNA binding mRNA were crucial for regulating the expression level. The correlation relationship between gene expression level and binding percentage multiplied by the minimum binding energy was found to show a good correlation between the thermodynamic parameters and the observed level of gene expression. The model has the potential to predict the sequence of asRNA and the approach will ultimately be applied to cyanobacteria to increase lipids production. Here, the long-term approach is to build metabolic switches from asRNA that can turn "on/off" various cellular programs and metabolic pathways at will in a fine-tuned manner. This will allow engineers to control metabolic activity in response to reactor conditions. / Master of Science

Biomolecular interactions are fundamentally important for a wide variety of biological processes. Understanding the temperature dependence of biomolecular interactions is hence critical for applications in fundamental sciences and drug discovery. Micro-Electro-Mechanical Systems (MEMS) technology holds great potential in facilitating temperature-dependent characterization of biomolecular interactions by providing on-chip microfluidic handling with drastically reduced sample consumption, and well controlled micro- or nanoscale environments in which biomolecules are effectively and efficiently manipulated and analyzed. This dissertation is focused on a high-through and miniaturized differential scanning calorimeter for thermodynamic study of bio-molecules using MEMS techniques. The dissertation firstly introduces the overall design and operation principles. This miniaturized DSC was fabricated based on a polyimide (PI) thin film. Highly temperature sensitive vanadium oxide was used as the thermistor material. A PDMS (Polydimethylsiloxane) microfluidic chamber was separately fabricated and then bonded firmly with the PI substrate by a stamp-and-stick method. Meanwhile, the micro heater design was optimized to reach better uniformity. A heating stage was constructed for fast and reliable scanning. In this study, we used syringes to deliver the 0.63 μL liquid sample into both the sample and reference chambers. All the testing processes were functionalized using the LabVIEW programs. The sensing material was also characterized. To seek a higher temperature coefficient of resistance (TCR) and less resistive behavior, explorations about various PVD (physical vapor deposition) parameters and annealing conditions were conducted for optimization. In this research, we found vanadium oxide deposited under certain conditions leads to the highest TCR value (a maximum of 2.51%/oC). To better understand the material’s property, we also did the XRD (X-ray Diffraction), SEM (Scanning electron microscope). The micro calorimeter was calibrated using a step thermal response. The time constant was around 3s, the thermal conductance was 0.6mW/K, and the sensitivity was 6.1V/W. The static power resolution of the device at equilibrium is 100 nW, corresponding to 250 nJ/K. These performances confirmed the design and material to be appropriate for both good thermal isolation and power sensitivity. We demonstrated the miniaturized DSC’s performance on several different kinds of protein samples: lysozyme, and mAb (monoclonal antibody) and a DVD IgG (double variable domain immunoglobulin G). The results were found to be reasonable by comparing it with the commercial DSC’s tests. Finally, this instrument may be ideal for incorporation into high throughput screening workflows for the relative comparison of thermal properties between large numbers of proteins when only small quantities are available. The micro-DSC has the potential to characterize the thermal stability of the protein sample with significantly higher throughput and less sample consumption, which could potentially reduce the time and cost for the drug formulation in the pharmaceutical industry. / Ph. D. / Virtually all biological phenomena depend on molecular interactions, which is either intra-molecular as protein folding/unfolding or intermolecular as in ligand binding. A basic biology problem is to understand the folding and denaturation processes of a protein: the kinetics, thermodynamics and how a protein unfolds and folds back into its native state. Both folding/unfolding and denaturation processes are associated with enthalpy changes. The thermodynamics of binding compounds helps a great deal to understand the nature and potency of such molecules and is essential in drug discovery. As a label-free and immobilization-free method, calorimetry can evaluate the Gibbs free energy, enthalpy, entropy, specific heat, and stoichiometry, and thus provides a fundamental understanding of the molecular interactions. Calorimetric systems including isothermal titration calorimeters (ITC) and differential scanning calorimeters (DSC) are the gold standard for characterizing molecular interactions. In this research, a micro DSC is developed for direct thermodynamic study of bio-molecules. Compared with the current commercial DSC, it is on a much smaller scale. It consumes much less sample and time in each DSC measurement. It can enable comprehensive high-content thermodynamics study in the early stage of drug discovery and formulation. It also enables direct, precise, and rapid evaluation of the folding and unfolding of the large biomolecules like proteins, DNAs, and enzymes without labeling or immobilization. It can also be used as a powerful tool to study the membrane proteins, which is often impractical or impossible before.

Yes / Arsenic (As) contamination of surface water has become a global concern, especially for the third world countries, and it is imperative to develop advanced materials and an effective treatment method to address the issue. In this paper, iron doped ZIF-8@MXene (Fe-ZIF-8@MXene) was prepared as a potential adsorbent to effectively and simultaneously remove As(III/V) from wastewater. To investigate this, Fe-ZIF-8@MXene was characterized before and after the removal of mixed As(III/V). The results of Fourier transform infrared (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), specific surface area (BET) and point of zero charge (pHpzc) showed that Fe-ZIF-8@MXene was prepared successfully and kept a stable structure after As(III) and As(V) adsorption. The particle size of Fe-ZIF-8@MXene was in the range of 0.5 μm to 2.5 μm, where its BET was 531.7 m2/g. For both contaminants, adsorption was found to follow pseudo-second-order kinetics and was best-fitted by the Langmuir adsorption model with correlation coefficients (R2) of 0.998 and 0.997, for As(III) and As(V), respectively. The adsorbent was then applied to remove As from two actual water samples, giving maximum removal rates of 91.07% and 98.96% for As(III) and As(V), respectively. Finally, removal mechanisms for As(III/V) by Fe-ZIF-8@MXene were also explored. During the adsorption, multiple complexes were formed under the effect of its abundant surface functional groups involving multiple mechanisms, which included Van der Waals force, surface adsorption, chemical complexation and electrostatic interactions. In conclusion, this study demonstrated that Fe-ZIF-8@MXene was an advanced and reusable material for simultaneous removal of As(III/V) in wastewater.

The current understanding of the mechanical properties and deformation behavior of some individual phases in titanium alloys is limited due to the fine scale at which these phases precipitate within the β-phase matrix. The α and ω phases represent the most widely observed phases in titanium alloys depending on the alloy composition and also the heat treatment procedure adopted during processing. The possibility of precipitating ω-phase depends on the content of the β-stabilizers within the system. Although a significant compositional partitioning occurs within ω-phase upon aging treatment, the knowledge of ω-phase mechanical properties as a function of composition is very limited. The initial part of the current work focuses on the effect of common β-stabilizers elements on the phase stability and mechanical properties of the ω-phase using first-principles calculations. A relation between the bonding nature, the phase stability, and elastic properties was proposed. Thereafter αʺ martensitic phase was investigated in Ti-Nb and Ti-Nb-O alloys. The phase stability and martensitic start temperature of αʺ-phase was studied as a function of Nb and oxygen content. Also, the effect of the lattice shear distortion induced by oxygen atom on stabilizing β-phase was investigated. Subsequently the effect of the β-stabilizers' elements on stacking faults energy and ductility in α-Ti alloys was studied. Both prismatic and basal slip system were investigated with different concentration of β-stabilizers at the slip plane. Lastly, while the Tadmor and Bernstein model was employed to predict the partial dislocation emission and twinning propensity, the Rice criterion was used to estimate the effect of different β-stabilizers on the ductility of α-Ti alloys.

The Fe-C-Cr-Mn-Ni-O system is of fundamental importance when describing the influence of oxygen on high alloyed steels. Both solid and liquid phases are of great interest: The solid phases regarding oxidation processes like the formation of oxide layers, inner oxidation, sintering processes and high temperature corrosion. The liquid phase is of interest concerning the interaction between steel and its slag in a metallurgical context. In this thesis the thermodynamic properties of this system is described using the Calphad technique. The main idea of the Calphad technique is to describe the Gibbs energy of all phases in the system as a function of temperature, pressure and composition using appropriate thermodynamic models. When thermodynamic descriptions of all phases taking part in the system are modelled and described in a database, the equilibrium state could be calculated with a software that minimizes the total Gibbs energy. Models within the compound energy formalism are used for all solution phases, among them the ionic two-sublattice liquid model, to describe both the metallic and oxide melts. All simple spinels (Cr3O4, FeCr2O4, Fe3O4, FeMn2O4, Mn3O4, MnCr2O4, NiCr2O4, NiFe2O4, NiMn2O4) within this system are described using a four-sublattice model. In this thesis several binary and ternary systems have been assessed or partly reassessed. The Fe-C-Cr-Mn-Ni-O database achieved can be used with an appropriate thermodynamic software to calculate thermodynamic properties, equilibrium states and phase diagrams. In general, the agreement between calculated and experimental values is good. / QC 20100723

<p>The main focus in the present work concerns calculations on steel/slag equilibria. Thermodynamic software and databases are now powerful and accurate enough to give reliable results when applied to complex metallurgical processes. One example is the decarburization process of high alloyed steels. It is shown that using advanced thermodynamic models, without a complicated kinetic description of the system, reasonable agreement with experimental data is obtained. The calculations are performed using the Thermo-Calc software.</p><p>Within this work a Java interface for Thermo-Calc has been implemented. Java gives graphical possibilities and a graphical interface has been created that facilitates calculations that involve both metallic phases as well as oxides and make them feasible also for an industrial user.</p>

The substance of present work is to provide standard thermodynamic functions (STF) of small size molecules for the calculation of the composition and thermodynamic properties of low-temperature plasma, and also method for such a calculation applying obtained STF under non-ideal plasma conditions. With a view to further application in modelling the phenomena in thermal plasma the range of pressures is limited to the region from 0.01 bar to 100 bar, and that of temperature to 298.15–50 kK. To obtain STF the method of partition function resulting from statistical mechanics was proposed. State of art in the given scientific area and theoretical basis of the statistical mechanics required for establishing of the proposed method together with discussion of partition function divergence problem have been reviewed. For the calculation of STF of diatomic molecules the method of direct summation has been employed, whereas, as for the larger size molecules, the rigid rotor and harmonic oscillator model have been generally adopted. The spectral data required for the calculations have been taken from literature, or, in selected cases, these have been computed by quantum chemistry ab initio techniques. The resulting STF have been included into already existing database system of thermodynamic properties and those can serve as input data for subsequent thermodynamic calculations. A general method has been worked out for the purpose of the computation of thermodynamic properties and composition of non-ideal homogenous plasma system in thermodynamic equilibrium. The method is based on minimizing total Gibbs energy to compute at constant pressure or Helmholtz energy to compute at constant volume. The computation algorithm was implemented into computer program and subsequently applied to the computation of the composition and thermodynamic properties of SF6 dissociation and ionization products using obtained STF.

The main focus in the present work concerns calculations on steel/slag equilibria. Thermodynamic software and databases are now powerful and accurate enough to give reliable results when applied to complex metallurgical processes. One example is the decarburization process of high alloyed steels. It is shown that using advanced thermodynamic models, without a complicated kinetic description of the system, reasonable agreement with experimental data is obtained. The calculations are performed using the Thermo-Calc software. Within this work a Java interface for Thermo-Calc has been implemented. Java gives graphical possibilities and a graphical interface has been created that facilitates calculations that involve both metallic phases as well as oxides and make them feasible also for an industrial user. / QC 20101118

L'interaction non-covalente entre un ligand et un récepteur selon un modèle clé-serrure constitue une des bases essentielles de tout système biologique. La présence de multiples clés et serrures sur les biomolécules conduit à des interactions multivalentes. Les lectines sont très fréquemment structurées en homo-multimères et sont donc des cibles de choix pour l'étude des interactions avec des structures multivalentes glycosylées. Ligands et récepteurs multivalents peuvent obéir à plusieurs mécanismes d'association conduisant à des profils thermodynamiques et cinétiques permettant de rationnaliser les améliorations spectaculaires d'affinité souvent observées. L'utilisation de ligands de faible valence et de petite taille permet une présentation contrôlée des sucres au travers d'une structure unique bien définie. Ces glycoclusters sont des plateformes adaptées à l'étude de l'influence de la topologie de la présentation des sucres sur l'interaction. La synthèse de glycoclusters a été optimisée selon une voie convergente de glycosylation puis de couplage par CuAAC permettant la synthèse de structures multi-glycosylées telles que des calix[4]arènes de différentes conformations, des peptoïdes linéaires et cycliques ou encore des porphyrines. Ces ligands ont été évalués par quatre techniques d'analyse des interactions (HIA, ELLA, SPR, ITC) principalement en présence de la lectine PA-IL de Pseudomonas aeruginosa mais également avec la Galectine-1 humaine et la lectine d'Erythrina cristagalli (légumineuse). Des glycoclusters de seconde génération ont été ensuite été préparés avec l'objectif d'optimiser les composantes enthalpiques et entropiques de l'interaction. Les résultats indiquent que de légères modifications de la présentation des sucres peuvent induire des mécanismes d'association différents. La conception de structures rigidifiées a révélé des profils thermodynamiques contre-intuitifs qui ont pu être modélisés. Par cette étude, plusieurs ligands ont montré des affinités sans précédent pour la lectine PA-IL. Le meilleur ligand multivalent de première génération a confirmé un potentiel thérapeutique prometteur in vivo. / Following Fischer's “lock-key“ concept, non-covalent interactions between a ligand and its receptor is one of the most fundamental process of any biological system. The presence of multiple keys and locks at the surface of many biomolecules leads to multivalent interactions. Lectins are appropriate partners for the study of multivalent interactions with multivalent glycoconjugates since lectins are generally organized as homomultimers. Association of ligands and receptors can occur through several mechanisms leading to distinct thermodynamic and kinetic patterns. Thermodynamic and kinetic parameters often rationalize the impressive affinity improvement observed in the context of multivalent interactions. Small and low valency multivalent ligands provide a neat organization of carbohydrates through a single well-defined structure. These glycoclusters are appropriate probes for studying the influence of the overall topology on the interaction. Glycocluster synthesis was optimized according to a convergent strategy consisting of a glycosidation reaction followed by multiple CuAAC couplings. This strategy yielded a library of glycoclusters based on conformers of calix[4]arenes, linear and cyclic peptoids and porphyrins scaffolds. Glycoclusters were evaluated thanks to a combination of four biochemical techniques (HIA, ELLA, SPR, ITC) mainly versus PA-IL, a tetrameric lectin from Pseudomonas aeruginosa. Further investigations of these ligands were performed with a plant lectin from Erythrina cristagalli and with human galectin-1. Second generation glycoclusters were prepared in order to optimize enthalpic and entropic contributions to the interaction. Results indicate that a slight modification of the glycocluster topology could induce different mechanisms. The design of glycoclusters with stiffened linkers highlights unexpected entropic patterns. Molecular modeling of these linkers provided rationalization of these entropic patterns on the basis of Boltzmann distribution. This work present glycoclusters with an unprecedented affinity for PA-IL. The best first generation glycocluster confirmed promising therapeutic potentialities in vivo.

For many decades zirconium alloys have been commonly used in the nuclear power industry as fuel cladding material. Besides their good corrosion resistance and acceptable mechanical properties the main reason for using these alloys is the low neutron absorption. Zirconium alloys are exposed to a very severe environment during the nuclear fission process and there is a demand for better design of this material. To meet this requirement a thermodynamic database is useful to support material designers. In this thesis some aspects of the development of a thermodynamic database for zirconium alloys are presented. A thermodynamic database represents an important facility in applying thermodynamic equilibrium calculations for a given material providing: 1) relevant information about the thermodynamic properties of the alloys e.g. amount and composition of phases, oxygen activity, heat capacity etc, and 2) significant information for the manufacturing process e.g. heat treatment temperature. The basic information in the database is first the unary data, i.e. pure elements; those are taken from the compilation of the Scientific Group Thermodata Europe (SGTE) and then the binary and ternary systems. All phases present in those binary and ternary systems are described by means of the Gibbs energy as a function of composition and temperature. Many of those binary systems have been taken from published or unpublished works and others have been assessed in the present work. The elements included in the databse are: C, Fe, Cr, Nb, Ni, Mo, O, Si, Sn, and Zr + H, and the assessment performed under this thesis are: Cr-Sn, Mo-Zr, Sn-Zr, Fe-Nb-Zr and Nb-O-Zr. All the calculations have been made using Thermo-Calc software and the representation of the Gibbs energy obtained by applying Calphad technique with some use of ab initio calculations. / QC 20100902