Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Deposizione elettrochimica di esacianoferrato di rame tramite un metodo "a due step"; caratterizzazione e valutazione delle prestazioni

In this thesis we have identified two electrochemical procedures for preparing two compounds of copper hexacyanoferrate (CuHCF) films with different compositions and structures. The deposition were carried out using a “two steps” method consisting in electrochemical oxidation of previously deposited metallic copper on carbon substrates (glassy carbon and graphite foil electrodes) in K3[Fe(CN)6] solution. Both films, CuHCF-methodA and CuHCF-methodB, were characterized by cyclic voltammetry (GC) and their study using XANES spectroscopy revealed evidence of different structures. Additionally, insertion and extraction of different cations (Na+, K+, Mg2+, Al3+ and Cs+) were performed and the results indicate that CuHCF-methodA has slightly better performances and operational stability than CuHCF-methodB. Data from galvanostatic charge-discharge tests confirme the latter observation. An application for amperometric detection of H2O2 and SEM micrographs are also reported for both films (method A and B). Comparing these results with a previous work of our research group, seems that the deposition of two different compounds using methodA and methodB is due to the different stoichiometry of ions Cu2+ e [Fe(CN)6]3– created near electrode surface during the dissolution step.

Atomistic simulations of 2D bicomponent self-assembly: from molecular recognition to self-healing

Supramolecular two-dimensional engineering epitomizes the design of complex molecular architectures through recognition events in multicomponent self-assembly. Despite being the subject of in-depth experimental studies, such articulated phenomena have not been yet elucidated in time and space with atomic precision. Here we use atomistic molecular dynamics to simulate the recognition of complementary hydrogen-bonding modules forming 2D porous networks on graphite. We describe the transition path from the melt to the crystalline hexagonal phase and show that self-assembly proceeds through a series of intermediate states featuring a plethora of polygonal types. Finally, we design a novel bicomponent system possessing kinetically improved self-healing ability in silico, thus demonstrating that a priori engineering of 2D self-assembly is possible.

Processing-structure-property relationships in solid-state shear pulverization: Parametric study of specific energy

Solid-state shear pulverization (SSSP) is a unique processing technique for mechanochemical modification of polymers, compatibilization of polymer blends, and exfoliation and dispersion of fillers in polymer nanocomposites. A systematic parametric study of the SSSP technique is conducted to elucidate the detailed mechanism of the process and establish the basis for a range of current and future operation scenarios. Using neat, single component polypropylene (PP) as the model material, we varied machine type, screw design, and feed rate to achieve a range of shear and compression applied to the material, which can be quantified through specific energy input (Ep). As a universal processing variable, Ep reflects the level of chain scission occurring in the material, which correlates well to the extent of the physical property changes of the processed PP. Additionally, we compared the operating cost estimates of SSSP and conventional twin screw extrusion to determine the practical viability of SSSP.

Processing-Structure-Property Relationships in Solid-State Shear Pulverization: Parametric Study of specific energy

Solid-state shear pulverization (SSSP) is a unique processing technique for mechanochemical modification of polymers, compatibilization of polymer blends, and exfoliation and dispersion of fillers in polymer nanocomposites. A systematic parametric study of the SSSP technique is conducted to elucidate the detailed mechanism of the process and establish the basis for a range of current and future operation scenarios. Using neat, single component polypropylene (PP) as the model material, we varied machine type, screw design, and feed rate to achieve a range of shear and compression applied to the material, which can be quantified through specific energy input (Ep). As a universal processing variable, Ep reflects the level of chain scission occurring in the material, which correlates well to the extent of the physical property changes of the processed PP. Additionally, we compared the operating cost estimates of SSSP and conventional twin screw extrusion to determine the practical viability of SSSP.

Adsorption behavior of redox-active suppressor additives: Combined electrochemical and STM studies

The redox chemistry and the related surface phase behavior of Safranine (SAF) and Janus Green B (JGB) have been studied by means of cyclic voltammetry in combination with in situ Scanning Tunneling Microscopy using HOPG (Highly Oriented Pyrolytic Graphite) and single crystalline Cu(1 0 0) as model substrates, both revealing different widths of the accessible potential windows. JGB and SAF serve as prototypical heterocyclic suppressor/leveler additives that are used for the metallization of 3D-TSVs (3D Through Silicon Vias) following a classical "leveling" concept. SAF can be considered as the reductive decomposition product of JGB that is formed at the copper/electrolyte interface upon electroplating. Both additives reveal a pronounced pH-dependent redox-chemistry with redox-transitions lying close to or even beyond the anodic limit of the copper potential window. Affected by these redox-processes are in particular the aromatic cores of those heterocycles that can be (quasi)reversibly reduced by a two electron transfer process within the potential window of copper. Therefore we identify the reduced form of those dyes as the active components for the suppressing/leveling effect in copper plating. STM data clearly shows a dye surface phase behavior that is crucially determined by its potential-dependent redox-chemistry. This will be exemplarily discussed for the SAF dye. On chloride-modified Cu(1 0 0) mono-reduced SAF forms a structurally well-defined monolayer of cationic stacking polymers. However, this coupled anion/cation layer reveals only minor suppressing capabilities with respect to the copper dissolution and deposition processes. Complete reduction of the aromatic heterocycle finally leads to the 3D precipitation of hydrophobic reaction products. 3D clusters of this SAF precipitate are discussed as the active structural motif for the suppressing effect of these dyes. (C) 2011 Elsevier Ltd. All rights reserved.

A gas ion source for radiocarbon measurements at 200 kV

The novel tabletop miniaturized radiocarbon dating system (MICADAS) at ETH Zurich features a hybrid Cs sputter negative ion source for the measurement of solid graphite and gaseous CO2 samples. The source produces stable currents of up to 6 mu A C- out of gaseous samples with an efficiency of 3-6%. A gas feeding system has been set up that enables constant dosing of CO2 into the Cs sputter ion source and ensures stable measuring conditions. The system is based on a syringe in which CO2 gas is mixed with He and then pressed continuously into the ion source at a constant flow rate. Minimized volumes allow feeding samples of 3-30 mu g carbon quantitatively into the ion source. In order to test the performance of the system, several standards and blanks have successfully been measured. The ratios of C-14/C-12 could be repeated within statistical errors to better than 1.0% and the C-13/C-12 ratios to better than 0.2%. The blank was < 1 pMC.

In-plane thermal conductivity modeling of carbon filled liquid crystal polymer based resins

Adding conductive carbon fillers to insulating thermoplastic resins increases composite electrical and thermal conductivity. Often, as much of a single type of carbon filler is added to achieve the desired conductivity, while still allowing the material to be molded into a bipolar plate for a fuel cell. In this study, varying amounts of three different carbons (carbon black, synthetic graphite particles, and carbon fiber) were added to Vectra A950RX Liquid Crystal Polymer. The in-plane thermal conductivity of the resulting single filler composites were tested. The results showed that adding synthetic graphite particles caused the largest increase in the in-plane thermal conductivity of the composite. The composites were modeled using ellipsoidal inclusion problems to predict the effective in-plane thermal conductivities at varying volume fractions with only physical property data of constituents. The synthetic graphite and carbon black were modeled using the average field approximation with ellipsoidal inclusions and the model showed good agreement with the experimental data. The carbon fiber polymer composite was modeled using an assemblage of coated ellipsoids and the model showed good agreement with the experimental data.

Characterization of thermal and mechanical properties of polypropylene-based composites for fuel cell bipolar plates and development of educational tools in hydrogen and fuel cell technologies

In this project we developed conductive thermoplastic resins by adding varying amounts of three different carbon fillers: carbon black (CB), synthetic graphite (SG) and multi-walled carbon nanotubes (CNT) to a polypropylene matrix for application as fuel cell bipolar plates. This component of fuel cells provides mechanical support to the stack, circulates the gases that participate in the electrochemical reaction within the fuel cell and allows for removal of the excess heat from the system. The materials fabricated in this work were tested to determine their mechanical and thermal properties. These materials were produced by adding varying amounts of single carbon fillers to a polypropylene matrix (2.5 to 15 wt.% Ketjenblack EC-600 JD carbon black, 10 to 80 wt.% Asbury Carbon's Thermocarb TC-300 synthetic graphite, and 2.5 to 15 wt.% of Hyperion Catalysis International's FIBRILTM multi-walled carbon nanotubes) In addition, composite materials containing combinations of these three fillers were produced. The thermal conductivity results showed an increase in both through-plane and in-plane thermal conductivities, with the largest increase observed for synthetic graphite. The Department of Energy (DOE) had previously set a thermal conductivity goal of 20 W/m·K, which was surpassed by formulations containing 75 wt.% and 80 wt.% SG, yielding in-plane thermal conductivity values of 24.4 W/m·K and 33.6 W/m·K, respectively. In addition, composites containing 2.5 wt.% CB, 65 wt.% SG, and 6 wt.% CNT in PP had an in–plane thermal conductivity of 37 W/m·K. Flexural and tensile tests were conducted. All composite formulations exceeded the flexural strength target of 25 MPa set by DOE. The tensile and flexural modulus of the composites increased with higher concentration of carbon fillers. Carbon black and synthetic graphite caused a decrease in the tensile and flexural strengths of the composites. However, carbon nanotubes increased the composite tensile and flexural strengths. Mathematical models were applied to estimate through-plane and in-plane thermal conductivities of single and multiple filler formulations, and tensile modulus of single-filler formulations. For thermal conductivity, Nielsen's model yielded accurate thermal conductivity values when compared to experimental results obtained through the Flash method. For prediction of tensile modulus Nielsen's model yielded the smallest error between the predicted and experimental values. The second part of this project consisted of the development of a curriculum in Fuel Cell and Hydrogen Technologies to address different educational barriers identified by the Department of Energy. By the creation of new courses and enterprise programs in the areas of fuel cells and the use of hydrogen as an energy carrier, we introduced engineering students to the new technologies, policies and challenges present with this alternative energy. Feedback provided by students participating in these courses and enterprise programs indicate positive acceptance of the different educational tools. Results obtained from a survey applied to students after participating in these courses showed an increase in the knowledge and awareness of energy fundamentals, which indicates the modules developed in this project are effective in introducing students to alternative energy sources.

Numerical modeling of the failure mechanisms in Si thin film anode for Li-ion batteries

In recent times, the demand for the storage of electrical energy has grown rapidly for both static applications and the portable electronics enforcing the substantial improvement in battery systems, and Li-ion batteries have been proven to have maximum energy storage density in all rechargeable batteries. However, major breakthroughs are required to consummate the requirement of higher energy density with lower cost to penetrate new markets. Graphite anode having limited capacity has become a bottle neck in the process of developing next generation batteries and can be replaced by higher capacity metals such as Silicon. In the present study we are focusing on the mechanical behavior of the Si-thin film anode under various operating conditions. A numerical model is developed to simulate the intercalation induced stress and the failure mechanism of the complex anode structure. Effect of the various physical phenomena such as diffusion induced stress, plasticity and the crack propagation are investigated to predict better performance parameters for improved design.

Processing and mechanical properties of cast aluminum containing scandium, zirconium, and ytterbium

A series of aluminum alloys containing additions of scandium, zirconium, and ytterbium were cast to evaluate the effect of partial ytterbium substitution for scandium on tensile behavior. Due to the high price of scandium, a crucible-melt interaction study was performed to ensure no scandium was lost in graphite, alumina, magnesia, or zirconia crucibles after holding a liquid Al-Sc master alloy for 8 hours at 900 °C in an argon atmosphere. The alloys were subjected to an isochronal aging treatment and tested for conductivity and Vickers microhardness after each increment. For scandium-containing alloys, peak hardnesses of 520-790 MPa, and peak tensile stresses of 138-234 MPa were observed after aging from 150-350 °C for 3 hours in increments of 50 °C, and for alloys without scandium, peak hardnesses of 217-335 MPa and peak tensile stresses of 45-63 MPa were observed after a 3 hour, 150 °C aging treatment. The hardness and tensile strength of the ytterbium containing alloy was found to be lower than in the alloy with no ytterbium substitution.

The Equilibrium Relations of Nickel Sulfide with Copper and Sodium Sulfides

The equilibrium relations of many of the metallic sulfides have long been a source of scientific and commer­cial interest, of particular interest, are the sulfides of nickel and copper, since the economic recovery of both of these useful metals, from their ores, involves the formation of a sulfide at some stage of the operations.

The Electrical Conductivity of the Copper-Aluminum Alloys.

Among the many aluminum alloys which have been studied are the binary copper-aluminum alloys. These have proven to be among the most useful of the alumi­num alloys thus far worked upon.

A Study of a Carbonaceous Gold Ore

The presence of graphite in the ore of the Missouri-McKee Mine has made its treatment by the methods now used quite unsatisfactory. The study was undertaken to de­velop a new flow sheet which would give a high recovery and yet be economical enough to handle low grade material.

SYNTHESIS OF GRAPHENE AND ITS APPLICATIONS FOR DYE-SENSITIZED SOLAR CELLS

Graphene, which is a two-dimensional carbon material, exhibits unique properties that promise its potential applications in photovoltaic devices. Dye-sensitized solar cell (DSSC) is a representative of the third generation photovoltaic devices. Therefore, it is important to synthesize graphene with special structures, which possess excellent properties for dye-sensitized solar cells. This dissertation research was focused on (1) the effect of oxygen content on the structure of graphite oxide, (2) the stability of graphene oxide solution, (3) the application of graphene precipitate from graphene oxide solution as counter electrode for DSSCs, (4) the development of a novel synthesis method for the three-dimensional graphene with honeycomb-like structure, and (5) the exploration of honeycomb structured graphene (HSG) as counter electrodes for DSSCs. Graphite oxide is a crucial precursor to synthesize graphene sheets via chemical exfoliation method. The relationship between the oxygen content and the structures of graphite oxides was still not explored. In this research, the oxygen content of graphite oxide is tuned by changing the oxidation time and the effect of oxygen content on the structure of graphite oxide was evaluated. It has been found that the saturated ratio of oxygen to carbon is 0.47. The types of functional groups in graphite oxides, which are epoxy, hydroxyl, and carboxylgroups, are independent of oxygen content. However, the interplanar space and BET surface area of graphite oxide linearly increases with increasing O/C ratio. Graphene oxide (GO) can easily dissolve in water to form a stable homogeneous solution, which can be used to fabricate graphene films and graphene based composites. This work is the first research to evaluate the stability of graphene oxide solution. It has been found that the introduction of strong electrolytes (HCl, LiOH, LiCl) into GO solution can cause GO precipitation. This indicates that the electrostatic repulsion plays a critical role in stabilizing aqueous GO solution. Furthermore, the HCl-induced GO precipitation is a feasible approach to deposit GO sheets on a substrate as a Pt-free counter electrode for a dye-sensitized solar cell (DSSC), which exhibited 1.65% of power conversion efficiency. To explore broad and practical applications, large-scale synthesis with controllable integration of individual graphene sheets is essential. A novel strategy for the synthesis of graphene sheets with three-dimensional (3D) Honeycomb-like structure has been invented in this project based on a simple and novel chemical reaction (Li2O and CO to graphene and Li2CO3). The simultaneous formation of Li2CO3 with graphene not only can isolate graphene sheets from each other to prevent graphite formation during the process, but also determine the locally curved shape of graphene sheets. After removing Li2CO3, 3D graphene sheets with a honeycomb-like structure were obtained. This would be the first approach to synthesize 3D graphene sheets with a controllable shape. Furthermore, it has been demonstrated that the 3D Honeycomb-Structured Graphene (HSG) possesses excellent electrical conductivity and high catalytic activity. As a result, DSSCs with HSG counter electrodes exhibit energy conversion efficiency as high as 7.8%, which is comparable to that of an expensive noble Pt electrode.