Thesis (doctoral)--Swedish University of Agricultural Sciences, 2007. / Thesis documentation sheet inserted. Includes appendix with four papers co-authored with others. Includes bibliographical references. Issued also electronically via World Wide Web in PDF format; online version lacks appendix.

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2006. / Thesis documentation sheet inserted. Appendix includes reproductions of six papers and manuscripts co-authored with others. Includes bibliographical references. Also issued electronically via World Wide Web in PDF format; online version lacks appendix of papers; ill. in online version displays in color.

The modeling of transport behavior of charged particles carried out in our laboratory is based on classical continuum electro kinetic theory. It is applied to a variety of systems from small electrolyte ions to macromolecules including peptides, DNA and nanoparticles. Systems range from weakly charged particles to highly charged ones. Transport properties studied include conductance, electrophoresis, and diffusion. In this dissertation, the conductance of polyvalent electrolytes ions is studied both by a “small ion” model [R.M. Fuoss, L. Onsager, J. Phys. Chem. 61 (1957) 668] and “large ion” model [R.W. O’Brien, L.R. White, J. Chem. Soc. Faraday Trans. 2 (74) (1978) 1607)]. Also, the coarse-grained continuum primitive model is developed and used to characterize the titration and electrical conductance behavior of aqueous solutions of fullerene hexa-malonic acid, which is a highly charged electrolyte with an absolute valence charge as high as 12. Free solution electrophoresis is closely related to conductance and a coarse-grained bead modeling methodology, BMM, developed in the Allison’s laboratory starting in 2006, is generalized to characterize peptide systems with respect to the charge, conformation, and possibly specific interactions with components of the BGE. For weakly charged peptides, the electrostatic potential is treated at the level of linear Poisson-Boltzmann equation, which predicts the electrophoretic mobility with considerable accuracy [S. Allison, H. Pei, U. Twahir, H. Wu, J. Sep. Sci., 2010, 33(16):2430-2438], but fails for highly charged systems. A new nonlinear Poisson-Boltzmann, NLPB-BM procedure is developed and applied to the free solution electrophoretic mobility of low molecular mass oligolysines. The difficulty of highly charged systems is twofold: more complex handeling of electrostatics and accounting for the relaxation effect. Both issues are addressed in this dissertation. A related problem we investigated deals with the retarding influence of a gel on the rotational motion of a macromolecule. This is investigated within the framework of the Effective Medium (EM) model and is applied to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. Modeling is also compared with experiment.

Many everyday materials, broadly classified as ``particulate media'', are at the heart of many industries and natural phenomena. Examples range from the storage and transport of bulk foods and aggregates such as grains and coal; the processing of pharmaceutical pills and the grinding coffee beans; to the mitigation and cost control of life-threatening events like landslides, earthquakes, and silo failures. The common theme connecting all these phenomena is the mechanical stability of the granular material that arises from interactions at the microscopic level of the grain scale, and how this influences collective properties at the bulk, macroscopic scale. In this dissertation, we present an extensive study of the mechanical properties of a physics-based model of granular particle systems in two dimensions using computer simulations. Specifically, we study the dynamics of an intruder particle that is driven through a dense, disordered packing of particles. This practical technique has the benefit of being amenable to experimental application which we expect will motivate future studies in the area. We find the `microrheology' of the intruder can be traced back to the properties of underlying, original, unperturbed packing, thereby providing a method to characterize the mechanical properties of the material that may otherwise be unavailable. To perform this study, we initially created mechanically stable granular packings of bidisperse discs, for several orders of magnitude of particle friction coefficient $\mu$, over a range in packing densities, or packing fractions $\phi$, in the vicinity of the critical packing fraction $\phi_c$, the density below which the packing is no longer stable. This range in $\phi$ translates to a range in packing pressures $P$, spanning several orders of magnitude down to the $P\rightarrow 0$ limit. For each packing, we apply a driving force to the intruder probe particle and find the critical force $F_{c}$, the minimum force required to induce motion of the probe as it is dragged through the system. We find that $F_{c}(\mu)$ for the different friction packings, scales with the packing pressure $P$ as a power-law according to: $F_{c}(\mu) - F_{c}^{o}(\mu) \sim P^{\beta(\mu)}$. The power-law exponent, $\beta(\mu)$ becomes friction dependent, but approaches the value, $\beta(\mu\to0) = 1.0 \pm 0.1$ in the zero-friction limit. $F_{c}^{o}(\mu)$ is the value of $F_{c}$ in the limit $P \to 0$, that similarly depends on the friction coefficient as, $F_{c}^{o}(\mu) \to 0$, when $\mu \to \infty$. We use this property of $F_{c}^{o}(\mu)$ to characterize the mechanical properties of different frictional packings. Another focus of this study is the `microrheology' of the intruder through force-velocity dependencies in $\mu=0$ systems at different $P$. For this case, the intruder is driven through the packing at a steady-state velocity $$, for driving forces above the critical force $F_D > F_c$. We introduce a scaling function that collapses the force-velocity curves onto a single master curve. This power law scaling of the collapsed curve as $P\rightarrow 0$ is reminiscent of a continuous phase transition, reinforcing the notion that the mechanical state of the system exhibits critical-like features. Furthermore, we also find an alternative scaling collapse of the form: $- \sim (F_{D} - F_{c})^{\alpha}$, where $$ represents a constant velocity term in the limit of small excess forcing, and the critical force $F_{c}$ now appears as fitting parameter that matches our explicit calculations. Thence, we are able to extract $F_{c}$ from a driven probe without a-priori having any knowledge about the state of the system. To further investigate the transition of the system through the different intruder force perturbations, we implemented a coarse graining (CG) technique that transforms our discrete particle interaction force information into continuous stress fields. Through this methodology, we are able to calculate the kinetic and contact stresses as the intruder is driven through the system. We are able to qualify and quantify the directional and distance dependencies of the stress response of the packing due to the driven probe via radial and azimuthal stress calculations. In particular, we find how the stress response not only captures the wake region behind the driven intruder, but also how the stress decays in the forward direction of the intruder, which follows universal behavior.

Molecular dynamics simulations are a theoretical method enabling to trace the movement of atoms within a system. The system studied is usually treated on the atomistic level, however its overall properties can be also described satisfactory if several atoms are handled as one particle (coarse-grained molecular dynamics). This thesis presents molecular modeling and (coarse-grained) molecular dynamics as tools for the description of different biologically relevant systems. The coarse-grained force field parameters had to be developed prior to characterization of the thylakoid membrane from cyanobacterium Synechocystis PCC6803. Two different compositions of the membrane were studied in order to reveal differences in their behavior. The PsbI subunit of photosystem II was embedded into the thylakoid membrane and its behavior, both as an isolated protein and as a cluster of several units, was described. The last system examined was the C-type lectin-like domain of NKR-P1, a surface receptor of natural killer cells. Attention was payed to its structural characterization.

O dimensionamento de sistemas de transporte hidráulico de polpas minerais exige especial atenção à medida que partículas grossas apresentam um comportamento de sedimentação no interior dos tubos. Dentro desta situação, a velocidade de transporte da polpa mineral deve ter magnitude suficiente para suspender e transportar os sólidos, evitando que os mesmos se depositem na base da tubulação. O bombeamento de polpas minerais em tubos horizontais contendo partículas grossas constituiu o objeto desta tese. Um levantamento sobre a literatura corrente foi realizado e, através de procedimentos experimentais, obteve-se um banco de dados para o modelamento da velocidade crítica (VC), isto é, a velocidade mínima em que ocorre a formação de um leito móvel na base do tubo, apresentando magnitude ligeiramente superior à velocidade de deposição VD, caracterizada pelo início da deposição das partículas na base dos dutos. Para a realização dos ensaios, foram construídas duas unidades experimentais de bombeamento de polpa mineral, onde foram estudadas as seguintes variáveis: i) gradiente de pressão por metro de tubo horizontal (\'delta\'P/L), ii) velocidade média do fluxo (V), iii) perfil de concentração de sólidos ao longo da seção transversal, iv) fator de forma através da função de esfericidade das partículas (\'psi\'), v) densidade do sólido e do líquido, vi) concentração volumétrica dapolpa mineral, vii) granulometria dos sólidos e viii) diâmetro da tubulação. A primeira unidade experimental foi montada com tubulação em PVC transparente de diâmetro interno de 25,4mm e a segunda unidade foi construída em PVC branco com um trecho de 2m em acrílico transparente, apresentando diâmetro interno de 50,8mm. A velocidade critica (VC) para cada condição estudada foi determinada visualmente, através das seções transparentes da tubulação. As amostras utilizadas neste trabalho foram: concentrados de apatita e hematita e o mineral quartzo. As frações granulométricas estudadas foram inseridas em duas classes de tamanho, sendo a primeira classe passante em 297µm e retida em 249µm e a segunda classe passante em 149µm e retida em 105µm. Os resultados permitiram determinar um novo modelo semiempírico para VC, alcançando desvios menores que 10% para as velocidades preditas em relação aos valores de velocidades observadas experimentalmente. / The design of hydraulic systems of slurry transport demands a special attention due to coarse particles present a settling behavior inside the pipes. In this situation, the transport velocity should have order of magnitude sufficient to promote the suspension and the transport of particles, avoiding the solids deposition at the bottom of pipe. The transport of mineral slurries containing coarse particles was the primary goal of the thesis. A survey of the available literature was done and through the experimental tests could be possible to raise a data bank in order to develop a new best fit correlation for the critical velocity (VC) which included the particle shape effect, through the sphericity function. VC could be defined as the minimum velocity where a moving bed of particles takes place at the bottom of the horizontal pipe and it is slightly above the deposition velocity VD, which could be characterized by a bed of stationary particles at the bottom of pipe. The research was conducted using two recirculating pipe test rigs with transparent PVC pipe of 25.4mm and 50.8mm internal diameter with slurry concentrations from 8% up to 27% by volume. The material used was apatite and hematite concentrates and quartz mineral, clustered in two classes of size range (-0.297+0.210mm; -0.149+0.105mm), where the variables were: i) Head losses per meter of horizontal pipe (\'delta\'P/L), ii) Mean transport velocity (V), iii) solids distribution profile, iv) particle shape effect, through the sphericity function (\'psi\'), v) density of particles and liquid, vi) Volumetric concentration of slurries, vii) particles size and viii) pipe diameter. The critical velocity (VC), for each studied condition, was visually determined through the transparent sections of the pipes. The results have yielded a new semi empirical model to predict the critical velocity, yielding a deviation of less than 10% from the observed values of experimental data for VC.

Single wall carbon nanotubes (SWCNTs) show a variety of unparalleled properties such as high electrical and thermal conductivity, high specific surface area (SSA) and a large stiffness under axial loads. One of the major challenges in tapping the vast potential of SWCNTs is to fabricate nanotube based macrostructures that retain the unique properties of nanotubes. Pristine SWCNT aerogels are highly porous, isotropic structures of nanotubes mediated via van der Waals (VDW) interactions at junctions. The mechanical behavior of such aerogels is examined in several experimental studies. However, it is necessary to supplement these studies with insights from simulations in order to develop a fundamental understanding of deformation behavior of SWCNT aerogels. In this study, the mechanical behavior of SWCNT networks is studied using a multi-scale modeling approach. The mechanics of an individual nanotube and interactions between few nanotubes are modeled using molecular dynamics (MD) simulations. The results from atomistic simulations are used to inform meso-scale and continuum scale finite element (FE) models. The deformation mechanism of pristine SWCNT networks under large compressive strain is deduced from insights offered by meso-scale simulations. It is found that the elasticity of such networks is governed by the bending deformation of nanotubes while the plastic deformation is governed by the VDW interactions between nanotubes. The stress response of the material in the elastic regime is dictated by the VDW stresses on nanotubes while in the plastic regime, both the VDW and axial deformation stresses on nanotubes drive the overall stress response. In this study, the elastic behavior of a random SWCNT network with any set of junction stiffness and network density is also investigated using FE simulations. It is found that the elastic deformation of such networks can be governed either by the deformation of the nanotubes (bending, axial compression) or deformation of the junctions. The junction stiffness and the network density determine the network deformation mode. The results of the FE study are also applicable to any stiff fiber network.

No description available.

Coarse-grained fabrics are comprised of multi-bit configurable logic blocks and configurable interconnect. This work is focused on area and energy optimization techniques for coarse-grained reconfigurable fabric architectures. In this work, a variety of design techniques have been explored to improve the utilization of computational resources and increase energy savings. This includes splitting, folding, multi-level vertical interconnect. In addition to this, I have also studied fully connected homogeneous and heterogeneous architectures, and 3D architecture. I have also examined some of the hybrid strategies of computation unit’s arrangements. In order to perform energy and area analysis, I selected a set of signal and image processing benchmarks from MediaBench suite. I implemented various fabric architectures on 90nm ASIC process from Synopsys. Results show area improvement with energy savings as compared to baseline architecture.

Medium chain fatty acids (MCFAs) are essential molecules for a wide range of pharmaceutical, biotechnological, and industrial applications. These are naturally occurring saturated or unsaturated fatty acids containing 6-12 carbons with complex and pH sensitive aggregation. Medium chain fatty acids such as capric acid (C10) or lauric acid (C12) have additionally been shown to exhibit antibacterial activity. A number of studies have observed the aggregation behavior of long chain fatty acid using the titration curves by molecular dynamic (MD) simulations.  In this study, we performed constant-pH coarse-grained MD simulations to determine pKa values and titration behavior using a two-states model for C10 and C12. In the simulations, pH was varied between 2 to 8 and pKa values were determined using the Hill equation. The pKa for C10 (capric acid) was found to be 4.8 and for C12 (lauric acid) 5.4, in good agreement with the literature values (4.9 and 5.3, respectively).