Earthquakes are natural calamities that occur as a result of sudden release of strain energy stored in fault planes. Earthquakes have been observed to cause huge damage to infrastructures and lives. Earthquakes result in development of fissures, abnormal or unequal movement of foundations, and loss of strength and stiffness of the soils. Liquefaction is attributed as a major cause for the loss of strength and stiffness of soil during earthquakes. In the past, liquefaction was attributed only to coarse-grained to medium-grained sand and was extensively studied but the fine-grained soils were generally considered as non-liquefiable. However, from observations during recent earthquakes, fine-grained soils having low plasticity (plasticity index (PI) <20) have experienced ground failures due to liquefaction or large deformations. Moreover, laboratory experiments show that not only saturated cohesionless soils but also fine-grained soils may liquefy if certain criteria are met. One of the parameters which influences the liquefaction characteristics of fine-grained soils is its plasticity. This study may become helpful in understanding the effect of plasticity on liquefaction resistance of fine-grained soils. The objective of this study were to investigate the (1) effect of plasticity on pore pressure built up and deformation characteristics of fine-grained soils, and (2) effects of cyclic shear stress on liquefaction resistance of fine-grained soils. A total of 24 tests were conducted using a stress controlled cyclic triaxial testing machine on identically prepared specimens at an initial effective confining pressure of 5.0psi. The plasticity index (PI) was varied from non-plastic (NP) to 14.53. Sil-Co-Sil #40, a non-plastic commercial silt (product of US Silica Company) and EPK Kaolin clay (product of Edgar Minerals Inc.) were used as base materials. These materials were mixed in different proportions to obtain desired plasticity index. Out of the twenty-four tests, eleven tests were conducted on clean silt samples. Among the tests on clean silt samples, four tests were conducted on specimens having a post consolidation void ratio of 0.74 to 0.76. Further, six tests were conducted on specimens having a post consolidation void ratio of 0.74 to 1.04 by using a cyclic stress ratio (CSR) of 0.2 and 0.25. Seventeen tests were grouped to study the influence of plasticity on liquefaction characteristics of fine-grained soil. The PI of specimens tested ranged from non-plastic (NP) to 14.53. Each of the specimens with a definite PI was tested at an initial confining pressure of 5.0 psi using a CSR of 0.2, 0.3, and 0.4. The results obtained from the tests were used to compare the effects of plasticity on liquefaction characteristics of fine-grained soils. Based on the limited tests conducted, it was observed that plasticity index had distinct influence on the cyclic strength of the samples. It was found that CSR required to cause a pre-determined strain in a given number of loading cycles reduces as the plasticity index increases from non-plastic (NP) to 3.46, but increases for soils having PI greater than 3.46. Moreover, the liquefaction resistance decreases with the increase in cyclic shear stress for all soils regardless of plasticity indices (PIs). The critical PI value corresponds to 15% of EPK clay content in the specimen which gives a PI of 3.46.

Master of Science / Civil Engineering / Stacey Tucker / Recent climate changes may affect the stability of our infrastructure in many ways. This study investigated the effects of fine-grained soil temperature on erosion rate. If climate change is shown to affect the erodibility of soils the impacts must be identified to monitor the stability of existing infrastructure, improve design of levees and structures founded in erosive environments, and to prevent sediment loss and stream meanders. Fine-grained soil erosion is complicated by the dynamic linkage of multiple parameters, including physical, biological and geochemical properties. This study held constant all parameters that influence fine-grained soil erodibility while only varying soil temperature in order to study the effects it has on erodibility. This study also confirmed previous findings that water temperature affects soil erodibility. The main objective of this study was to investigate the effects of fine-grained soil temperature on erosion rate. This study also instrumented a turbidity sensor to reliably map soil erosion. Based on this research, the conclusion was made that an increase in soil temperature increases soil erosion rate. The turbidity sensor was a valuable tool for comparing soil erosion. Future studies should investigate the effects soil temperatures below room temperature, the magnitude of temperature increase or decrease, and the effects of cyclic heating and cooling on fine grained soil erodibility.

abstract: Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can provide tremendous insight into how the fine details of chemistry, molecular architecture, and microstructure affect many physical properties; however, they face well-known restrictions in their applicable temporal and spatial scales. These limitations have motivated the development of computationally-efficient, coarse-grained methods to investigate how microstructural details affect thermophysical properties. In this dissertation, I summarize my research work in structure-based coarse-graining methods to establish the link between molecular-scale structure and macroscopic properties of two different polymers. Systematically coarse-grained models were developed to study the viscoelastic stress response of polyurea, a copolymer that segregates into rigid and viscous phases, at time scales characteristic of blast and impact loading. With the application of appropriate scaling parameters, the coarse-grained models can predict viscoelastic properties with a speed up of 5-6 orders of magnitude relative to the atomistic MD models. Coarse-grained models of polyethylene were also created to investigate the thermomechanical material response under shock loading. As structure-based coarse-grained methods are generally not transferable to states different from which they were calibrated at, their applicability for modeling non-equilibrium processes such as shock and impact is highly limited. To address this problem, a new model is developed that incorporates many-body interactions and is calibrated across a range of different thermodynamic states using a least square minimization scheme. The new model is validated by comparing shock Hugoniot properties with atomistic and experimental data for polyethylene. Lastly, a high fidelity coarse-grained model of polyethylene was constructed that reproduces the joint-probability distributions of structural variables such as the distributions of bond lengths and bond angles between sequential coarse-grained sites along polymer chains. This new model accurately represents the structure of both the amorphous and crystal phases of polyethylene and enabling investigation of how polymer processing such as cold-drawing and bulk crystallization affect material structure at significantly larger time and length scales than traditional molecular simulations. / Dissertation/Thesis / Doctoral Dissertation Mechanical Engineering 2016

We envisage a fine-grained access control solution that allows a user's access privilege to be linked to the confidence level (hereafter referred to as the assurance level) in identifying the user. Such a solution would be particularly attractive to a large-scale distributed resource sharing environment, where resources are likely to be more diversified and may have varying levels of sensitivity and resource providers may wish to adjust security protection levels to adapt to resource sensitivity levels or risk levels in the underlying environment. However, existing electronic authentication systems largely identify users through the verification of their electronic identity (ID) credentials. They take into account neither assurance levels of the credentials, nor any other factors that may affect the assurance level of an authentication process, and this binary approach to access control may not provide cost-effective protection to resources with varying sensitivity levels. To realise the vision of assurance level linked access control, there is a need for an authentication framework that is able to capture the confidence level in identifying a user, expressed as an authentication Level of Assurance (LoA), and link this LoA value to authorisation decision-making. This research investigates the feasibility of estimating a user's LoA at run-time by designing, prototyping and evaluating an authentication model that derives an LoA value based upon not only users' ID credentials, but also other factors such as access location, system environment and authentication protocol used. To this aim, the thesis has identified and analysed authentication attributes, processes and procedures that may influence the assurance level of an authentication environment. It has examined various use-case scenarios of authentication in Grid environments (a well-known distributed system) and investigated the relationships among the attributes in these scenarios. It has then proposed an authentication model, namely a generic e-authentication LoA derivation model (GEA-LoADM). The GEA-LoADM takes into account multiple authentication attributes along with their relationships, abstracts the composite effect by the multiple attributes into a generic value called the authentication LoA, and provides algorithms for the run-time derivation of LoA values. The algorithms are tailored to reflect the relationships among the attributes involved in an authentication instance. The model has a number of valuable properties, including flexibility and extensibility; it can be applied to different application contexts and supports easy addition of new attributes and removal of obsolete ones. The prototypes of the algorithms and the model have been developed. The performance and security properties of the LoA derivation algorithms and the model are analysed here and evaluated based on the prototypes. The performance costs of the GEA-LoADM are also investigated and compared against conventional authentication mechanisms, and the security of the model is tested against various attack scenarios. A case study has also been conducted using a live system, the Multi-Agency Information Sharing (MAIS) system.

Diverse fiber-forming proteins are found in nature that accomplish a wide range of functions including signaling, cell adhesion, and mechanical support. Unique sequence characteristics of these proteins often lead to their specialized roles. However, these proteins also share a common organizational hierarchy in primary and secondary structures that strongly influence both their intramolecular folding and intermolecular interactions. Based on what is known regarding protein fiber assembly of silk peptides, shear-induced elongation of the molecular strands drives interchain secondary structure crystallization via anisotropic alignment, which creates a molecular superstructure that forms the basis a fiber network. In this work, the hypothesis is this type of protein fiber assembly is not unique to silk sequences and that other proteins can be spun into fibers in similar fashion while maintaining unique functionality given by their specialized amino acid sequences such as RGD, GX1X2, and so forth. This was investigated by modeling the manner in which hydrophobic and hydrophilic blocks of amino acids create interacting secondary structures at the chain level when exposed to shear. It was determined computationally and then verified experimentally that fiber spinning success is most likely to occur after shear processing if the protein sequence exhibits a balance of hydrophobic and hydrophilic content and has sufficient length. Applied to the biological scale, both pure and mixed solutions of proteins such as fibronectin, laminin, and silk fibroin were spun into fibers. In particular, alloy protein fibers of silk fibroin mixed with fibronectin exhibited the characteristic mechanical integrity of silk and the bioactivity of fibronectin. This simple method of creating protein fibers with hybrid characteristics is significantly faster, less expensive, and less technically intensive than chimeric protein production, which purports to do the same. This finding also provides insight into a fundamental means by which protein fibers may be assembled in vivo by taking advantage of the thermodynamically favorable assembly of peptide sequences at the chain level under proper molecular orientation. Taken together, a high throughput means of producing a wide-range of pure and hybrid protein fibers has been developed for various biological applications and research investigations into the fibrous elements of biology.

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Molecular Dynamics (MD) is a simulation technique widely used by computational chemists and biologists to simulate and observe the physical properties of a system of particles or molecules. The method provides invaluable three-dimensional structural and transport property data for macromolecules that can be used in applications such as the study of protein folding and drug design. The most time-consuming and inefficient routines in MD packages, particularly for large systems, are the ones involving the computation of intermolecular energy and forces for each molecule. Many fully atomistic systems such as CHARMM and NAMD have been refined over the years to improve their efficiency. But, simulating complex long-time events such as protein folding remains out reach for atomistic simulations. The consensus view amongst computational chemists and biologists is that the development of a coarse-grained (CG) MD package will make the long timescales required for protein folding simulations possible. The shortcoming of this method remains an inability to produce accurate dynamics and results that are comparable with atomistic simulations. It is the objective of this dissertation to develop a coarse-grained method that is computationally faster than atomistic simulations, while being dynamically accurate enough to produce structural and transport property data comparable to results from the latter. Firstly, the accuracy of the Gay-Berne potential in modelling liquid benzene in comparison to fully atomistic simulations was investigated. Following this, the speed of a course-grained condensed phase benzene simulation employing a Gay-Berne potential was compared with that of a fully atomistic simulation. While coarse-graining algorithmically reduces the total number of particles in consideration, the execution time and efficiency scales poorly for large systems. Both fully-atomistic and coarse-grained developers have accelerated packages using high-performance parallel computing platforms such as multi-core CPU clusters, Field Programmable Gate Arrays (FPGAs) and Graphics Processing Units (GPUs). GPUs have especially gained popularity in recent years due to their massively parallel architecture on a single chip, making them a cheaper alternative to a CPU cluster. Their relatively shorter development time also gives them an advantage over FPGAs. NAMD is perhaps the most popular MD package that employs efficient use of a single GPU or a multi-GPU cluster to conduct simulations. The Scientific Computing Research Unit’s in-house generalised CG code, the Free Energy Force Induced (FEFI) coarse-grained MD package, was accelerated using a GPU to investigate the achievable speed-up in comparison to the CPU algorithm. To achieve this, a parallel version of the sequential force routine, i.e. the computation of the energy, force and torque per molecule, was developed and implemented on a GPU. The GPU-accelerated FEFI package was then used to simulate benzene, which is almost exclusively governed by van der Waal’s forces (i.e. dispersion effects), using the parameters for the Gay-Berne potential from a study by Golubkov and Ren in their work “Generalized coarse-grained model based on point multipole and Gay-Berne potentials”. The coarse-grained condensed phase structural properties, such as the radial and orientational distribution functions, proved to be inaccurate. Further, the transport properties such as diffusion were significantly more unsatisfactory compared to a CHARMM simulation. From this, a conclusion was reached that the Gay-Berne potential was not able to model the subtle effects of dispersion as observed in liquid benzene. In place of the analytic Gay-Berne potential, a more accurate approach would be to use a multidimensional free energy-based potential. Using the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method, a four-dimensional Free Energy Volume (FEV) for two interacting benzene molecules was computed for liquid benzene. The focal point of this dissertation was to use this FEV as the coarse-grained interaction potential in FEFI to conduct CG simulations of condensed phase liquid benzene. The FEV can act as a numerical potential or Look-Up Table (LUT) from which the interaction energy and four partial derivatives required to compute the forces and torques can be obtained via numerical methods at each step of the CG MD simulation. A significant component of this dissertation was the development and implementation of four-dimensional LUT routines to use the FEV for accurate condensed phase coarse-grained simulations. To compute the energy and partial derivatives between the grid points of the surface, an interpolation algorithm was required. A four-dimensional cubic B-spline interpolation was developed because of the method’s superior accuracy and resistance to oscillations compared with other polynomial interpolation methods. When The algorithm’s introduction into the FEFI CG MD package for CPUs exhausted the single-core CPU architecture with its large number of interpolations for each MD step. It was therefore impractical for the high throughput interpolation required for MD simulations. The 4D cubic B-spline algorithm and the LUT routine were then developed and implemented on a GPU. Following evaluation, the LUT was integrated into the FEFI MD simulation package. A FEFI CG simulation of liquid benzene was run using the 4D FEV for a benzene molecular pair as the numerical potential. The structural and transport properties outperformed the analytical Gay-Berne CG potential, more closely approximating the atomistic predicted properties. The work done in this dissertation demonstrates the feasibility of a coarse-grained simulation using a free energy volume as a numerical potential to accurately simulate dispersion effects, a key feature needed for protein folding.

After a major flooding disaster, construction materials will be scarce during early recovery stages and any material of reasonable quality would be useful. Instead of importing higher quality material from sites a considerable distance away, on-site material may be useable. This thesis explores usage of specialty portland cements, and in some cases polymer fibers, as stabilization additives to fine grained soils with elevated moisture contents. The primary objective of this thesis is to develop strength, modulus, and ductility trends for a variety of soil types, cementitious materials, cementitious material contents, and moisture contents, and to use the data to compare specialty grind portland cements to commercially available portland cement from the same production facility. The secondary objective is to evaluate the effect of polymer fibers combined with portland cement for the same mixtures. Over 1300 Unconfined Compression (UC) tests were conducted to complete these two objectives.

The essential cellular functions of the mitochondrion require the exchange of a wide variety of molecules across its two membranes, which is carried out by different membrane proteins.The Voltage-Dependent Anion Channel (VDAC) located in the mitochondrial outer membrane (MOM) is responsible for the passage of various ions and small molecules to and from the intermembrane space. It is also involved in the regulation of cellular processes through its interactions with lipids or other proteins.At the MOM level, we studied the transport, through VDAC, of small inorganic ions and of thiamine pyrophosphate (TPP), an essential cofactor. Using different simulation methods such as Brownian dynamics (BD), All-Atom (AA) molecular dynamics (MD) and Coarse-Grained (CG) MD, we investigated the effect of two factors on the regulation of VDAC ion selectivity: ionic strength and membrane lipid composition. All simulation types show that VDAC becomes less selective towards anions with increasing salt concentration. The simulations further suggest that the selectivity mechanism occurs due to the filtering of some basic residues that point into the pore lumen. Furthermore, MD simulations show that the lipid composition of the membrane modulates the distribution of ions inside VDAC. In a comparison of POPE versus POPC bilayer, this regulation occurs through the more persistent interactions of some acidic residues located on both edges of the β-barrel with POPE head groups which, in turn, alters the electrostatic potential in the lumen which consequently affects the pore selectivity. CG MD simulations show that this mechanism also occurs in a mixed POPE/POPC bilayer by an enrichment of POPE on VDAC surface.In order to simulate the transport of the TPP, force field parameters have been developed and validated. Simulations of the translocation of TPP through VDAC show analogies with the mechanism used by other previously studied metabolites, in particular with ATP. At the mitochondrial inner membrane level, the mechanism of TPP transport by the specific thiamine pyrophosphate transporter (TPPT) shows significant similarities with the mechanism proposed for other members of the mitochondrial carrier family to which TPPT belongs. They mainly are the energetics arising from the alternating formation and disruption of two salt bridge networks, one on the matrix side and the other on the cytosolic side, and the interactions, of an ionic nature, formed by TPP during its binding in TPPT central cavity. Furthermore, the energy contribution provided by the cytosolic network establishes a weaker barrier than that of the matrix network, which may support the hypothesis of a uniport activity of TPPT. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished