Erosion of a river bed has important implications with respect to scour around river structures such as bridges, transport of contaminants attached to the sediment, and disruption or destruction of aquatic habitats. Erosion occurs when the resistive strength of the sediment is overcome by the hydrodynamic forces produced by the flow of water. This resistance to erosion in a sediment originates from gravity or interparticle forces for coarse sediment (sand and gravel) and fine sediment (silt and clay), respectively. Since the erosion of fine sediment depends on the combination of many interparticle forces, and this combination fluctuates widely amongst different fine sediments, past studies have had difficulty finding a consistent method to estimate fine sediment erosion. This study analyzes sediments that fall in the transition size range between fine and coarse sediments and compares the findings with those from fine sediments (Wang 2013) and sandy coarse sediments (Navarro 2004, Hobson 2008), in order to correlate the erosion rates of both sediment types to their physical characteristics. In this study, kaolin-sand mixtures were prepared by mixing various percentages of Georgia kaolin by weight ranging from 30% to 100% with industrial fine sand and tap water. Geotechnical and other tests of sediment properties were performed to measure water content, bulk density, grain size distribution, temperature, pH, and conductivity of these mixtures. Hydraulic flume experiments measured the erosion rates of each sediment and these rates were used to estimate the critical shear stress correlating to that mixture. Relationships between the physical properties of the sediment and critical shear stress were developed by multiple regression analysis. An alternative option of estimating the critical shear stress by a weighted equation, which uses the combination of fine sediment erosion and coarse sediment erosion equations separately, was explored and found to be a viable and accurate option to estimating both coarse and fine sediment erosion from the same parameters and equation. The results from this study can be used to estimate sediment erodibility and thus river bed stability based on simple tests of physical properties of the river bed sediment and will help predict scour around bridges and other flow obstructions.

This thesis considers coarse-grained models of DNA and RNA, developed in particular to study nanotechnological applications as well as some important biophysical processes. We first introduce sequence-dependent thermodynamics into a previously developed coarse-grained rigid base-pair model of DNA. This model is then used to study sequence-dependent effects in multiple DNA systems including: the heterogeneous stacking transition of single strands, the fraying of a duplex, the effects of stacking strength in the loop on the melting temperature of hairpins, the force-extension curve of single strands, and the structure of a kissing-loop complex. We further apply the DNA model to study in detail the properties of an autonomous unidirectionally propagating DNA nanotechnological device, called the ``burnt bridges motor''. We then apply the coarse-graining methods developed for the DNA model to construct a new sequence-dependent coarse-grained model of RNA, which aims to capture basic thermodynamic, structural and mechanical properties of RNA molecules. We test the model by studying its thermodynamics for a variety of secondary structure motifs and also consider the force-extension properties of an RNA duplex. This RNA model allows for efficient simulations of a variety of RNA systems up to hundreds or even thousands of base-pairs. Its versatility is further demonstrated by studying the thermodynamics of a pseudoknot folding, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin.

A molecular dynamics coarse-grained block copolymer (BCP) model was developed and used to studied directed self-assembly (DSA), especially in regards to applications for semiconductor manufacturing. Most of the thesis is spent investigating the effect that guiding layer properties and block copolymer properties have on line roughness and defect density in a BCP-DSA process. These two effects are perhaps the most critical in making BCP-DSA a cost efficient industrial process. It is found that guiding patterns have little effect on line roughness and in fact that the BCP heals the majority of roughness in the underlying pattern. BCP properties have a larger effect on line roughness. Segregation strength (as measured by χN, where χ is the Flory- Huggins interaction parameter and N is the degree of polymerization) resulted in a larger than expected increase in line roughness when χN was low. Polydispersity resulted in a moderate increase in line roughness. In regards to equilibrium defect density, free energy calculations showed that χ was the primary determining factor, not χN as many expected. Equilibrium defect density was found to decrease exponentially with increasing χ. Defect density is also found to scale exponentially with polydispersity. Concerning defect heal rate, which can increase the real defect rate of a process if said rate is too low, it is found that increasing χN linearly increased the barrier to defect healing, which means that the defect heal rate decreases exponentially. However, for thin films this is only true for χN > ~ 50. Below χN ~ 50, the barrier is approximately constant. These results give excellent guidance to the type of materials and processes necessary to optimize a BCP-DSA process. A simulation technique designed to more efficiently sample over energy barriers called protracted noise dynamics for polymer systems was developed and studied. It was found that a decrease in simulation time of up to 4 orders of magnitude was achieved. The effect of box size on allowable pitches for a lamellar forming BCP was derived and demonstrated. It was found that more elongated boxes yielded more possible pitches and more accurate results. A short study on the effect of multiblock copolymers on the location of the order-disorder transition was also carried out and it was found that multiblock copolymers had small effect on the ODT. The distribution of chain conformations was also calculated.

In this study, we consider electrostatics contributed from the molecules in the ionic solution. It plays a significant role in determining the binding affinity of molecules and drugs. We develop the overall framework of computing electrostatic properties for three-dimensional molecular structures, including potential, energy, and forces. These properties are derived from Poisson-Boltzmann equation, a partial differential equation that describes the electrostatic behavior of molecules in ionic solutions. In order to compute these properties, we derived new boundary integral equations and designed a boundary element algorithm based on the linear time fast multipole method for solving the linearized Poisson-Boltzmann equation. Meanwhile, a higher-order parametric formulation called algebraic spline model is used for accurate approximation of the unknown solution of the linearized Poisson-Boltzmann equation. Based on algebraic spline model, we represent the normal derivative of electrostatic potential by surrounding electrostatic potential. This representation guarantees the consistent relation between electrostatic potential and its normal derivative. In addition, accurate numerical solution and fast computation for electrostatic energy and forces are also discussed. In addition, we described our hierarchical modeling and parameter optimization of molecular structures. Based on this technique, we can control the scalability of molecular models for electrostatic computation. The numerical test and experimental results show that the proposed techniques offer an efficient and accurate solution for solving the electrostatic problem of molecules. / text

Structure and mechanical properties of DNA play a key role in its biological functioning. A lot of well-established conclusions about the DNA structure and its sequence-dependent variabil- ity came from various experimental and computational studies of the Dickerson-Drew dodecamer (DD), a prototypic B-DNA molecule of the sequence (5')CGCGAATTCGCG(3'). In this study we present a detailed analysis of structural and mechan- ical properties of DD based on extensive atomistic molecular dynamics (MD) simulations with explicit representation of wa- ter and ionic environment. We analyze three simulated systems covering different ionic conditions and water models. Two MD trajectories are reported for the first time, one of them being 2.4 µs long. An extensive comparsion with one recent NMR struc- ture and four recent X-ray structures is made. It is found that the end basepairs can adopt two different pairing motifs dur- ing the simulation: the canonical Watson-Crick pair or a non- canonical trans Watson-Crick/Sugar Edge pair. These states can significantly influence the structure of DD even at the third step from the end. A clear relationship is found between the BI/BII backbone substates and the basepair step conformation. A model of rigid bases is used to study mechanical properties of the DNA. The non-local...

Structural and mechanical properties of nucleic acids play a key role in a wide range of biological processes, as well as in the field of nucleic acid nanotechnology. The thesis presents results of several studies focused on modelling these properties. Extensive unrestrained atomic-resolution molecular dynamics (MD) simulations are used to investigate structural dynamics of nucleic acids, and to parametrize their mechanical models. The deformation energy is assumed to be a general quadratic function of suitably chosen internal coordinates. Two types of models are employed which differ in the level of coarse- graining. The first one is based on the description of conformation at the level of individual bases and the second, coarser one is used to study global bending and twisting flexibility. The models are applied to explain mechanical properties of A-tracts in the context of DNA looping and nucleosome positioning, to characterize twist-stretch cou- pled deformations in DNA and RNA, and to predict changes in the properties of damaged DNA that are likely to be relevant for damage recognition and repair. Besides that, we propose a general model of DNA allostery, applied to study the effect of minor groove binding of small ligands and the allosteric coupling between proteins mediated by the DNA. A careful...

La complexité des systèmes embarqués et des applications impose des besoins croissants en puissance de calcul et de consommation énergétique. Couplé au rendement en baisse de la technologie, le monde académique et industriel est toujours en quête d'accélérateurs matériels efficaces en énergie. L'inconvénient d'un accélérateur matériel est qu'il est non programmable, le rendant ainsi dédié à une fonction particulière. La multiplication des accélérateurs dédiés dans les systèmes sur puce conduit à une faible efficacité en surface et pose des problèmes de passage à l'échelle et d'interconnexion. Les accélérateurs programmables fournissent le bon compromis efficacité et flexibilité. Les architectures reconfigurables à gros grains (CGRA) sont composées d'éléments de calcul au niveau mot et constituent un choix prometteur d'accélérateurs programmables. Cette thèse propose d'exploiter le potentiel des architectures reconfigurables à gros grains et de pousser le matériel aux limites énergétiques dans un flot de conception complet. Les contributions de cette thèse sont une architecture de type CGRA, appelé IPA pour Integrated Programmable Array, sa mise en œuvre et son intégration dans un système sur puce, avec le flot de compilation associé qui permet d'exploiter les caractéristiques uniques du nouveau composant, notamment sa capacité à supporter du flot de contrôle. L'efficacité de l'approche est éprouvée à travers le déploiement de plusieurs applications de traitement intensif. L'accélérateur proposé est enfin intégré à PULP, a Parallel Ultra-Low-Power Processing-Platform, pour explorer le bénéfice de ce genre de plate-forme hétérogène ultra basse consommation. / Emerging trends in embedded systems and applications need high throughput and low power consumption. Due to the increasing demand for low power computing and diminishing returns from technology scaling, industry and academia are turning with renewed interest toward energy efficient hardware accelerators. The main drawback of hardware accelerators is that they are not programmable. Therefore, their utilization can be low is they perform one specific function and increasing the number of the accelerators in a system on chip (SoC) causes scalability issues. Programmable accelerators provide flexibility and solve the scalability issues. Coarse-Grained Reconfigurable Array (CGRA) architecture consisting of several processing elements with word level granularity is a promising choice for programmable accelerator. Inspired by the promising characteristics of programmable accelerators, potentials of CGRAs in near threshold computing platforms are studied and an end-to-end CGRA research framework is developed in this thesis. The major contributions of this framework are: CGRA design, implementation, integration in a computing system, and compilation for CGRA. First, the design and implementation of a CGRA named Integrated Programmable Array (IPA) is presented. Next, the problem of mapping applications with control and data flow onto CGRA is formulated. From this formulation, several efficient algorithms are developed using internal resources of a CGRA, with a vision for low power acceleration. The algorithms are integrated into an automated compilation flow. Finally, the IPA accelerator is augmented in PULP - a Parallel Ultra-Low-Power Processing-Platform to explore heterogeneous computing.

"Recently, hydrogel have found to be promising biomaterials since their porous structure and hydrophilicity enables them to absorb a large amount of water. In this study the role of water on the mechanical properties of hydrogel are studied using ab-initio molecular dynamics (MD) and coarse-grained simulations. Condensed-Phased Optimized Molecular Potential (COMPASS) and MARTINI force fields are used in the all-atom atomistic models and coarse-grained simulations, respectively. The crosslinking process is modeled using a novel approach by cyclic NPT and NVT simulations starting from a high temperature, cooling down to a lower temperature to model the curing process. Radial distribution functions for different water contents (20%, 40%, 60% and 80%) have shown the crosslinks atoms are more hydrophilic than the other atoms. Diffusion coefficients are quantified in different water contents and the effect of crosslinking density on the water diffusion is studied. Elasticity parameters are computed by constant strain energy minimization in mechanical deformation simulations. It is shown that an increase in the water content results in a decrease in the elastic. Finally, continuum hyper elastic model of contact lens is studied for three different loading scenarios using Finite Element Model. "

Protein misfolding and aggregation are the cause of many problems within the biopharmaceutical industry and medical fields. Although many experimental studies have been implemented in vivo in order to understand this process, the mechanism occurs in time and length scales inaccessible to conventional experiments. On the other hand, computational studies have shown significant improvement in elucidating key aspects of the aggregation pathways and gain insights to the folding behavior of the proteins. Consequently, this makes computational modeling an ideal complement to experiment in understanding the generic behavior and mechanisms of aggregation. This study is concerned with DynamO, a coarse-grained, off-lattice, general event-driven discontinuous molecular-dynamics simulation package. This simulator offers a unique opportunity to gain insight into the process of protein aggregation by displaying the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than O(NlogN) scaling found in most standard algorithms. The study was split into two loosely related projects: in the first project, a computer model was developed in which the effect of model parameters on folding behavior and characteristics of isolated peptides is investigated. The model parameters include chain stiffness (an overlap parameter defined as the ratio of the hard-core diameter to bond length 'sigma/l'), range of interaction potential 'Gamma', sequence, and chains length 'N '. Based on the model chosen from systems of isolated chains, aggregation in multichain systems is studied. In another project, we simulate various square-well fluid systems with different ranges of interaction potential in order to understand the phase behavior of proteins due to its relevance to aggregation and many bioprocessing events. Changing the model parameters shows different folding behaviors. The model-chains with 64 residues, Gamma equal to 1.1 and sigma/l equal to 1.9 is the least computationally expensive model displaying all the characteristics found in real proteins. We introduce a new order parameter which divides the conformational space into folded and unfolded ensemble-structures, this order parameter corresponds to a transition in the folding behavior of the chains. We define a native state ensemble as an ensemble of structures with small deviation in contact maps for spheres inaccessible to the solvent defined as the core of the chain. This native ensemble corresponds to the structures exhibiting low-temperature fluctuations simulating the 'breathing motions' of real proteins which is considered responsible for their catalytic activities. On the other hand, the non-native ensemble unfolds at higher temperatures, which increases the propensity for aggregation by forming intermolecular contacts, and therefore reproduce the behavior of proteins under severe solution conditions which occurs in bio- processing (this includes high concentration, temperature, pressure, pH ...). The behavior of multichain systems shows that it is possible to correlate the aggregation propensity of chains at room temperature from the behavior of chains in isolated system at the collapse temperature, which in turn correlate with the stability of the low-T ensemble. In the second project, we developed a more efficient way of calculating the critical temperature in SW fluids even for strongly short-ranged systems which are especially difficult to simulate. In the supercritical region, every isotherm obeys the linear equation for the pressure with a high precision within the bounds of uncertainty. The linear equation pm = p0 + Rm with Rm being the constant isothermal rigidity (dp/d)T . The constant rigidity can be used to estimate directly a critical temperature (Tc) and critical pressure (pc), respectively, and also to obtain the pressures and densities of the percolation loci based on an empirical quadratic nature of change in pressure with densities outside the percolation loci. Identifying the critical temperature and how it depends on the pair potential is very important in formulations with a growing need to predict when the solution will go opalescent.

La dynamique moléculaire gros-grain nous permet d'étudier l'interface polymère / silice. En particulier, nous comparons les comportements divergents du poly(acrylamide) (PAAm) et du poly(N,Ndimethylacrylamide) (PDMA) sur la surface de silice. Tout d'abord, nous montrons que les comportements macroscopiques du PAAm et du PDMA sont correctement représentés par un modèle contenant un solvant explicite. Nous utilisons ensuite la méthode d'énergie libre umbrella sampling afin d'examiner le détachement du PAAm et du PDMA de la surface de silice et d'étudier les caractéristiques importantes qui permettent ou non à la chaîne de polymère de rester adsorbée sur la surface de silice. Nous soulignons l'importance des interactions intra moléculaires au sein du polymère ainsi que les interactions polymère/surface qui déterminent l'adsorption du polymère sur la silice. De manière surprenante, les interactions solvant/polymère et solvant/surface ne sont pas des critères discriminants lors de l'adsorption des polymères sur la surface. Les polymères sont finalement contraints de s'adsorber sur deux surfaces de silice séparées de 200 Å. Ce système nous permet d'analyser l'évolution de la labilité des monomères ainsi que la force appliquée par les monomères sur la surface quand la distance entre les deux surfaces augmente. / Polymer/silica interface is investigated using coarse-grained molecular dynamics simulations. In particular, the different behavior of poly(acrylamide) (PAAm) and of poly(N,N-dimethylacrylamide) (PDMA) on the silica surface is compared. First, we show that the macroscopic behavior of PAAm and of PDMA is correctly represented by a model containing an explicit solvent. Then, the umbrella sampling free energy method is used to probe the detachment of PAAm and of PDMA from a silica surface and to investigate important features that allow - or not - the polymer chain to remain adsorbed on the silica surface. We proved that intramolecular interactions within the polymer and polymer/surface interactions are of first importance for the polymer chain to adsorb on silica. Surprisingly, solvent/polymer as well as solvent/surface interactions are not discriminating criteria. Polymer chains are finally constrained to a particular configuration where one chain is adsorbed on two silica surfaces that are 200 Å apart. This yields interesting insights into the evolution of the monomers lability and of the surface/polymer strength interaction when the two silica surfaces are moved apart.