Recently an effective usage of the chip area plays an essential role for System-on-Chip (SOC) designs. Nowadays on-chip memories take up more than 50%of the total die-area and are responsible for more than 40% of the total energy consumption. Cache memory alone occupies 30% of the on-chip area in the latest microprocessors. This thesis project “System Level Exploration of RRAM for SRAM Replacement” describes a Resistive Random Access Memory (RRAM) based memory organizationfor the Coarse Grained Reconfigurable Array (CGRA) processors. Thebenefit of the RRAM based memory organization, compared to the conventional Static-Random Access Memory (SRAM) based memory organization, is higher interms of energy and area requirement. Due to the ever-growing problems faced by conventional memories with Dynamic Voltage Scaling (DVS), emerging memory technologies gained more importance. RRAM is typically seen as a possible candidate to replace Non-volatilememory (NVM) as Flash approaches its scaling limits. The replacement of SRAMin the lowest layers of the memory hierarchies in embedded systems with RRAMis very attractive research topic; RRAM technology offers reduced energy and arearequirements, but it has limitations with regards to endurance and write latency. By reason of the technological limitations and restrictions to solve RRAM write related issues, it becomes beneficial to explore memory access schemes that tolerate the longer write times. Therefore, since RRAM write time cannot be reduced realistically speaking we have to derive instruction memory and data memory access schemes that tolerate the longer write times. We present an instruction memory access scheme to compromise with these problems. In addition to modified instruction memory architecture, we investigate the effect of the longer write times to the data memory. Experimental results provided show that the proposed architectural modifications can reduce read energy consumption by a significant frame without any performance penalty.

Application-specific optimization of embedded systems becomes inevitable to satisfy the market demand for designers to meet tighter constraints on cost, performance and power. On the other hand, the flexibility of a system is also important to accommodate the short time-to-market requirements for embedded systems. To compromise these incompatible demands, coarse-grained reconfigurable architecture (CGRA) has emerged as a suitable solution. A typical CGRA requires many processing elements (PEs) and a configuration cache for reconfiguration of its PE array. However, such a structure consumes significant area and power. Therefore, designing cost-effective CGRA has been a serious concern for reliability of CGRA-based embedded systems. As an effort to provide such cost-effective design, the first half of this work focuses on reducing power in the configuration cache. For power saving in the configuration cache, a low power reconfiguration technique is presented based on reusable context pipelining achieved by merging the concept of context reuse into context pipelining. In addition, we propose dynamic context compression capable of supporting only required bits of the context words set to enable and the redundant bits set to disable. Finally, we provide dynamic context management capable of reducing reduce power consumption in configuration cache by controlling a read/write operation of the redundant context words In the second part of this dissertation, we focus on designing a cost-effective PE array to reduce area and power. For area and power saving in a PE array, we devise a costeffective array fabric addresses novel rearrangement of processing elements and their interconnection designs to reduce area and power consumption. In addition, hierarchical reconfigurable computing arrays are proposed consisting of two reconfigurable computing blocks with two types of communication structure together. The two computing blocks have shared critical resources and such a sharing structure provides efficient communication interface between them with reducing overall area. Based on the proposed design approaches, a CGRA combining the multiple design schemes is shown to verify the synergy effect of the integrated approach. Experimental results show that the integrated approach reduces area by 23.07% and power by up to 72% when compared with the conventional CGRA.

The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA.

The present work addresses issues related to the derivation of reduced models of atomistic systems, their statistical calibration, and their relation to atomistic models of materials. The reduced model, known in the chemical physics community as a coarse-grained model, is calibrated within a Bayesian framework. Particular attention is given to developing likelihood functions, assigning priors on coarse-grained model parameters, and using data from molecular dynamics representations of atomistic systems to calibrate coarse-grained models such that certain physically relevant atomistic observables are accurately reproduced. The developed Bayesian framework is then applied in three case studies of increasing complexity and practical application. A freely jointed chain model is considered first for illustrative purposes. The next example entails the construction of a coarse-grained model for a liquid heptane system, with the explicit design goal of accurately predicting a vapor-liquid transfer free energy. Finally, a coarse-grained model is developed for an alkylthiophene polymer that has been shown to have practical use in certain types of photovoltaic cells. The development therein employs Bayesian decision theory to select an optimal CG potential energy function. Subsequently, this model is subjected to validation tests in a prediction scenario that is relevant to the performance of a polyalkylthiophene-based solar cell. / text

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Molecular dynamics simulations of the liquid crystal phases of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine (2PhP) and 5-(4-butyloxyphenyl)-2-octyloxy-pyrimidine (5PhP) are the focus of this thesis. The 2PhP and 5PhP mesogens display different liquid crystalline phase sequences, despite having very similar molecular structures. Specifically, both mesogens consist of aromatic phenyl and pyrimidine cores in between two flexible alkoxy tails, but they differ in the preferred core conformation. A multi-site coarse-grained model, in which the aromatic rings are represented by soft quadrupolar ellipsoids and the alkoxy chains are given a united atom representation, is proposed in this thesis. A parameterization route for the intra- and intermolecular potentials appropriate for liquid crystal simulations is developed. The ab initio based derivation of suitable molecular models for the two mesogens is discussed in detail, with particular emphasis on capturing proper phenyl-pyrimidine interactions which proved to be essential to correctly represent core-core interactions between neighboring molecules. A systematic determination of suitable Gay-Berne (GB) parameters has been adopted for the aromatic rings of 2PhP and 5PhP. To account for the pi-electron cloud below and above the ring plane, a quadrupole was added perpendicular to the ring. In the end, four parameterizations for aromatic rings have been selected for the simulations. Model characterization via pair interactions proved to be valuable in identifying and analyzing the short range structure in the phases. Extensive molecular dynamics simulations of these fluids at various temperatures are performed. Intermolecular structure and order, in aromatic core and the flexible tail regions, are analyzed. Intermolecular structure is divided into contributions parallel and perpendicular to the layers, as indicated by a layer normal or by a director, to differentiate smectic A (SmA) from smectic C (SmC). The presence of a ring quadrupole in the molecular model is shown to be essential to the correct reproduction of the experimentally observed phases. Simulations correctly indicate phases in agreement with experiment: SmC and SmA phases for 2PhP, and only a SmA phase for 5PhP. / Thesis (Ph.D, Chemistry) -- Queen's University, 2009-10-27 20:23:37.89

In this study, the behavior of partially saturated coarse-grained soil packings was studied as a function of solid surface composition and aqueous salt concentration. The substrates tested were PTFE and soda lime glass, while the aqueous electrolytes consisted of NaCl and CaCl2 in differing concentrations. In order to gain a fundamental understanding of the unsaturated soils system, the two phase intersections of gas-liquid and solid-liquid were studied. The effect of varying aqueous electrolytes on the gas-liquid interface was analyzed by testing the surface tension while systematically varying the electrolyte concentration, while the effect on the solid/liquid/gas interface was studied by altering the surface hydrophobicity and aqueous solution concentration. In order to extend the analysis to soil fabrics, four ideal coarse gained packings were subdivided into their smallest repeating units. These repeating units, along with the measured dependence of the contact angles and surface tension on salt types, allowed an estimation of the equilibrium behavior of the capillary rise and tensile strength within a uniform coarse-grained fabric.

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.

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.

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