Scheduling, placement, and routing are important steps in Very Large Scale Integration (VLSI) design. Researchers have developed numerous techniques to solve placement and routing problems. As the complexity of Application Specific Integrated Circuits (ASICs) increased over the past decades, so did the demand for improved place and route techniques. The primary objective of these place and route approaches has typically been wirelength minimization due to its impact on signal delay and design performance. With the advent of Field Programmable Gate Arrays (FPGAs), the same place and route techniques were applied to FPGA-based design. However, traditional place and route techniques may not work for Coarse-Grained Reconfigurable Architectures (CGRAs), which are reconfigurable devices offering wider path widths than FPGAs and more flexibility than ASICs, due to the differences in architecture and routing network. Further, the routing network of several types of CGRAs, including the Field Programmable Object Array (FPOA), has deterministic timing as compared to the routing fabric of most ASICs and FPGAs reported in the literature. This necessitates a fresh look at alternative approaches to place and route designs. This dissertation presents a finite domain constraint-based, delay-aware placement and routing methodology targeting an FPOA. The proposed methodology takes advantage of the deterministic routing network of CGRAs to perform a delay aware placement.

In this dissertation, an experimental and numerical study of dense coarse solids-liquid flows has been performed. The experimental work mainly involved pressure drop measurements in a vertical flow loop. A limited number of measurements of solids velocity profiles were also obtained in the upward flow section of the flow loop. The numerical work involved simulations of coarse particles-in-water flows in vertical and horizontal pipes. The vertical flow simulations were performed using the commercial CFD software, ANSYS CFX-4.4, while ANSYS CFX-10 was used to simulate the flows in the horizontal pipes. The simulations were performed to investigate the applicability of current physically-based models to very dense coarse-particle flows.<p> In the experimental study, measurements of pressure drop and local solids velocity profiles were obtained. The experiments were conducted in a 53 mm diameter vertical flow loop using glass beads of 0.5 mm and 2.0 mm diameter solids for concentration up to 45%. The liquid phase was water. The measured pressure drop exhibited the expected dependence on bulk velocity and solids mean concentration. The wall shear stress was determined by subtracting the gravitational contribution from the measured pressure drop. For flow with the 0.5 mm particles at high bulk velocities, the values of the wall shear stress were essentially similar for each concentration in the upward flow sections but more variation, indicating the effect of concentration, was noted in the downward flow section. At lower bulk velocities, the wall shear stresses with the 0.5 mm glass beads-water flow showed a dependence on concentration in both test sections. This was attributed to an increase in the slip velocity. For the large particle (2.0 mm glass beads), similar observations were made but the effect of concentration was much less in the upward test section. In the downward test section, the wall shear stress for the flow of the 2.0 mm glass beads increased by almost a constant value for the bulk velocities investigated. The solids velocity profiles showed that the solids velocity gradient is large close to the wall. In addition, the solids velocity profiles indicated that the slip velocity increased at lower velocities due to increase in the bulk concentration in the upward flow section.<p> For the vertical flow simulations, different physical models based on the kinetic theory of granular flows were programmed and implemented in ANSYS CFX-4.4. These models, referred to as the kf-ef-ks-es, kf-ef-ks-es-Ts and kf-ef-ks-kfs models, were investigated by focusing on the closure laws for the solids-phase stress. The treatment of the granular temperature Ts depends on whether small- or large-scale fluctuating motion of the particles is considered. The models were implemented via user-Fortran routines. The predicted results were compared with available experimental results. The predicted solids-phase velocity profiles matched the measured data quite well close to the pipe wall but over-predicted it in the core region. The solids concentration, on the other hand, was significantly under-predicted for concentrations higher than 10%. Variations in the predictions of the phasic turbulent kinetic energy and the eddy viscosity were noted; the effect of solids concentration on them was mixed. A general conclusion drawn from the work is that a more accurate model is required for accurate and consistent prediction of coarse particle flows at high concentrations (less than 10%). In a related study, attention was given to wall boundary conditions again focusing on the effect of the solids-phase models at the wall. Comparison between numerical predictions, using some of the existing wall boundary condition models for the solids phase in particulate flows, with experimental results indicated that the physical understanding of the influence of the fluid and solids-phase on each other and their effect on frictional head loss is far from complete. The models investigated failed to reproduce the experimental results. At high solids concentration, it was apparent from the present study that the no-slip and free-slip wall boundary conditions are not appropriate for liquid-solid flows.<p> For the horizontal flow case, three-dimensional simulations were performed with a focus on the velocity and concentration distributions. Medium and coarse sand-in-water flows in three pipe diameters were considered to investigate the default solids stress models in ANSYS CFX-10. Simulations were performed for three cases by considering: 1) no additional solids-phase stress, i.e. no model for Ts; 2) a zero equation, and 3) an algebraic equilibrium model for the granular temperature. The model predictions were compared to experimental results. The effect of particle size, solids-phase concentration, and pipe diameter was explored using the algebraic equilibrium model. All the cases for the models considered exhibited the characteristic features of horizontal coarse particle slurry flows. The zero equation and the algebraic equilibrium model for the granular temperature produced similar results that were not significantly different from the prediction obtained when no solids-phase stress was considered. The comparison with experimental results was mixed. Locally, the measured solids-phase velocity distributions were over-predicted, whereas the solids concentration was reasonably reproduced in the core of all the pipes. The concentration at the bottom and top walls were over-, and under-predicted, respectively. This was attributed to the inappropriate phasic wall boundary condition models available.

Single-molecule spectroscopy has provided a means to uncover pathways and heterogeneities that were previously hidden beneath the ensemble average. Such heterogeneity, however, is often obscured by the artifacts of experimental noise and the occurrence of undesired processes within the experimental medium. This has subsequently caused in the need for new analytical methodologies. It is particularly important that objectivity be maintained in the development of new analytical methodology so that bias is not introduced and the results improperly characterized. The research presented herein identifies two such sources of experimental uncertainty, and constructs objective approaches to reduce their effects in the experimental results. The first, photoblinking, arises from the occupation of dark electronic states within the probe molecule, resulting in experimental data that is distorted by its contribution. A method based in Bayesian inference is developed, and is found to nearly eliminate photoblinks from the experimental data while minimally affecting the remaining data and maintaining objectivity. The second source of uncertainty is electronic shot-noise, which arises as a result of Poissonian photon collection. A method based in wavelet decomposition is constructed and applied to simulated and experimental data. It is iii found that, while making only one assumption, that photon collection is indeed a Poisson process, up to 75% of the shot-noise contribution may be removed from the experimental signal by the wavelet-based procedure. Lastly, in an effort to connect model-based approaches such as molecular dynamics simulation to model-free approaches that rely solely on the experimental data, a coarse-grained molecular model of a molecular ionic fluorophore diffusing within an electrostatically charged polymer brush is constructed and characterized. It is found that, while the characteristics of the coarse-grained simulation compare well with atomistic simulations, the model is lacking in its representation of the electrostatically-driven behavior of the experimental system.

In this dissertation, an experimental and numerical study of dense coarse solids-liquid flows has been performed. The experimental work mainly involved pressure drop measurements in a vertical flow loop. A limited number of measurements of solids velocity profiles were also obtained in the upward flow section of the flow loop. The numerical work involved simulations of coarse particles-in-water flows in vertical and horizontal pipes. The vertical flow simulations were performed using the commercial CFD software, ANSYS CFX-4.4, while ANSYS CFX-10 was used to simulate the flows in the horizontal pipes. The simulations were performed to investigate the applicability of current physically-based models to very dense coarse-particle flows.<p> In the experimental study, measurements of pressure drop and local solids velocity profiles were obtained. The experiments were conducted in a 53 mm diameter vertical flow loop using glass beads of 0.5 mm and 2.0 mm diameter solids for concentration up to 45%. The liquid phase was water. The measured pressure drop exhibited the expected dependence on bulk velocity and solids mean concentration. The wall shear stress was determined by subtracting the gravitational contribution from the measured pressure drop. For flow with the 0.5 mm particles at high bulk velocities, the values of the wall shear stress were essentially similar for each concentration in the upward flow sections but more variation, indicating the effect of concentration, was noted in the downward flow section. At lower bulk velocities, the wall shear stresses with the 0.5 mm glass beads-water flow showed a dependence on concentration in both test sections. This was attributed to an increase in the slip velocity. For the large particle (2.0 mm glass beads), similar observations were made but the effect of concentration was much less in the upward test section. In the downward test section, the wall shear stress for the flow of the 2.0 mm glass beads increased by almost a constant value for the bulk velocities investigated. The solids velocity profiles showed that the solids velocity gradient is large close to the wall. In addition, the solids velocity profiles indicated that the slip velocity increased at lower velocities due to increase in the bulk concentration in the upward flow section.<p> For the vertical flow simulations, different physical models based on the kinetic theory of granular flows were programmed and implemented in ANSYS CFX-4.4. These models, referred to as the kf-ef-ks-es, kf-ef-ks-es-Ts and kf-ef-ks-kfs models, were investigated by focusing on the closure laws for the solids-phase stress. The treatment of the granular temperature Ts depends on whether small- or large-scale fluctuating motion of the particles is considered. The models were implemented via user-Fortran routines. The predicted results were compared with available experimental results. The predicted solids-phase velocity profiles matched the measured data quite well close to the pipe wall but over-predicted it in the core region. The solids concentration, on the other hand, was significantly under-predicted for concentrations higher than 10%. Variations in the predictions of the phasic turbulent kinetic energy and the eddy viscosity were noted; the effect of solids concentration on them was mixed. A general conclusion drawn from the work is that a more accurate model is required for accurate and consistent prediction of coarse particle flows at high concentrations (less than 10%). In a related study, attention was given to wall boundary conditions again focusing on the effect of the solids-phase models at the wall. Comparison between numerical predictions, using some of the existing wall boundary condition models for the solids phase in particulate flows, with experimental results indicated that the physical understanding of the influence of the fluid and solids-phase on each other and their effect on frictional head loss is far from complete. The models investigated failed to reproduce the experimental results. At high solids concentration, it was apparent from the present study that the no-slip and free-slip wall boundary conditions are not appropriate for liquid-solid flows.<p> For the horizontal flow case, three-dimensional simulations were performed with a focus on the velocity and concentration distributions. Medium and coarse sand-in-water flows in three pipe diameters were considered to investigate the default solids stress models in ANSYS CFX-10. Simulations were performed for three cases by considering: 1) no additional solids-phase stress, i.e. no model for Ts; 2) a zero equation, and 3) an algebraic equilibrium model for the granular temperature. The model predictions were compared to experimental results. The effect of particle size, solids-phase concentration, and pipe diameter was explored using the algebraic equilibrium model. All the cases for the models considered exhibited the characteristic features of horizontal coarse particle slurry flows. The zero equation and the algebraic equilibrium model for the granular temperature produced similar results that were not significantly different from the prediction obtained when no solids-phase stress was considered. The comparison with experimental results was mixed. Locally, the measured solids-phase velocity distributions were over-predicted, whereas the solids concentration was reasonably reproduced in the core of all the pipes. The concentration at the bottom and top walls were over-, and under-predicted, respectively. This was attributed to the inappropriate phasic wall boundary condition models available.

A Variational Transport Theory Method for Two-Dimensional Reactor Core Calculations Scott W. Mosher 110 Pages Directed by Dr. Farzad Rahnema It seems very likely that the next generation of reactor analysis methods will be based largely on neutron transport theory, at both the assembly and core levels. Signifi-cant progress has been made in recent years toward the goal of developing a transport method that is applicable to large, heterogeneous coarse-meshes. Unfortunately, the ma-jor obstacle hindering a more widespread application of transport theory to large-scale calculations is still the computational cost. In this dissertation, a variational heterogeneous coarse-mesh transport method has been extended from one to two-dimensional Cartesian geometry in a practical fashion. A generalization of the angular flux expansion within a coarse-mesh was developed. This allows a far more efficient class of response functions (or basis functions) to be employed within the framework of the original variational principle. New finite element equations were derived that can be used to compute the expansion coefficients for an individual coarse-mesh given the incident fluxes on the boundary. In addition, the non-variational method previously used to converge the expansion coefficients was developed in a new and more thorough manner by considering the implications of the fission source treat-ment imposed by the response expansion. The new coarse-mesh method was implemented for both one and two-dimensional (2-D) problems in the finite-difference, multigroup, discrete ordinates approximation. An efficient set of response functions was generated using orthogonal boundary conditions constructed from the discrete Legendre polynomials. Several one and two-dimensional heterogeneous light water reactor benchmark problems were studied. Relatively low-order response expansions were used to generate highly accurate results using both the variational and non-variational methods. The expansion order was found to have a far more significant impact on the accuracy of the results than the type of method. The varia-tional techniques provide better accuracy, but at substantially higher computational costs. The non-variational method is extremely robust and was shown to achieve accurate re-sults in the 2-D problems, as long as the expansion order was not very low.

The coarse-grained configurational-bias Monte Carlo (CG-CBMC) simulation was employed to study the structural behaviors of methyl methacrylate (MMA) oligomers adsorbed on grooved substrate due to molecular dynamics (MD) simulation is probably trapped at some local energy minima and difficult to carry out over a long enough time to allow relaxation of chain motion for an enormous polymeric system. Therefore, the CG-CBMC simulation was adopted in the present study. In this study, three types of chains are classified according to their positions relative to the groove. Type 1, Type 2, and Type 3 represent the entire MMA-oligomer within the groove, the MMA-oligomer partially within the groove, and the oligomer outside the groove, respectively. The orientational order parameters of Type 1 and Type 2 oligomers decrease with the increase of groove width, but the orientational order parameter of Type 3 oligomers is approximately equal to 0.1. In addition, observation of the orientational order parameters of Type 1 oligomers interacting with the grooved substrate at different interaction strengths decrease with increasing the groove width. Furthermore, the orientational order parameters of Type 1 oligomers within the narrowest (20 Å) and the widest (35 Å) groove with different depths were determined. For the narrowest groove, the arrangement of Type 1 oligomers will be influenced by the groove width. However, in the case of the widest groove, the orientational order parameter of Type 1 oligomers is approximately equal to 0.2. This study can help engineers clarify the characteristics and phenomena of physical adsorption of the molecules, as well as contributing to the application of recent technology.

In this study the incipient motion of coarse solitary particles having different specific weights and shapes was investigated. A tilting flume of rectangular cross-section having a net working length of 12 m was used through the experiments. The slope of the channel and the discharge in the channel are the two basic variable parameters that determine the initiation of motion. Particles made of cement and mixture of cement and iron dust in certain ratios were used in the experiments with an obstructing element of various heights right behind the particles. Dimensionless hydraulic parameters determined from theoretical analysis were related to each other. Velocity profiles over the flow depths were measured and flow conditions corresponding to critical conditions were evaluated in terms of critical velocities and shear velocities. The findings of this study were compared with the results of similar studies given in the literature.

Proteine spielen auf der zellulären Ebene eines Organismus eine fundamentale Rolle. Sie sind quasi die „Maschinen“ der Zelle. Ihre Bedeutung wird nicht zuletzt in ihrem Namen deutlich, welcher 1838 erstmals von J. Berzelius verwendet wurde und „das Erste“, „das Wichtigste“ bedeutet. Proteine sind aus Aminosäuren aufgebaute Moleküle. Unter physiologischen Bedingungen besitzen sie eine definierte dreidimensionale Gestalt, welche für ihre biologische Funktion bestimmend ist. Es wird heutzutage davon ausgegangen, dass diese dreidimensionale, stabile Struktur von Proteinen eindeutig durch die Abfolge der einzelnen Aminosäuren, der Sequenz, bestimmt ist. Diese Abfolge ist für jedes Protein in der Desoxyribonukleinsäure (DNS) gespeichert. Es ist allerdings eines der größten ungelösten Probleme der letzten Jahrzehnte, wie die Beziehung zwischen Sequenz und 3D-Struktur tatsächlich aussieht. Die Beantwortung dieser Fragestellung erfordert interdisziplinäre Ansätze aus Biologie, Informatik und Physik. In dieser Arbeit werden mit Hilfe von Methoden der theoretischen (Bio-) Physik einige der damit verbundenen Aspekte untersucht. Das Hauptaugenmerk liegt dabei auf Wechselwirkungen der einzelnen Aminosäuren eines Proteins untereinander, wofür in dieser Arbeit ein entsprechendes Energiemodell entwickelt wurde. Es werden Grundzustände sowie Energielandschaften untersucht und mit experimentellen Daten verglichen. Die Stärke der Wechselwirkung einzelner Aminosäuren erlaubt zusätzlich Aussagen über die Stabilität von Proteinen bezüglich mechanischer Kräfte. Die vorliegende Arbeit unterteilt sich wie folgt: Kapitel 2 dient der Einleitung und stellt Proteine und ihre Funktionen dar. Kapitel 3 stellt die Modellierung der Proteinstrukturen in zwei verschiedenen Modellen vor, welche in dieser Arbeit entwickelt wurden, um 3D-Strukturen von Proteinen zu beschreiben. Anschließend wird in Kapitel 4 ein Algorithmus zum Auffinden des exakten Energieminimums dargestellt. Kapitel 5 beschäftigt sich mit der Frage, wie eine geeignete diskrete Energiefunktion aus experimentellen Daten gewonnen werden kann. In Kapitel 6 werden erste Ergebnisse dieses Modells dargestellt. Der Frage, ob der experimentell bestimmte Zustand dem energetischen Grundzustand eines Proteins entspricht, wird in Kapitel 7 nachgegangen. Die beiden Kapitel 8 und 9 zeigen die Anwendung des Modells an zwei Proteinen, dem Tryptophan cage protein als dem kleinsten, stabilen Protein und Kinesin, einem Motorprotein, für welches 2007 aufschlussreiche Experimente zur mechanischen Stabilität durchgeführt wurden. Kapitel 10 bis 12 widmen sich Membranproteinen. Dabei beschäftigt sich Kapitel 10 mit der Vorhersage von stabilen Bereichen (sog. Entfaltungsbarrieren) unter externer Krafteinwirkung. Zu Beginn wird eine kurze Einleitung zu Membranproteinen gegeben. Im folgenden Kapitel 11 wird die Entfaltung mit Hilfe des Modells und Monte-Carlo-Techniken simuliert. Mit dem an Membranproteine angepassten Wechselwirkungsmodell ist es möglich, den Einfluss von Mutationen auch ohne explizite strukturelle Informationen vorherzusagen. Dieses Thema wird in Kapitel 12 diskutiert. Die Beziehung zwischen Primär- und Tertiärstruktur eines Proteins wird in Kapitel 13 behandelt. Es wird ein Ansatz skizziert, welcher in der Lage ist, Strukturbeziehungen zwischen Proteinen zu detektieren, die mit herkömmlichen Methoden der Bioinformatik nicht gefunden werden können. Die letzten beiden Kapitel schließlich geben eine Zusammenfassung bzw. einen Ausblick auf künftige Entwicklungen und Anwendungen des Modells.

Biological molecules are essential parts of organisms and participate in a variety of biological processes within cells. Understanding the relationship between sequence, structure, and function of biological molecules are of fundamental importance in life science and the health care industry. In this dissertation, a multi-scale approach was utilized to develop coarse-grained molecular models for protein and RNA simulations. By simplifying the atomistic representation of a biomolecular system, the coarse-grained approach enables the molecular dynamics simulations to reveal the biological processes, which occur on the time and length scales that are inaccessible to the all-atom models. For RNA, an "intermediate" coarse-grained model was proposed to provide both accuracy and efficiency for RNA 3D structure modeling and prediction. The overall potential parameters were derived based on structural statistics sampled from experimental structures. For protein, a general, transferable coarse-grain framework based on the Gay-Berne potential and electrostatic point multipole expansion was developed for polypeptide simulations. Next, an advanced atomistic model was developed to model electrostatic interaction with high resolution and incorporates electronic polarization effect that is ignored in conventional atomistic models. The last part of my thesis work involves applying all-atom molecular simulations to address important questions and problems in biophysics and structural biology. For example, the interaction between protein and miRNA, the recognition mechanism of antigen and antibody, and the structure dynamics of protein in mixed denaturants. / text

Polymer Nanocomposites (PNC) are a new class of materials characterized by their large interfacial areas between the host polymer and nanofiller. This unique feature, due to the size of the nanofiller, is understood to be the cause of enhanced mechanical, electrical, optical, and barrier properties observed of PNCs, relative to the properties of the unfilled polymer. This interface can determine the miscibility of the nanofiller in the polymer, which, in turn, influences the PNC's properties. In addition, this interface alters the polymer's structure near the surface of the nanofiller resulting in heterogeneity of local properties that can be expressed at the macroscopic level. Considering the polymer-nanoparticle interface significantly influences PNC properties, it is apparent that some atomistic level of detail is required to accurately predict the behavior of PNCs. Though an all-atom simulation of a PNC would be able to accomplish the latter, it is an impractical approach to pursue even with the most advanced computational resources currently available. In this contribution, we develop (1) an equilibrium coarse-graining method to predict nanoparticle dispersion in a polymer melt, (2) a dynamic coarse-graining method to predict rheological properties of polymer-nanoparticle melt mixtures, and (3) a numerical approach that includes interfacial layer effects and polymer rigidity when predicting barrier properties of PNCs. In addition to the above, we study how particle and polymer characteristics affect the interfacial layer thickness as well as how the polymer-nanoparticle interface may influence the entanglement network in a polymer melt. More specifically, we use a mean-field theory approach to discern how the concentration of a semiflexible polymer, its rigidity and the particle's size determine the interfacial layer thickness, and the scaling laws to describe this dependency. We also utilize molecular dynamics and simulation techniques on a model PNC to determine if the polymer-nanoparticle interaction can influence the entanglement network of a polymer melt. / text