Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution

Molecular dynamics simulations have been used to explore the conformational flexibility of a PNA·DNA·PNA triple helix in aqueous solution. Three 1.05 ns trajectories starting from different but reasonable conformations have been generated and analyzed in detail. All three trajectories converge within about 300 ps to produce stable and very similar conformational ensembles, which resemble the crystal structure conformation in many details. However, in contrast to the crystal structure, there is a tendency for the direct hydrogen-bonds observed between the amide hydrogens of the Hoogsteen-binding PNA strand and the phosphate oxygens of the DNA strand to be replaced by water-mediated hydrogen bonds, which also involve pyrimidine O2 atoms. This structural transition does not appear to weaken the triplex structure but alters groove widths and so may relate to the potential for recognition of such structures by other ligands (small molecules or proteins). Energetic analysis leads us to conclude that the reason that the hybrid PNA/DNA triplex has quite different helical characteristics from the all-DNA triplex is not because the additional flexibility imparted by the replacement of sugar−phosphate by PNA backbones allows motions to improve base-stacking but rather that base-stacking interactions are very similar in both types of triplex and the driving force comes from weak but definate conformational preferences of the PNA strands.

Parallel vector processing of multidimensional orthogonal transforms for digital signal processing applications

The performance of the parallel vector implementation of the one- and two-dimensional orthogonal transforms is evaluated. The orthogonal transforms are computed using actual or modified fast Fourier transform (FFT) kernels. The factors considered in comparing the speed-up of these vectorized digital signal processing algorithms are discussed and it is shown that the traditional way of comparing th execution speed of digital signal processing algorithms by the ratios of the number of multiplications and additions is no longer effective for vector implementation; the structure of the algorithm must also be considered as a factor when comparing the execution speed of vectorized digital signal processing algorithms. Simulation results on the Cray X/MP with the following orthogonal transforms are presented: discrete Fourier transform (DFT), discrete cosine transform (DCT), discrete sine transform (DST), discrete Hartley transform (DHT), discrete Walsh transform (DWHT), and discrete Hadamard transform (DHDT). A comparison between the DHT and the fast Hartley transform is also included.(34 refs)

A Framework for the Automation of Discrete-Event Simulation Experiments

Simulation is an important resource for researchers in diverse fields. However, many researchers have found flaws in the methodology of published simulation studies and have described the state of the simulation community as being in a crisis of credibility. This work describes the project of the Simulation Automation Framework for Experiments (SAFE), which addresses the issues that undermine credibility by automating the workflow in the execution of simulation studies. Automation reduces the number of opportunities for users to introduce error in the scientific process thereby improvingthe credibility of the final results. Automation also eases the job of simulation users and allows them to focus on the design of models and the analysis of results rather than on the complexities of the workflow.

The Design of XML-Based Model and Experiment Description Languages for Network Simulation

The Simulation Automation Framework for Experiments (SAFE) is a project created to raise the level of abstraction in network simulation tools and thereby address issues that undermine credibility. SAFE incorporates best practices in network simulationto automate the experimental process and to guide users in the development of sound scientific studies using the popular ns-3 network simulator. My contributions to the SAFE project: the design of two XML-based languages called NEDL (ns-3 Experiment Description Language) and NSTL (ns-3 Script Templating Language), which facilitate the description of experiments and network simulationmodels, respectively. The languages provide a foundation for the construction of better interfaces between the user and the ns-3 simulator. They also provide input to a mechanism which automates the execution of network simulation experiments. Additionally,this thesis demonstrates that one can develop tools to generate ns-3 scripts in Python or C++ automatically from NSTL model descriptions.

Visualization Techniques For The Analysis Of Network Simulation Results

The Simulation Automation Framework for Experiments (SAFE) streamlines the de- sign and execution of experiments with the ns-3 network simulator. SAFE ensures that best practices are followed throughout the workflow a network simulation study, guaranteeing that results are both credible and reproducible by third parties. Data analysis is a crucial part of this workflow, where mistakes are often made. Even when appearing in highly regarded venues, scientific graphics in numerous network simulation publications fail to include graphic titles, units, legends, and confidence intervals. After studying the literature in network simulation methodology and in- formation graphics visualization, I developed a visualization component for SAFE to help users avoid these errors in their scientific workflow. The functionality of this new component includes support for interactive visualization through a web-based interface and for the generation of high-quality, static plots that can be included in publications. The overarching goal of my contribution is to help users create graphics that follow best practices in visualization and thereby succeed in conveying the right information about simulation results.

Combustion of Biogas in a Gas Turbine Simulation

Research was to investigate the effects of increasing levels of carbon dioxide addition to the combustion of methane with air. Using an atmospheric-pressure, swirl-stabilized dump combustor, emissions data and flame stability limitations were measured and analyzed.

Design Simulation for Solar Energy Research and Education

Solar research is primarily conducted in regions with consistent sunlight, severely limiting research opportunities in many areas. Unfortunately, the unreliable weather in Lewisburg, PA, can prove difficult for such testing to be conducted. As such, a solar simulator was developed for educational purposes for the Mechanical Engineering department at Bucknell University. The objective of this work was to first develop a geometric model to evaluate a one sun solar simulator. This was intended to provide a simplified model that could be used without the necessity of expensive software. This model was originally intended to be validated experimentally, but instead was done using a proven ray tracing program, TracePro. Analyses with the geometrical model and TracePro demonstrated the influence the geometrical properties had results, specifically the reflector (aperture) diameter and the rim angle. Subsequently, the two were approaches were consistent with one another for aperture diameters 0.5 m and larger, and for rim angles larger than 45°. The constructed prototype, that is currently untested, was designed from information provided by the geometric model, includes a metal halide lamp with a 9.5 mm arc diameter and parabolic reflector with an aperture diameter of 0.631 meters. The maximum angular divergence from the geometrical model was predicted to be 30 mRadians. The average angular divergence in TraceProof the system was 19.5 mRadians, compared to the sun’s divergence of 9.2 mRadians. Flux mapping in TracePro showed an intensity of 1000 W/m2 over the target plane located 40 meters from the lamp. The error between spectrum of the metal halide lamp and the solar spectrum was 10.9%, which was found by comparing their respective Plank radiation distributions. The project did not satisfy the original goal of matching the angular divergence of sunlight, although the system could still to be used for optical testing. The geometric model indicated performance in this area could be improved by increasing the diameter of the reflector, as well as decreasing the source diameter. Although ray tracing software provides more information to analyze the simulator system, the geometrical model is adequate to provide enough information to design a system.

Reynolds-stress turbulence model in the KIVA code for engine simulation

A Reynolds-Stress Turbulence Model has been incorporated with success into the KIVA code, a computational fluid dynamics hydrocode for three-dimensional simulation of fluid flow in engines. The newly implemented Reynolds-stress turbulence model greatly improves the robustness of KIVA, which in its original version has only eddy-viscosity turbulence models. Validation of the Reynolds-stress turbulence model is accomplished by conducting pipe-flow and channel-flow simulations, and comparing the computed results with experimental and direct numerical simulation data. Flows in engines of various geometry and operating conditions are calculated using the model, to study the complex flow fields as well as confirm the model’s validity. Results show that the Reynolds-stress turbulence model is able to resolve flow details such as swirl and recirculation bubbles. The model is proven to be an appropriate choice for engine simulations, with consistency and robustness, while requiring relatively low computational effort.

Topological changes in 2D simplicial meshes for the simulation of fractures

A method for the introduction of strong discontinuities into a mesh will be developed. This method, applicable to a number of eXtended Finite Element Methods (XFEM) with intra-element strong discontinuities will be demonstrated with one specific method: the Generalized Cohesive Element (GCE) method. The algorithm utilizes a subgraph mesh representation which may insert the GCE either adaptively during the course of the analysis or a priori. Using this subgraphing algorithm, the insertion time is O(n) to the number of insertions. Numerical examples are presented demonstrating the advantages of the subgraph insertion method.

Simulation of four stroke engine cycle for a 4 - valve pentroof engine in KIVA 3VR2

The main purpose of this project is to understand the process of engine simulation using the open source CFD code called KIVA. This report mainly discusses the simulation of the 4-valve Pentroof engine through KIVA 3VR2. KIVA is an open source FORTRAN code which is used to solve the fluid flow field in the engines with the transient 2D and 3D chemically reactive flow with spray. It also focuses on the complete procedure to simulate an engine cycle starting from pre- processing until the final results. This report will serve a handbook for the using the KIVA code.

Investigating the effect of construction management strategies on project greenhouse gas emissions using interactive simulation

The challenges posed by global climate change are motivating the investigation of strategies that can reduce the life cycle greenhouse gas (GHG) emissions of products and processes. While new construction materials and technologies have received significant attention, there has been limited emphasis on understanding how construction processes can be best managed to reduce GHG emissions. Unexpected disruptive events tend to adversely impact construction costs and delay project completion. They also tend to increase project GHG emissions. The objective of this paper is to investigate ways in which project GHG emissions can be reduced by appropriate management of disruptive events. First, an empirical analysis of construction data from a specific highway construction project is used to illustrate the impact of unexpected schedule delays in increasing project GHG emissions. Next, a simulation based methodology is described to assess the effectiveness of alternative project management strategies in reducing GHG emissions. The contribution of this paper is that it explicitly considers projects emissions, in addition to cost and project duration, in developing project management strategies. Practical application of the method discussed in this paper will help construction firms reduce their project emissions through strategic project management, and without significant investment in new technology. In effect, this paper lays the foundation for best practices in construction management that will optimize project cost and duration, while minimizing GHG emissions.

Dynamic modeling, simulation and control design of a parafoil-payload system for ship launched aerial delivery system (SLADS)

The objective of this research was to develop a high-fidelity dynamic model of a parafoilpayload system with respect to its application for the Ship Launched Aerial Delivery System (SLADS). SLADS is a concept in which cargo can be transfered from ship to shore using a parafoil-payload system. It is accomplished in two phases: An initial towing phase when the glider follows the towing vessel in a passive lift mode and an autonomous gliding phase when the system is guided to the desired point. While many previous researchers have analyzed the parafoil-payload system when it is released from another airborne vehicle, limited work has been done in the area of towing up the system from ground or sea. One of the main contributions of this research was the development of a nonlinear dynamic model of a towed parafoil-payload system. After performing an extensive literature review of the existing methods of modeling a parafoil-payload system, a five degree-of-freedom model was developed. The inertial and geometric properties of the system were investigated to predict accurate results in the simulation environment. Since extensive research has been done in determining the aerodynamic characteristics of a paraglider, an existing aerodynamic model was chosen to incorporate the effects of air flow around the flexible paraglider wing. During the towing phase, it is essential that the parafoil-payload system follow the line of the towing vessel path to prevent an unstable flight condition called ‘lockout’. A detailed study of the causes of lockout, its mathematical representation and the flight conditions and the parameters related to lockout, constitute another contribution of this work. A linearized model of the parafoil-payload system was developed and used to analyze the stability of the system about equilibrium conditions. The relationship between the control surface inputs and the stability was investigated. In addition to stability of flight, one more important objective of SLADS is to tow up the parafoil-payload system as fast as possible. The tension in the tow cable is directly proportional to the rate of ascent of the parafoil-payload system. Lockout instability is more favorable when tow tensions are large. Thus there is a tradeoff between susceptibility to lockout and rapid deployment. Control strategies were also developed for optimal tow up and to maintain stability in the event of disturbances.

Three dimensional finite element simulation of polymer melting and flow in a single-screw extruder : optimization of screw channel geometry

Single-screw extrusion is one of the widely used processing methods in plastics industry, which was the third largest manufacturing industry in the United States in 2007 [5]. In order to optimize the single-screw extrusion process, tremendous efforts have been devoted for development of accurate models in the last fifty years, especially for polymer melting in screw extruders. This has led to a good qualitative understanding of the melting process; however, quantitative predictions of melting from various models often have a large error in comparison to the experimental data. Thus, even nowadays, process parameters and the geometry of the extruder channel for the single-screw extrusion are determined by trial and error. Since new polymers are developed frequently, finding the optimum parameters to extrude these polymers by trial and error is costly and time consuming. In order to reduce the time and experimental work required for optimizing the process parameters and the geometry of the extruder channel for a given polymer, the main goal of this research was to perform a coordinated experimental and numerical investigation of melting in screw extrusion. In this work, a full three-dimensional finite element simulation of the two-phase flow in the melting and metering zones of a single-screw extruder was performed by solving the conservation equations for mass, momentum, and energy. The only attempt for such a three-dimensional simulation of melting in screw extruder was more than twenty years back. However, that work had only a limited success because of the capability of computers and mathematical algorithms available at that time. The dramatic improvement of computational power and mathematical knowledge now make it possible to run full 3-D simulations of two-phase flow in single-screw extruders on a desktop PC. In order to verify the numerical predictions from the full 3-D simulations of two-phase flow in single-screw extruders, a detailed experimental study was performed. This experimental study included Maddock screw-freezing experiments, Screw Simulator experiments and material characterization experiments. Maddock screw-freezing experiments were performed in order to visualize the melting profile along the single-screw extruder channel with different screw geometry configurations. These melting profiles were compared with the simulation results. Screw Simulator experiments were performed to collect the shear stress and melting flux data for various polymers. Cone and plate viscometer experiments were performed to obtain the shear viscosity data which is needed in the simulations. An optimization code was developed to optimize two screw geometry parameters, namely, screw lead (pitch) and depth in the metering section of a single-screw extruder, such that the output rate of the extruder was maximized without exceeding the maximum temperature value specified at the exit of the extruder. This optimization code used a mesh partitioning technique in order to obtain the flow domain. The simulations in this flow domain was performed using the code developed to simulate the two-phase flow in single-screw extruders.

Implementation of a phenomenological evaporation model into a porous network simulation for water management in low temperature fuel cells

A phenomenological transition film evaporation model was introduced to a pore network model with the consideration of pore radius, contact angle, non-isothermal interface temperature, microscale fluid flows and heat and mass transfers. This was achieved by modeling the transition film region of the menisci in each pore throughout the porous transport layer of a half-cell polymer electrolyte membrane (PEM) fuel cell. The model presented in this research is compared with the standard diffusive fuel cell modeling approach to evaporation and shown to surpass the conventional modeling approach in terms of predicting the evaporation rates in porous media. The current diffusive evaporation models used in many fuel cell transport models assumes a constant evaporation rate across the entire liquid-air interface. The transition film model was implemented into the pore network model to address this issue and create a pore size dependency on the evaporation rates. This is accomplished by evaluating the transition film evaporation rates determined by the kinetic model for every pore containing liquid water in the porous transport layer (PTL). The comparison of a transition film and diffusive evaporation model shows an increase in predicted evaporation rates for smaller pore sizes with the transition film model. This is an important parameter when considering the micro-scaled pore sizes seen in the PTL and becomes even more substantial when considering transport in fuel cells containing an MPL, or a large variance in pore size. Experimentation was performed to validate the transition film model by monitoring evaporation rates from a non-zero contact angle water droplet on a heated substrate. The substrate was a glass plate with a hydrophobic coating to reduce wettability. The tests were performed at a constant substrate temperature and relative humidity. The transition film model was able to accurately predict the drop volume as time elapsed. By implementing the transition film model to a pore network model the evaporation rates present in the PTL can be more accurately modeled. This improves the ability of a pore network model to predict the distribution of liquid water and ultimately the level of flooding exhibited in a PTL for various operating conditions.