Browsing by Subject "Simulation"

Utilizing the power of Monte Carlo simulations, a novel, semi-empirical method for investigating the performance of organic photovoltaics (OPVs) in resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE) films is explored. Emulsion-based RIR-MAPLE offers a unique and powerful alternative to solution processing in depositing organic materials for use in solar cells: in particular, its usefulness in controlling the nanoscale morphology of organic thin films and the potential for creating novel hetero-structures make it a suitable experimental backdrop for investigating trends through simulation and gaining a better understanding of how different thin film characteristics impact OPV device performance.

The work presented in this dissertation explores the creation of a simulation tool that relies heavily on measureable properties of RIR-MAPLE films that impact efficiency and can be used to inform film deposition and dictate the paths for future improvements in OPV devices. The original nanoscale implementation of the Monte Carlo method for investigating OPV performance is transformed to enable direct comparison between simulation and experimental external quantum efficiency results. Next, a unique microscale formulation of the Dynamic Monte Carlo (DMC) model is developed based on the observable, fundamental differences between the morphologies of RIR-MAPLE and solution-processed bulk heterojunction (BHJ) films. This microscale model enables us to examine the sensitivity of device performance to various structural and electronic properties of the devices. Specifically, using confocal microscopy, we obtain an average microscale feature size for the RIR-MAPLE P3HT:PC61BM (1:1) BHJ system that represents a strategic starting point for utilizing the DMC as an empirical tool.

Building on this, the RIR-MAPLE P3HT:PC61BM OPV system is studied using input simulation parameters obtained from films with different material ratios and overall device structures based on characterization techniques such as grazing incidence-wide angle X-ray scattering (GI-WAXS) and X-ray photoelectron spectroscopy (XPS). The results from the microscale DMC simulation compare favorably to experimental data and allow us to articulate a well-informed critique on the strengths and limitations of the model as a predictive tool. The DMC is then used to analyze a different RIR-MAPLE BHJ system: PCPDTBT:PC71BM, where the deposition technique itself is investigated for differences in the primary solvents used during film deposition.

Finally, a multi-scale DMC model is introduced where morphology measurements taken at two different size scales, as well as structural and electrical characterization, provide a template that mimics the operation of OPVs. This final, semi-empirical tool presents a unique simulation opportunity for exploring the different properties of RIR-MAPLE deposited OPVs, their effects on OPV performance and potential design routes for improving device efficiencies.

As the largest cave of Buddhist art with thousands of murals spanning ten dynasties, the Dunhuang Mogao cave has been described as a “peerless cave” because of its fabulous frescos and handcrafted delicate sculptures. However, tourism and in-cave human activities had damaged the frescos; only a few caves are now open with limited accessibility for global visitors and the public. In addition, Dunhuang Cave authorities set strict rules to exclude some people, such as people in wheelchairs, to protect the murals and sculptures from possible damage. This thesis project aims to address this problem by modeling how digital environments might provide universal access to the cave by marginalized and excluded groups. The thesis project includes two separate digital sections: a Unity VR (Virtual Reality) immersive experience and a web-based Story Map with a three-dimensional view of selected murals. The thesis project not only provides an immersive experience for worldwide visitors but also unlocks the door for the possibilities of preserving cultural heritage by using innovative digital methods. Through the use of Maya and Steam, the Unity game engine can be used to curate a virtual space by placing the audience into well-textured 3D cave models, while the web-based story map can be used to contextualize basic background knowledge and provides a comprehensive text explanation of the Silk Road and Buddhist culture to inform the user’s understanding of what they are seeing. Overall, this thesis demonstrates endeavors to discover more possibilities and opportunities for historical and cultural heritage protection while not losing access.

Consumers often lack objective information about product acquisition costs. In such cases, consumers must rely on estimates of acquisition costs in making their choices. The current work examines the influence of mental simulations of product acquisition on estimates of acquisition costs. We suggest that simulations of product acquisition lead estimates to reflect the influence of consumers' current physical states on the experience of a particular cost. Specifically, carrying a heavy burden leads consumers to estimate higher distances to targets when they engage in simulation of walking to targets, but not when they do not engage in such simulation.

Simulation can be either deliberate or spontaneous. Deliberate simulation is engaged when consumers intentionally simulate an action. Spontaneous simulation requires particular conditions for its occurrence, but does not require conscious intent. The specific conditions for the occurrence of spontaneous simulation are the availability of situational inputs and that action be possible in the given situation. We support these ideas in a series of studies.

Study 1 demonstrates preference shifts that occur as a consequence of participants carrying heavy burdens. Participants in this study shifted their preference from an option located a visible but undefined distance away towards one that was available at their current location. Study 2 supports the theory that this shift occurs as a consequence of alterations in estimates of acquisition costs by showing that burdened participants estimate distances as greater than do unburdened participants.

Study 3 provides evidence for the role of mental simulation in producing such changes in estimated acquisition costs by showing that the distance expansion first demonstrated in study 2 occurs when targets are visible, but not when targets are not visible. This result is consistent with the central contention of this dissertation that visibility is critical for spontaneous simulation. Together, the studies support the role of spontaneous simulation in burden leading to distance expansion. Study 4 provides further support for the role of simulation in producing the effects of physical state on estimated acquisition costs by showing deliberate simulation results in similar distance to that of spontaneous simulation.

Studies 5 and 6 further demonstrate the dual roles of spontaneous and deliberate simulation on distance expansion. They show that expansion does not occur when targets are not reachable because they are up in the air (study 5). However, deliberate simulation of realistic (climbing - study 5) or unrealistic (flying - study 6) action restores distance expansion in those circumstances, supporting the role of simulation in leading to consideration of physical state in estimated acquisition costs.

The final study ties together these results by demonstrating the effects of both spontaneous and deliberate simulation in a single setting. Varying both the availability of conditions supporting spontaneous simulation and instructions for deliberate simulation the study allows an examination of the comparative effects of the two types of simulation and of their potential interaction. The study finds that deliberate simulation may produce effects that are larger than those of spontaneous simulation, but spontaneous simulation does not seem to enhance the effects of deliberate simulation.

Computer simulation and modeling is a powerful tool for the analysis of physical systems; in this work we consider the use of computer modeling and optimization in improving the focusing properties of a variety of charged particle optics systems. The combined use of several software packages and custom computer code allows for modeling electrostatic and magnetostatic fields and the trajectory of particles through them. Several applications of this functionality are shown. The pieces of code which are shown are the starting point of an integrated charged particle simulation and optimization tool with focus on optimization. The applications shown are mass spectrographs and electron energy spectrographs. Simulation allowed additional information about the systems in question to be determined.In this work, coded apertures are shown to be compatible with sector instruments, though architectural challenges exist. Next, simulation allowed for the discovery of a new class of mass spectrograph which addresses these challenges and is compatible with computational sensing, allowing for both high resolution and high sensitivity, with a 1.8x improvement in spot size. Finally, a portion of this new spectrograph was adapted for use as an electron energy spectrograph, with a resolution 9.1x and energy bandwidth 2.1x that of traditional instruments.

Computational phantoms are set to play an important role in imaging research. As medicine moves increasingly towards providing individualized, patient-specific care, it is imperative that simulations be completed on patient-specific anatomy, rather than a reference standard. To that end, there is need for a variety of realistic phantoms for clinical studies.

This work adds to the existing extended cardiac and torso (XCAT) adult phantom series (two phantoms based on visual human data) by building new models based on adult patient computed tomography (CT) image data. These CT datasets were obtained from Duke University's patient CT database.

Each image-set was segmented using in-house segmentation software, defining bony structures and large organs within the field of view. 3D non-uniform rational b-spline (NURBS) surfaces were fitted to the segmented data. Using the multi-channel large diffeomorphic deformation metric mapping (MC-LDDMM) network, a transform was calculated to morph an existing XCAT model to the segmented patient geometry. Fifty-eight adult XCAT models were added to the phantom library.

In addition to the expanding the XCAT library, the feasibility of incorporating texture was investigated. Currently, the XCAT phantom structures are assumed to be homogeneous. This can lead to unrealistic appearance when the phantoms are combined with imaging simulations, particularly in CT. The purpose of this project was to capture anatomical texture and test it in a simulated phantom. Image data from the aforementioned patient CT database served as the source of anatomical texture.

The images were de-noised using anisotropic diffusion. Next, several regions of interest (ROIs) were taken from the liver and lungs of CT images. Using the ROIs as a source of texture, a larger stochastic texture image-set was created using the Image Quilting algorithm.

The visual human adult male XCAT phantom was voxelized at the same resolution as the texture image. The voxels inside the liver were directly replaced by the corresponding voxels of texture. Similarly for the lung, the voxels between the existing lung bronchi/blood vessels and the lung wall were replaced by texture voxels. This procedure was performed using ten different patient CT image-sets as sources of texture.

To validate the similarity of the artificial textures to the source textures, reconstructions of the adult male XCAT phantom with added textures were compared to the clinical images via receiver operator characteristic (ROC) analysis, a two-sample t-test, equivalence test, and through comparing absolute differences between scores.

It was concluded that this framework provides a valuable tool in which anatomical texture can be incorporated into computational phantoms. It is anticipated that this step towards making many anatomically variable virtual models indicative of a patient populace and making these models more realistic will be useful in medical imaging research, especially for studies relating to image quality.

As silicon-based microelectronics approaches its fundamental physical limit, molecular electronics is emerging as a promising candidate for future ultra-dense electronic devices with individual molecules as active device components. The emerging of molecular spintronics, which exploits the spin-dependent charge transport through organic materials, further demonstrate the promising future of molecular electronics. This dissertation describes the charge transport and spin-spin electronic coupling properties of an extraordinary class of molecular wires, alkyne-bridged porphyrin arrays. Chapter one provides a general background of molecular electronics and molecular wires, as well as the basics of electron paramagnetic resonance (EPR). Chapter two describes utilizing highly conjugated (porphinato)metal-based oligomers (PMn structures) as molecular wire components of nanotransfer printed (nTP) molecular junctions; electrical characterization of these “bulk” nTP devices highlights device resistances that depend on PMn wire length. This study demonstrates the ability to fabricate “bulk” and scalable electronic devices in which function derives from the electronic properties of discrete single molecules, and underscores how a critical device function—wire resistance—may be straightforwardly engineered by PMn molecular composition. Chapter three describe the electronic exchange coupling between two unpaired spin on Cu(II) ions in meso-meso alkyne-bridged multi[copper(II) porphyrin] (mmPCu2). Spin and conformational dynamics in symmetric mmPCu2 have been studied in toluene solution at variable temperature using EPR spectroscopy. Comparison of the dimer EPR spectra to those of Cu porphyrin monomers shows clear evidence of an isotropic exchange interaction (Javg) in these biradicaloid structures, manifested by a significant line broadening in the dimer spectra. Comparison of ethyne and butadiyne alkyne bridges reveals a remarkable sensitivity to orbital interactions between the spacer and the metal, which is reflected in measurements of Javg as a function of temperature. The results suggest that orbital symmetry relationships may be more important than previously recognized in the design of optimized molecular spintronic devices. Chapter four reports a study of β-β linked bis[(porphinato)copper(II)] complexes (ββPCu2), which exhibit very different electronic structures compared to their mm linked analogs. By using electron paramagnetic resonance (EPR) spectroscopy, this study exhibits that a wide range (3 orders of magnitude) of the average electronic spin-spin exchange coupling can be achieved by varying the length of bridges and points of connections between the porphyrin rings. The pathways for mmPCu2 and ββPCu2 complexes were also investigated, with the ββPCu2 complexes exhibiting a dominant σ-type pathway and the mmPCu2 complexes showing a dominant π-type pathway.

Purpose: Optical-CT imaging with radiochromic dosimeters is a powerful method of evaluating 3D dose distributions at high resolution and sensitivity. Current optical-CT systems require large quantities of refractively matched fluid surrounding the dosimeter in order to minimize refraction artifacts. The use of a refractively matched solid polyurethane solid-tank, in place of a fluid bath, has the potential to greatly increase practical convenience, reduce cost, and improve the efficacy of flood corrections. This thesis aims to investigate the feasibility of solid-tank optical-CT imaging for 3D dosimetry, and to use computer simulation to investigate optimal design and scanning parameters.

Methods: A Matlab based ray-tracing simulation platform, ScanSim, was used to model a parallel-source imaging system through a cubic polyurethane solid-tank containing a central cylindrical hollow into which cylindrical PRESAGE® radiochromic dosimeters can be placed. A small amount of fluid surrounds the dosimeter in the tank. ScanSim's capabilities were expanded from previous work to include the geometry and physics of dry scanning. Two imaging methods were investigated, representing a telecentric detector and an ideal detector: in the latter, all light rays are collected and used in reconstruction. In order to characterize the efficacy of these systems, and dependence on refractive index (RI) mismatches between dosimeter, solid-tank, and fluid, simulations were run for a variety of dosimeter (RI = 1.5-1.47), and fluid (RI = 1.55-1.0) combinations. Additional simulations examined the effect of increasing gap size (1-5mm) between the dosimeter and solid-tank well. For the telecentric setup, the effects of changing the lens tolerance (0.5-5.0 degrees) were also investigated. The metric for evaluation of efficacy is the usable radius, which is defined as the distance from the dosimeter center where the measured and true (known) dose differs by less than 2%.

Results: As the refractive index mismatch between the dosimeter and tank increases from 0-0.02, the telecentric system showed a significant decrease in the usable radius from 97.6% to 50.2% compared to a decrease from 97.6% to 96.4% for the ideal system. When the three media are perfectly matched, the telecentric system and ideal system perform identically. For mismatched dosimeter and solid-tank in a telecentric system, the optimal fluid match has a refractive index lower than either the tank or dosimeter, decreasing non-linearly from 1.5-1.34 as the dosimeter-tank refractive mismatch increases from 0 to 0.02. Media mismatches between the dosimeter and solid-tank also exacerbate the effects of changing the gap size, with no apparent quantifiable relationship. Generally, the optimal fluid match is closer to the dosimeter RI when the gap size is large (>3mm). Increasing the telecentric lens tolerance improves the usable radius for all refractive media combinations, and approaches the behavior of the ideal system for tolerances >5.0°.

The biological reduction of N2 to NH3 catalyzed by molybdenum nitrogenase requires eight steps to finish a completed catalysis cycle. This reaction cycle is associated with ATP-driven electron transfer (ET) from the Fe protein to the MoFe protein, and part of ET is experimentally confirmed to be ‘conformationally gated’. Although the overall sequence of ET in nitrogenase has been studied for decades, the nature of coupling between ET pathways and nucleotides binding/protein-protein docking is still unclear, especially from theoretical aspects. Here, we have utilized submicrosecond classical molecular dynamics simulations to allow the ADP-bound and ATP-bound nitrogenases to simulate their conformations in real biological systems. Then the Pathways plugin implemented by Balabin et al was employed to calculate the ET coupling and visualize the ET pathways between the F-cluster and the P-cluster in nitrogenase. The comparison of the ET couplings (the F-cluster to the P-cluster) we calculated and the edge-to-edge distance between the ET donor and acceptor suggests that the coupling pathways grow in strength more that that would be expected from simple distance changes. This result additionally indicates the electron of Fe protein is protected prior to the ATP binding and the protein-protein docking, using pathway switching effects.

Magnetic field inhomogeneity results in image artifacts including signal loss, image blurring and distortions, leading to decreased diagnostic accuracy. Conventional multi-coil (MC) shimming method employs both RF coils and shimming coils, whose mutual interference induces a tradeoff between RF signal-to-noise (SNR) ratio and shimming performance. To address this issue, RF coils were integrated with direct-current (DC) shim coils to shim field inhomogeneity while concurrently emitting and receiving RF signal without being blocked by the shim coils. The currents applied to the new coils, termed iPRES (integrated parallel reception, excitation and shimming), were optimized in the numerical simulation to improve the shimming performance. The objectives of this work is to offer a guideline for designing the optimal iPRES coil arrays to shim the abdomen.

In this thesis work, the main field () inhomogeneity was evaluated by root mean square error (RMSE). To investigate the shimming abilities of iPRES coil arrays, a set of the human abdomen MRI data was collected for the numerical simulations. Thereafter, different simplified iPRES(N) coil arrays were numerically modeled, including a 1-channel iPRES coil and 8-channel iPRES coil arrays. For 8-channel iPRES coil arrays, each RF coil was split into smaller DC loops in the x, y and z direction to provide extra shimming freedom. Additionally, the number of DC loops in a RF coil was increased from 1 to 5 to find the optimal divisions in z direction. Furthermore, switches were numerically implemented into iPRES coils to reduce the number of power supplies while still providing similar shimming performance with equivalent iPRES coil arrays.

The optimizations demonstrate that the shimming ability of an iPRES coil array increases with number of DC loops per RF coil. Furthermore, the z direction divisions tend to be more effective in reducing field inhomogeneity than the x and y divisions. Moreover, the shimming performance of an iPRES coil array gradually reach to a saturation level when the number of DC loops per RF coil is large enough. Finally, when switches were numerically implemented in the iPRES(4) coil array, the number of power supplies can be reduced from 32 to 8 while keeping the shimming performance similar to iPRES(3) and better than iPRES(1). This thesis work offers a guidance for the designs of iPRES coil arrays.

Inter-Vehicle Communication (IVC) is a vital part of Intelligent Transportation System (ITS), which has been extensively researched in recent years. Dedicated Short Range Communication (DSRC) is being seriously considered by automotive industry and government agencies as a promising wireless technology for enhancing transportation safety and efficiency of road utilization. In the DSRC based vehicular ad hoc networks (VANETs), the transportation safety is one of the most crucial features that needs to be addressed. Safety applications usually demand direct vehicle-to-vehicle ad hoc communication due to a highly dynamic network topology and strict delay requirements. Such direct safety communication will involve a broadcast service because safety information can be beneficial to all vehicles around a sender. Broadcasting safety messages is one of the fundamental services in DSRC. In order to provide satisfactory quality of services (QoS) for various safety applications, safety messages need to be delivered both timely and reliably. To support the stringent delay and reliability requirements of broadcasting safety messages, researchers have been seeking to test proposed DSRC protocols and suggesting improvements. A major hurdle in the development of VANET for safety-critical services is the lack of methods that enable one to determine the effectiveness of VANET design mechanism for predictable QoS and allow one to evaluate the tradeoff between network parameters. Computer simulations are extensively used for this purpose. A few analytic models and experiments have been developed to study the performance and reliability of IEEE 802.11p for safety-related applications. In this thesis, we propose to develop detailed analytic models to capture various safety message dissemination features such as channel contention, backoff behavior, concurrent transmissions, hidden terminal problems, channel fading with path loss, multi-channel operations, multi-hop dissemination in 1-Dimentional or 2-Dimentional traffic scenarios. MAC-level and application-level performance metrics are derived to evaluate the performance and reliability of message broadcasting, which provide insights on network parameter settings. Extensive simulations in either Matlab or NS2 are conducted to validate the accuracy of our proposed models.

In this work, the simulation (forward problem) and reconstruction (inverse problem) in Thermoacoustic Tomography (TAT) are studied using a pseudospectral time-domain (PSTD) method with 4th-order time integration.

The objective of the TAT simulation is to solve for the thermoacoustic pressure field in an inhomogeneous medium. Using the PSTD method, the spatial derivatives of pressure field and particle velocity can be obtained using fast fourier transform (FFT). Since the Fourier transforms used to represent the spatial derivatives of smooth functions are exact, only 2 points per wavelength are needed in the spatial discretization. The time integration is achieved by a 4th-order method to effectively reduce the computational time. The results of the algorithm are validated by analytical solutions. Perfectly Matched Layers (PMLs) are applied to absorb the outgoing waves and avoid ``wraparound'' effect. The maximum attenuation coefficient of the PMLs has an optimum value to minimize the reflections due to discretization and wraparound effect for 2D and 3D problems. Different PML profiles are also compared, quadratic profile is chosen because it can minimize the overall reflection. Spatial smoothing is needed for PSTD to avoid Gibbs' phenomenon in the modeling of a point source, and the effect of the smoothing function is studied.

In the TAT reconstruction problem, the PSTD method is used to reconstruct the thermoacoustic sources by solving the thermoacoustic wave equations in a reversed temporal order within the framework of time reversal imaging. The back-propagated pressure waves then refocus at the spatial locations of the original sources. Most other TAT reconstruction algorithms are based on the assumption that the tissue medium is acoustically homogeneous. In practice, however, even the mild tissue inhomogeneity will cause large phase errors and cause spatial misplacement and distortion of the sources. The proposed PSTD method utilizes a two-step process to solve this problem. In the first step, a homogeneous time reversal reconstruction is performed. Since an inhomogeneity itself is usually a source because of spatially dependent electrical conductivity (thus microwave absorption), the spatial location and the shape of the inhomogeneity can be estimated. In the second step, the updated acoustic property map is loaded followed by an inhomogeneous reconstruction. Numerical results show that this method greatly improves the reconstruction results. Images with improved quality are reconstructed from experimental data.

A 3D PSTD algorithm is developed and validated. Numerical results show that the PSTD algorithm with the 4th-order time integration is capable of simulating large 3D acoustic problems accurately and efficiently. A 3D breast phantom model is used to study the inhomogeneous reconstruction in 3D. Improved results over the homogeneous method are observed.

A preliminary study of the Thermoacoustic Tomography (TAT) using continuous-wave (CW) modulated microwaves is summarized. The theoretical background, system configuration, experiment setup, and measurement results are presented.

The two years of Master of Science in Statistical and Economic Modeling program is the most rewarding time ever in my life. This thesis acts as a portfolio of project and applied experience while I am enrolled in the Master of Science in Statistical and Economic Modeling program. This thesis will summarize my graduate study in two parts: Simulation Study of Exchangeability for Binary Data, and Summary of Summer Internship at Center for Responsible Lending. The project of Simulation Study of Exchangeability for Binary Data contains materials from a team project, which jointly performed by Sheng Jiang, Xuan Sun and me. Abstracts for both projects are below in order.

(1) Simulation Study of Exchangeability for Binary Data

To investigate tractable Bayesian tests on exchangeability, this project considers special cases of nonexchangeable random sequences: Markov chains. Asymptotic results of Bayes factor (BF) are derived. When null hypothesis is true, Bayes Factor in favor of the null goes to infinity at geometric rate (true odds is not one half). When null hypothesis is not true, Bayes Factor in favor of the null goes to 0 faster than geometric rate. The results are robust under misspecifications. Simulation studies are employed to see the performance of the test when the sample size is small, prior beliefs change and true parameters change.

(2) Summary of Summer Internship at Center for Responsible Lending

My summer internship deals with a survey data from Social Science Research Solution about auto financing. The dataset includes about one thousand valid responses and 114 variables for each response. My efforts on exploratory statistic analysis unfolded many interesting findings. For example, African Americans and Latinos are receiving 2.02% higher APR on average than white buyers, excluding the effects of relevant variables. And what's more, a Fisher's Exact Test of Significance is widely used to discover the significance of a series of variables. Results are presented in organized neat tables. Findings are included in weekly reports. One example finding is that warranty add-­‐‑ons of a financed car has significant impacts on all three aspects of a loan, which is Annual Percent Rate, Loan Amount, and Monthly Payment.

In magnetic resonance microscopy, insufficient signal-to-noise ratio currently limits imaging performance. Superconducting probes can potentially increase the sensitivity of the magnetic resonance experiment. However, many superconducting probes failed to entirely deliver the expected increase in signal-to-noise ratio.

We present a method based on finite-element radiofrequency simulations. The radiofrequency model computes several figures of merit of a probe, namely: i) the resonant frequency, ii) the impedance, iii) the magnetic field homogeneity, iv) the filling factor, and v) the sensitivity. The probe is constituted by several components. The method calculates the electromagnetic losses induced by every component within the probe, and identifies the component limiting the sensitivity of the probe. Subsequently, the probe design can be improved iteratively.

We show that the sensitivity of an existing superconducting Helmholtz pair can be improved by increasing the filling factor of the probe and cooling the radiofrequency shield, which was implemented in the design of a new superconducting probe. The second probe exhibits a sensitivity three times as high, leading to improved imaging performance.