Browsing by Subject "Simulations"
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Item Computational and experimental studies of biomolecules(2018-10-08) Cheng, Sara Yuengee; Florin, Ernst-Ludwig; Ren, Pengyu; Gordon, Vernita; Marder, Michael; Russell, RickIntegrating experiments and computational modeling is critical for understanding the structure and dynamics of biomolecules. Beyond providing validation for experimental results, computational modeling, that incorporates accurate physical models and enhanced sampling methods, can provide insight into the mechanisms underlying experimental observations. I will present four projects where experiments and computational modeling were used together, to understand mechanisms underlying the structure and dynamics of biomolecules. The first project involves using enhanced sampling to improve the efficiency of calculating the hydration free energies of small molecules using a polarizable force field. These predictions are compared with a conventional free energy method, and excellent agreement is found between the methods. The second project involves using atomic molecular dynamics simulations to determine the molecular mechanism underlying the ability of nanosensor to detect point-mutations in a DNA sequence. By analyzing the nearest-neighbor hydrogen bonding profile, from simulations of the nanosensor, a molecular mechanism was proposed to explain the experimental data. The third project involves the incorporation of non-canonical hydrogen bonding in a RNA coarse-grained model in order to improve 3D structure prediction. This new model is applied to study the sequence-dependent stability of several RNAs including RNA G-quadruplexes. The final project involves the development of a new single-molecule assay to measure local transitions in nucleic acid structures using ultrashort DNA tethers. This project involves collaboration with an experimental biochemistry group to design the DNA tethers and to prepare single-molecule samples. All projects involve the development of new methods to understand the 3D structure and dynamics of biomoleculesItem Connecting the dots : tracking galaxy evolution using constant cumulative number density at 3(2015-12) Jaacks, Jason Dale; Finkelstein, Steven L.; Bromm, VolkerUsing the cosmological smoothed particle hydrodynamical code GADGET-3 we make a realistic assessment of the technique of using constant cumulative number density as a tracer of galaxy evolution. We find that over a redshift range of 3Item Investigation of surfactant-polymer flooding simulation using two-phase and three-phase microemulsion phase behavior models(2021-08-16) Alhotan, Muhammad Mansour; Sepehrnoori, Kamy, 1951-; Delshad, MojdehThe vast global demand for energy coupled with the decreasing oil production capabilities of maturing fields raises the need for Enhanced Oil Recovery (EOR) technologies. Much of the oil in these maturing fields are yet to be extracted and remains in the reservoir as residual oil. Chemical EOR (CEOR) is a widely known and effective method in extracting the remaining oil in the reservoir post-secondary flooding. Surfactant-polymer flooding is a type of CEOR that enhances oil recovery by applying mobility control, forming micelles, and reducing interfacial tension. Simulation of CEOR floods before field application is essential to avoid deployment obstacles and to ensure the good design of the chemical formulations. In this thesis, reservoir simulators that utilize two-phase microemulsion model (CMG-STARS) and three-phase microemulsion model (UTCHEMRS & INTERSECT) are used to simulate surfactant-polymer flooding to determine and compare their results. Different models are used in the simulators to describe the physical behavior of injected chemicals inside the reservoir. Therefore, these models were examined and matched when possible. An extensive study was performed on the relative permeability models of INTERSECT and UTCHEMRS. For simulations, the physical behavior models of polymer and surfactant were constructed and validated on a 1D scale reservoir model. Then, the reservoir model was extended to a 3D model, where the physical models and results were further validated. Finally, simulations were conducted in a field-scale reservoir containing 680,400 grids, where results were compared and analyzed. The results for the relative permeability study demonstrated that the INTERSECT relative permeability model is complex, and more information is required to follow the sequence of equations and their dependencies. For the simulation, the 1D and 3D model results suggest an excellent match between the different simulators in modeling surfactant-polymer floods. In the case of the field-scale model, the simulators matched in terms of oil recovery and produced and injected total fluids while having similar average reservoir pressures.Item The macro- and micro-instabilities in the pedestal region of the Tokamak(2015-05) Ma, Jingfei; Morrison, Philip J.; Horton, C. W. (Claude Wendell), 1942-; Berk, Herbert; Fitzpatrick, Richard; Hallock, GaryIn this paper, we present the theoretical and numerical studies of the linear characteristics and nonlinear transport features of the instabilities driven by the steep profile gradient and edge current in the pedestal region of the tokamak. Two important instabilities, the peeling-ballooning (P-B) modes (macro-instability) and the drift-Alfven modes (micro-instability), are studied using the fluid analysis and the BOUT++ codes. In particular, the edge-localized modes (ELMs), which appear to be the energy burst in the nonlinear stage of the peeling-ballooning mode, are numerically studied and the results are compared with the experimental measurement. In addition, the features of the impurity transport in the edge region of the tokamak are theoretically analyzed. Firstly, we explore the fundamental characteristics of the P-B modes and the ELM bursts numerically using the three-field reduced MHD model under the BOUT++ framework, in the shifted-circular geometry, i.e. the limiter tokamak geometry. In the linear simulations, the growth rate and real frequency and the mode structure versus the toroidal mode number (n) are shown. The features of the ELM bursts are shown in the nonlinear simulations, including the time evolution of the relative energy loss (ELM size) and the pedestal profile. Secondly, two original research projects related to the P-B modes and the ELM burst are described. One is the study of the scaling law between the relative energy loss of ELMs and the edge collisionality. We generate a sequence of shifted-circular equilibria with different edge collisionality varying over four orders of magnitude using EFIT. The simulation results are in good agreement with the multi-tokamak experimental data. Another is the study of the differences of the linear behaviors of the P-B modes between the standard and snowflake divertor configurations. Using DIII-D H-mode ElMing equilibria, we found that the differences are due to the local magnetic shear change at the outboard midplane, which is the result of the realization of the snowflake configuration. Finally, the micro-instability, the drift-Alfven instability in the pedestal region of the DIII-D tokamak is studied. A modified six-field Landau fluid model under BOUT++ framework is used to study the linear characteristics and transport features of the drift-Alfven modes. Based on the DIII-D H-mode discharge, a sequence of divertor tokamak equilibria with different pedestal height is generated by the ’VARYPED’ tool for our studies. Qualitative agreement is obtained between theoretical analysis and the simulation results in the linear regime. Moreover, the heat transport induced by the drift-Alfven turbulence is explored and the convection level is estimated for both ions and electrons.Item Molecular simulations of noncovalent interactions in complex biological systems(2019-09-19) First, Jeremy Todd; Webb, Lauren J.; Baiz, Carlos R; Elber, Ron; Makarov, Dmitrii E; Ren, PengyuMolecular dynamics (MD) simulations have proven to be useful for understanding the complex and dynamic interactions between atoms in biomolecular systems. The dynamic movement of each atom, for up to tens of thousands of atoms, can be calculated in MD simulations on timescales from femtoseconds up to microseconds. While many biological phenomena occur in larger systems and on timescales still out of reach of MD simulations, this dynamic range far exceeds those of any experimental technique. However as a theoretical calculation, the simulations must be benchmarked against experimental information to know if they are accurate. Simulations designed to predict structure, for example, are often benchmarked against structural information in the protein databank. Emerging relevant biological phenomena, such as biomolecules at surfaces, interfaces, or in non-aqueous solvents, are difficult to characterize structurally and thus are underrepresented in the structural datasets used for benchmarks; the reliability of MD simulations in these more complex environments is uncertain. Similarly, calculations of more specific properties such as electric field are unreliable, since experimental data of electric fields in biomolecules are scarce. This is in part due to the fact that the interpretation of experimental measurements of electric field, such as ∆pK [subscript a] or vibrational Stark effect (VSE) shifts, are complicated by their susceptibility to local interactions. While calculating electric fields remains a challenge, the accurate modeling of molecular structure can aid in the interpretation of such experiments, eventually allowing for robust electric field measurements to be used to parameterize electrostatic-centered force fields that can accurately calculate and predict electric fields in complex biomolecular structures. The work herein investigates the reliability of MD simulations of biomolecules at complex interfaces, demonstrating a protocol to test and validate force fields in complex environments. Additionally, we investigate the effect of local interactions on the ability of nitriles to act as VSE probes. We establish specific hydrogen bonding as a dominant factor in nitrile vibrational spectra and provide evidence of a control experiment that may be used to diagnose the hydrogen bonding status of the nitrile probe. Finally, we provide an example of the importance of electric field measurements (and thus the importance of experiments to diagnose hydrogen bonding to nitriles) by providing evidence that electrostatic contributions control the rate of intrinsic hydrolysis of GTP in p²¹H-Ras, where altered electric fields in the active site change the rate of hydrolysis causing tumorigenesis. This work demonstrates the importance of simultaneous investigation of biological phenomena in silico and in vitro. When combined, experiments and calculations compliment each other to provide a mutual feedback loop that increases the molecular level understanding of how the dynamic motion of atoms can cooperatively achieve an observed outcomeItem Monte-Carlo simulations of a comptonization model for the photospheric process(2015-08) Hernandez, Roberto Amilcar; Dicus, Duane A.; Kumar, PawanThis thesis presents the results of numerical simulations of an InverseCompton scattering model for the photospheric process. We use a Monte-Carlo method to simulate the processing and broadening of Planckian radiation below the Thomson photosphere of hot relativistic outflows. A new numerical code was developed and allowed us to explore a completely new region of the parameter space, in particular a higher and more realistic photon-to-electron ratio. The results may be relevant to the prompt emission of Gamma-ray Bursts (GRBs), Tidal Disruption Events (TDEs), and other high-energy transients where optically thick outflows are present.Item Physics-based material constitutive models for the simulation of high-temperature forming of magnesium alloy AZ31(2012-08) Carpenter, Alexander James; Taleff, Eric M.; Bourell, David L.; Kovar, Desiderio; Seepersad, Carolyn C.; Engelhardt, Michael D.Magnesium sheet alloys, such as wrought AZ31, have material properties that make them an attractive option for use in automotive and aircraft components. However, the low ductility of magnesium alloys at room temperature necessitates the use of high-temperature forming to manufacture complex components. Finite-element-method (FEM) simulations can assist in determining the optimum processing parameters for high-temperature forming, but only if an accurate material constitutive model is used. New material constitutive models describing the deformation behavior of AZ31 sheet at 450°C are proposed. These models account for both active deformation mechanisms at this temperature: grain-boundary-sliding creep and five-power dislocation-climb creep. Phenomena affecting these deformation mechanisms, such as material anisotropy and grain growth, are also investigated. This physics-based approach represents an improvement over previous material models, which require nonphysical parameters and can only predict forming for a limited range of conditions. Tensile tests are conducted to obtain data used in fitting constitutive models. New models are used in FEM simulations of both tensile tests and biaxial gas-pressure bulge tests. Simulation results are compared to experimental data for validation and determination of model accuracy.Item Prospects for directly detecting the first supernovae, and their impact on early star formation(2016-05) Hummel, Jacob Alexander; Bromm, Volker; Milosavljevic, Milos; Wheeler, J. Craig; Finkelstein, Steven; Yoshida, NaokiThe formation of the first stars in the Universe marked a pivotal moment in cosmic history, initiating the transition from the simple initial conditions of the big bang to the complex structures we see today. Ionizing radiation produced by these so-called Population III stars began the process of reionization, and the supernovae marking their deaths initiated the process of chemical enrichment. We assess the prospects for direct detection of the first supernovae should they happen to end their lives as extremely energetic pair-instability supernovae, which should be within the detection limits of the upcoming James Webb Space Telescope. Using a combination of semi-analytic models and cosmological simulations to estimate their source density, we find that the primary obstacle to observing such events is their scarcity, not their faintness. The first supernovae and the compact remnants they leave behind also produce significant amounts of high-energy X-rays and cosmic rays able to travel through the predominantly neutral intergalactic medium and build up a cosmic background. To better understand how these violent explosions impact subsequent episodes of metal-free star formation, we employ ab-initio, cosmological hydrodynamics simulations to model the formation of stars in a minihalo at z = 20-30 under the influence of both an X-ray and cosmic ray background. The presence of an ionizing background---whether X-rays or cosmic rays---serves to expedite the collapse of gas to high densities by enhancing molecular hydrogen cooling, thus allowing stars to form at substantially earlier epochs in strongly irradiated minihalos. The mass of the stars thus formed however appears to be quite robust, maintaining a characteristic mass of order a few tens of solar masses even as the strength of the ionizing background varies by several orders of magnitude. Finally, we describe the novel software developed to enable this research. These tools for manipulating and analyzing simulation data have been released as the open-source GAdget DataFrame Library: gadfly.Item Quantification of the confidence that can be placed in land-surface model predictions : applications to vegetation and hydrologic processes(2009-08) Gulden, Lindsey Elizabeth; Yang, Zong-liangThe research presented here informs the confidence that can be placed in the simulations of land-surface models (LSMs). After introducing a method for simplifying a complex, heterogeneous land-cover dataset for use in LSMs, I show that LSMs can realistically represent the spatial distribution of heterogeneous land-cover processes (e.g., biogenic emission of volatile organic compounds) in Texas. LSM-derived estimates of biogenic emissions are sensitive (varying up to a factor of 3) to land-cover data, which is not well constrained by observations. Simulated emissions are most sensitive to land-cover data in eastern and central Texas, where tropospheric ozone pollution is a concern. I further demonstrate that interannual variation in leaf mass is at least as important to variation in biogenic emissions as is interannual variation in shortwave radiation and temperature. Model estimates show that more-humid regions with less year-to-year variation in precipitation have lower year-to-year variation in biogenic emissions: as modeled mean emissions increase, their mean-normalized standard deviation decreases. I evaluate three parameterizations of subsurface hydrology in LSMs (with (1) a shallow, 10-layer soil; (2) a deeper, many-layered soil; and (3) a lumped aquifer model) under increasing parameter uncertainty. When given their optimal parameter sets, all three versions perform equivalently well when simulating monthly change in terrestrial water storage. The most conceptually realistic model is least sensitive to errant parameter values. However, even when using the most conceptually realistic model, parameter interaction ensures that knowing ranges for individual parameters is insufficient to guarantee realistic simulation. LSMs are often developed and evaluated at data-rich sites but are then applied in regions where data are sparse or unavailable. I present a framework for model evaluation that explicitly acknowledges perennial sources of uncertainty in LSM simulations (e.g., parameter uncertainty, meteorological forcing-data uncertainty, evaluation-data uncertainty) and that evaluates LSMs in a way that is consistent with models’ typical application. The model performance score quantifies the likelihood that a representative ensemble of model performance will bracket observations with high skill and low spread. The robustness score quantifies the sensitivity of model performance to parameter error or data error. The fitness score ranks models’ suitability for broad application.Item Quantum simulations on the physics of quasi-two-dimensional electronics systems for device applications(2019-05) Wu, Xian (Ph. D. in electrical and computer engineering); Register, Leonard F.; Banerjee, Sanjay K; Tutuc, Emanuel; Yu, Edward T; MacDonald, Allan HThe underlying physics of various quasi-two-dimensional (quasi-2D) electronics systems and associated quantum effects is studied using numerical simulations based on quantum mechanical theories. These systems and effects are the foundation for novel devices that potentially could outperform the CMOS devices for particular or general applications in the long term. The single-electron resonant tunneling in the double-monolayer transition metal dichalcogenide (TMD) system is the basis of the proposed interlayer tunnel field-effect transistor (ITFET). I simulate this system using a quantum transport method with a multiband model for the TMD material. Gate-controllable interlayer tunneling peaks are presented suggesting the theoretical feasibility of realizing TMD-based ITFETs. The spatially-indirect exciton condensation in a bulk double-monolayer TMD system is then studied under equilibrium condition. The operation of the proposed bilayer pseudospin field-effect transistor (BiSFET) and the bilayer pseudospin junction transistor (BiSJT) relies on the existence of this many-body quantum effect. Using the self-consistent Hartree-Fock approximation, I simulate the formation of the exciton condensates and study the dependence of the condensation strength on various parameters. Based on the equilibrium exciton condensate properties, I subsequently study the current-voltage characteristics of a voltage-biased four-terminal double-monolayer TMD system with the presence of the exciton condensates in this energy gapped (in contrast to previously considered graphene) system using quantum transport simulations. The potential of and possible issues with pseudospin devices based on this system are addressed. Approaches to experimentally verify the formation of the exciton condensates are also suggested. Finally, I study the current-phase relation (CPR) in a multiterminal Josephson junction (MT-JJ) system with 2D semiconductor layer as the weak link. Quantum simulations based on the BCS mean-field theory are conducted. The simulation results suggest a simplified macroscopic model to describe the CPR. Using this simplified model, I study a current-biased MT-JJ system, and illustrate the possibility for, e.g., gain/fan-out in appropriately designed MT-JJs. Such MT-JJs potentially could be adapted to design ultra-low-power current-controlled transistors in cryogenic computing with circuits operating at voltages on the scale of superconducting energy gap divided by the electron charge eItem A simulation approach to studying the relationship between landscape features and social system on the genetic structure of a tamarin primate population(2013-05) Valencia Rodriguez, Lina Maria; Di Fiore, Anthony, Ph. D.Landscape genetics is an emerging field that seeks to understand how specific landscape features and microevolutionary processes such as gene flow, genetic drift, and selection interact to shape the amount and spatial distribution of genetic variation. This study explores, through agent based simulations, how the specific mating and social system of tamarin primates (genus Saguinus) influences population genetic structure and patterns of relatedness within and among groups of this primate species, which might affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. I use a spatially-explicit agent-based population genetics simulation model (GENESYS) configured to reflect the particular social system of tamarin monkeys (i.e. small group size, limited numbers of breeders per group, frequent twin births, and short dispersal distances) to assess whether the isolation by distance model of genetic differentiation expected in an unfragmented landscape can be distinguished from the isolation by barrier model expected in a fragmented landscape. GENESYS allows a user to explore the effects of social structure and landscape features on the population genetic structure of social animals, such as primates. I simulated two different landscapes containing an otherwise equivalent population of tamarins. In the first setup I simulated a homogeneous landscape unconstrained by any barriers to gene flow, while for the second setup, a barrier to gene flow restricted dispersal from one half of the landscape to the other. I found that the particular mating system of tamarin results in the rapid genetic differentiation of its social groups and consequently its populations. Social groups in the continuous landscape indeed revealed an isolation by distance pattern, while social groups on the fragmented landscape yielded instead an isolation by barrier model, where the barrier rather than geographic distance per se influenced the spatial genetic structure of the population. The results from this study suggest that features of the tamarin social system influence population genetic structure, which could affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. To more fully address that issue, future studies should focus on a range of different primate social systems.Item Simulations and reduced models for microtearing modes in the Tokamak pedestals(2022-07-26) Curie, Max Tian; Tenerani, Anna; Hatch, David R.; Fitzpatrick, Richard; Michoski, Craig; Morrison, Philip JRenewable energy can not only help to clean the environment but also create a more peaceful world. Fusion has the potential to provide clean energy with abundant resources. The high energy density (per-footprint) nature of fusion makes it appealing in highly urbanized areas, such as Singapore, which complements wind and solar power. Magnetic confinement fusion (MCF) is one of the most promising routes to thermonuclear fusion energy. Among the prospective MCF configurations, the Tokamak is the most widely implemented scheme. A host of instabilities are suppressed in H-mode (high-confinement mode) plasmas in Tokamaks due to high flow shear and/or steep density gradients in the pedestal (the edge of the plasma). This produces higher confinement and thus better performance than L-mode (low-confinement mode) operation. Transport and instabilities in the pedestal of the plasma are studied more intensively using gyrokinetic simulations thanks to the improvement of computational and experimental capabilities. Recent studies show that the magnetic fluctuations from microtearing modes (MTM) can be commonly observed in magnetic spectrograms [1– 12]. and contribute significant electron heat transport [13–15]. This thesis further investigates MTMs in the pedestal through 3 projects: • Direct comparison between nonlinear gyrokinetic simulations (GENE) and a newly installed magnetic diagnostic Faradayeffect Radial Interferometer-Polarimeter (RIP) [2, 16, 17]. Such a comparison provides strong evidence of the MTM’s importance in the Tokamak pedestal. • A package based on a global reduced model for MTM stability [18, 19] called the slab-like MTM (SLiM) package [20]. This model provides a tool for rapid MTM stability assessment. Applications of its usage will be described in the thesis: determining the stability of MTM, poloidal mode numbers, and equilibrium reconstruction. • Equilibrium reconstruction based on the SLiM model. Neural networks were trained for faster MTM stability assessment. This allows for extensive variations of nominal equilibrium quantities in order to better match the experimentally-observed magnetic frequencies in discharges and hopefully produce more accurate equilibrium reconstructions.