Dissertations / Theses on the topic 'Models and simulations of design'
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Pohl, Thomas. "Design of adaptable simulation models." Thesis, Sheffield Hallam University, 2006. http://shura.shu.ac.uk/20240/.
Full textOchs, David S. "Design of detailed models for use in fast aeroelastic simulations of permanent-magnet direct-drive wind turbines." Thesis, Kansas State University, 2012. http://hdl.handle.net/2097/15042.
Full textDepartment of Electrical and Computer Engineering
Ruth Douglas Miller
This thesis presents the design of two models for permanent-magnet direct-drive wind turbines. The models are of a 10 kW and a 5 MW wind turbine, which are representative of residential scale and commercial scale turbines respectively. The models include aerodynamic and mechanical simulations through the FAST software, as well as concurrent electrical simulations through the SimPowerSystems toolbox for MATLAB/Simulink. The aim is to provide wind turbine designers and researchers with a comprehensive simulation tool that they can use to design and test many different aspects of a wind turbine. The particular novelty of these models is their high level of detail in electromechanical simulations. For each model, a generator speed controller was designed in a reference frame attached to the generator’s rotor, and was executed with a 3-phase active rectifier using space-vector pulse-width modulation. Also for each model, active and reactive power controllers were designed in a reference frame synchronous with the grid, and were executed with a 3-phase inverter using space-vector pulse-width modulation. Additionally, a blade pitch controller was designed for the 5 MW model. Validation of the models was carried out in the MATLAB/Simulink environment with satisfactory results.
Craig, David Latch. "Perceptual simulation and analogical reasoning in design." Diss., Georgia Institute of Technology, 2001. http://hdl.handle.net/1853/23940.
Full textLi, Zhiyong. "Data-Driven Adaptive Reynolds-Averaged Navier-Stokes k - ω Models for Turbulent Flow-Field Simulations." UKnowledge, 2017. http://uknowledge.uky.edu/me_etds/93.
Full textKini, Satish D. "An approach to integrating numerical and response surface models for robust design of production systems." Columbus, Ohio : Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1080276457.
Full textTitle from first page of PDF file. Document formatted into pages; contains xviii, 220 p.; also includes graphics (some col.). Includes abstract and vita. Advisor: R. Shivpuri, Dept. of Industrial, Welding and Systems Engineering. Includes bibliographical references.
Han, Sangmok. "A design tool for reusing integration knowledge in simulation models." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/85771.
Full textCataloged from PDF version of thesis.
Includes bibliographical references (pages 88-89).
In the academic field of computer-aided product development, the role of the design tool is to support engineering designers to develop and integrate simulation models. Used to save time and costs in product development process, the simulation model, however, introduces additional costs for its development and integration, which often become considerably large due to the fact that many, complex simulation models need to be integrated. Moreover, the result of integration and the effort taken during the integration process are often not reused for other product development projects. In this paper, we attempt to develop a design tool that can capture integration knowledge and make the knowledge reusable for other design tasks. More specifically, we are interested in the two kinds of integration knowledge: the first captured in the form of a graph structure associating simulation models, called the integration structure, and the second generalized from script codes into rule-based patterns, called the integration code pattern. An integration mechanism and a pattern generalization algorithm have been developed and incorporated into a design tool utilizing a new integration model called catalog model, a model that enables us to reuse the integration structure and code patterns of one model to quickly build another. Application scenarios have demonstrated the effectiveness of the design tool: The same integration task could be performed in less time, and repetitive and error-prone elements in the task were substantially reduced as a result of reusing integration knowledge in the simulation models.
by Sangmok Han.
S.M.
Yasar, Orten Pinar. "Numerical Analysis, Design And Two Port Equivalent Circuit Models For Split Ring Resonator Arrays." Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12611620/index.pdf.
Full texts HFSS software that is based on the finite elements method (FEM). Some of these structures are constructed over low-loss dielectric substrates and their complex scattering parameters are measured to verify the numerical simulation results. The major purpose of this study has been to establish equivalent circuit models to estimate the behavior of SRR structures in a simple and computationally efficient manner. For this purpose, individual single ring SRR cells with multiple splits are modeled by appropriate two-port RLC resonant circuits paying special attention to conductor and dielectric loss effects. Results obtained from these models are compared with the results of HFSS simulations which use either PEC/PMC (perfect electric conductor/perfect magnetic conductor) type or perfectly matched layer (PML) type boundary conditions. Interactions between the elements of SRR arrays such as the mutual inductance and capacitance effects as well as additional dielectric losses are also modeled by proper two-port equivalent circuits to describe the overall array behavior and to compute the associated transmission spectrum by simple MATLAB codes. Results of numerical HFSS simulations, equivalent circuit model computations and measurements are shown to be in good agreement.
Muthukrishnan, Gayathri. "Utilizing Hierarchical Clusters in the Design of Effective and Efficient Parallel Simulations of 2-D and 3-D Ising Spin Models." Thesis, Virginia Tech, 2004. http://hdl.handle.net/10919/9944.
Full textMaster of Science
Zhang, Bo. "Design, modelling and simulation of a novel micro-electro-mechanical gyroscope with optical readouts." Thesis, Cape Peninsula University of Technology, 2007. http://hdl.handle.net/20.500.11838/1101.
Full textMicro Electro-Machnical Systems (MEMS) applications are fastest development technology present. MEMS processes leverage mainstream IC technologies to achieve on chip sensor interface and signal processing circuitry, multi-vendor accessibility, short design cycles, more on-chip functions and low cost. MEMS fabrications are based on thin-film surface microstructures, bulk micromaching, and LIGA processes. This thesis centered on developing optical micromaching inertial sensors based on MEMS fabrication technology which incorporates bulk Si into microstructures. Micromachined inertial sensors, consisting of the accelerometers and gyroscopes, are one of the most important types of silicon-based sensors. Microaccelerometers alone have the second largest sales volume after pressure sensors, and it is believed that gyroscopes will soon be mass produced at the similar volumes occupied by traditional gyroscopes. A traditional gyroscope is a device for measuring or maintaining orientation, based on the principle of conservation of angular momentum. The essence of the gyroscope machine is a spinning wheel on an axle. The device, once spinning, tends to resist changes to its orientation due to the angular momentum of the wheel. In physics this phenomenon is also known as gyroscopic inertia or rigidity in space. The applications are limited by the huge volume. MEMS Gyroscopes, which are using the MEMS fabrication technology to minimize the size of gyroscope systems, are of great importance in commercial, medical, automotive and military fields. They can be used in cars for ASS systems, for anti-roll devices and for navigation in tall buildings areas where the GPS system might fail. They can also be used for the navigation of robots in tunnels or pipings, for leading capsules containing medicines or diagnostic equipment in the human body, or as 3-D computer mice. The MEMS gyroscope chips are limited by high precision measurement because of the unprecision electrical readout system. The market is in need for highly accurate, high-G-sustainable inertial measuring units (IMU's). The approach optical sensors have been around for a while now and because of the performance, the mall volume, the simplicity has been popular. However the production cost of optical applications is not satisfaction with consumer. Therefore, the MEMS fabrication technology makes the possibility for the low cost and micro optical devices like light sources, the waveguide, the high thin fiber optical, the micro photodetector, and vary demodulation measurement methods. Optic sensors may be defined as a means through which a measurand interacts with light guided in an optical fiber (an intrinsic sensor) or guided to (and returned from) an interaction region (an extrinsic sensor) by an optical fiber to produce an optical signal related to the parameter of interest. During its over 30 years of history, fiber optic sensor technology has been successfully applied by laboratories and industries worldwide in the detection of a large number of mechanical, thermal, electromagnetic, radiation, chemical, motion, flow and turbulence of fluids, and biomedical parameters. The fiber optic sensors provided advantages over conventional electronic sensors, of survivability in harsh environments, immunity to Electro Magnetic Interference (EMI), light weight, small size, compatibility with optical fiber communication systems, high sensitivity for many measurands, and good potential of multiplexing. In general, the transducers used in these fiber optic sensor systems are either an intensity-modulator or a phase-modulator. The optical interferometers, such as Mach-Zehnder, Michelson, Sagnac and Fabry-Perot interferometers, have become widely accepted as a phase modulator in optical sensors for the ultimate sensitivity to a range of weak signals. According to the light source being used, the interferometric sensors can be simply classified as either a coherence interferometric sensor if a the interferometer is interrogated by a coherent light source, such as a laser or a monochromatic light, or a lowcoherence interferometric sensor when a broadband source a light emitting diode (LED) or a superluminescent diode (SLD), is used. This thesis proposed a novel micro electro-mechanical gyroscope system with optical interferometer readout system and fabricated by MEMS technology, which is an original contribution in design and research on micro opto-electro-mechanical gyroscope systems (MOEMS) to provide the better performances than the current MEMS gyroscope. Fiber optical interferometric sensors have been proved more sensitive, precision than other electrical counterparts at the measurement micro distance. The MOMES gyroscope system design is based on the existing successful MEMS vibratory gyroscope and micro fiber optical interferometer distances sensor, which avoid large size, heavy weight and complex fabrication processes comparing with fiber optical gyroscope using Sagnac effect. The research starts from the fiber optical gyroscope based on Sagnac effect and existing MEMS gyroscopes, then moving to the novel design about MOEMS gyroscope system to discuss the operation principles and the structures. In this thesis, the operation principles, mathematics models and performances simulation of the MOEMS gyroscope are introduced, and the suitable MEMS fabrication processes will be discussed and presented. The first prototype model will be sent and fabricated by the manufacture for the further real time performance testing. There are a lot of inventions, further research and optimize around this novel MOEMS gyroscope chip. In future studying, the research will be putted on integration three axis Gyroscopes in one micro structure by optical sensor multiplexing principles, and the new optical devices like more powerful light source, photosensitive materials etc., and new demodulation processes, which can improve the performance and the interface to co-operate with other inertial sensors and navigation system.
Wiedemann, Michael. "Robust parameter design for agent-based simulation models with application in a cultural geography model." Thesis, Monterey, California : Naval Postgraduate School, 2010. http://edocs.nps.edu/npspubs/scholarly/theses/2010/Jun/10Jun%5FWiedemann.pdf.
Full textThesis Advisor(s): Johnson, Rachel T. ; Second Reader: Baez, Francisco R, "June 2010." Description based on title screen as viewed on July 15, 2010. Author(s) subject terms: Cultural Geography, Agent-Based Model (ABM), Irregular Warfare (IW), Theory of planned Behavior (TpB), Baysian Belief Nets (BBN), Counterinsurgency Operations (COIN), Stability Operations, Discrete Event Simulation (DES), Design of Experiments (DOX), Robust Parameter Design (RPD). Includes bibliographical references (p. 69-70). Also available in print.
Martin, Christopher John. "A new tool for the validation of dynamic simulation models." Thesis, n.p, 1995. http://ethos.bl.uk/.
Full textShariat, Yazdi Hamed [Verfasser]. "Statistical analysis and simulation of design models evolution / Hamed Shariat Yazdi." Siegen : Universitätsbibliothek der Universität Siegen, 2015. http://d-nb.info/1076911692/34.
Full textJiang, Lin. "Novel catalysts by computational enzyme design /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9248.
Full textQuirante, Natalia. "Rigorous Design of Chemical Processes: Surrogate Models and Sustainable Integration." Doctoral thesis, Universidad de Alicante, 2017. http://hdl.handle.net/10045/74373.
Full textHiggs, Jessica Marie. "Ion Trajectory Simulations and Design Optimization of Toroidal Ion Trap Mass Spectrometers." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6652.
Full textQian, Zhiguang. "Computer experiments [electronic resource] : design, modeling and integration /." Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/11480.
Full textBrito, A. E. S. C. "Configuring Simulation Models Using CAD Techniques: A New Approach to Warehouse Design." Thesis, Cranfield University, 1992. http://dspace.lib.cranfield.ac.uk/handle/1826/4640.
Full textRampersad, Kevin. "The rapid design of simulation models using cladistics and template based modelling." Thesis, Cranfield University, 2012. http://dspace.lib.cranfield.ac.uk/handle/1826/7756.
Full textSvensson, Marcus, and Daniel Haraldsson. "Integrating Design Optimization in the Development Process using Simulation Driven Design." Thesis, Linköpings universitet, Maskinkonstruktion, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-157374.
Full textRiley, Matthew E. "Quantification of Model-Form, Predictive, and Parametric Uncertainties in Simulation-Based Design." Wright State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=wright1314895435.
Full textSan, Jose Angel. "Analysis, design, implementation and evaluation of graphical design tool to develop discrete event simulation models using event graphs and SIMKIT." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2001. http://handle.dtic.mil/100.2/ADA397405.
Full textThesis advisor(s): Buss, Arnold; Miller, Nita. "September 2001." Includes bibliographical references (p. 109-110). Also available in print.
Klostermeier, Christian. "Investigation into the capability of large eddy simulation for turbomachinery design." Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/252106.
Full textZhang, Mingyang 1981. "Macromodeling and simulation of linear components characterized by measured parameters." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=112589.
Full textMumpower, Gregory D. "Improving product and process design integration through representation and simulation of manufacturing processes." Thesis, Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/17039.
Full textLópez, Benítez Miguel. "Spectrum usage models for the analysis, design and simulation of cognitive radio networks." Doctoral thesis, Universitat Politècnica de Catalunya, 2011. http://hdl.handle.net/10803/33282.
Full textPalmer, Kurt D. "Data collection plans and meta models for chemical process flowsheet simulators." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/24511.
Full textKaczorowski, Przemyslaw Robert. "Thermal-based multi-objective optimal design of liquid cooled power electronic modules." Thesis, Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/16448.
Full textSwinerd, C. "On the design of hybrid simulation models, focussing on the agent-based system dynamics combination." Thesis, Cranfield University, 2014. http://dspace.lib.cranfield.ac.uk/handle/1826/8645.
Full textRoure, Océane. "NUMERICAL SIMULATIONS OF FRICTION-INDUCED NOISE OF AUTOMOTIVE WIPER SYSTEMS." Thesis, KTH, MWL Marcus Wallenberg Laboratoriet, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-180252.
Full textÜnver, Hakkı Özgür. "A comparative study of Lotka-Volterra and system dynamics models for simulation of technology industry dynamics." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/44705.
Full textIncludes bibliographical references (leaves 78-80).
Scholars have developed a range of qualitative and quantitative models for generalizing the dynamics of technological innovation and identifying patterns of competition between rivals. This thesis compares two predominant approaches in the quantified modeling of technological innovation and competition. Multi-mode framework, based on the Lotka-Volterra equation barrowed from biological ecology, provide a rich setting for assessing the interaction between two or more technologies. A more recent approach uses System Dynamics to model the dynamics of innovative industries. A System Dynamics approach enables the development of very comprehensive models, which can cover multiple dimensions of innovation, and provides very broad insights for innovative and competitive landscape of an industry. As well as comparing these theories in detail, a case study is also performed on both of them. The phenomenal competition between two technologies in the consumer photography market; the recent battle between digital and film camera technology, is used as a test case and simulated by both models. Real market data is used as inputs to the simulations. Outputs are compared and interpreted with the realities of the current market conditions and predictions of industry analysts. Conclusions are derived on the strengths and weaknesses of both approaches. Directions for future research on model extensions incorporating other forms of innovation are given, such as collaborative interaction in SME networks.
by Hakkı Özgür Ünver.
S.M.
Satish, Prabhu Nachiketh, and Ranjan Tunga Sarapady. "Evaluation of parametric CAD models from a manufacturing perspective to aid simulation driven design." Thesis, Linköpings universitet, Maskinkonstruktion, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-167724.
Full textLee, Chun-Sho. "A process simulation model for the manufacture of composite laminates from fiber-reinforced, polyimide matrix prepreg materials." Diss., Virginia Tech, 1993. http://hdl.handle.net/10919/40298.
Full textPh. D.
Pavurala, Naresh. "Oral Drug Delivery -- Molecular Design and Transport Modeling." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/53505.
Full textPh. D.
Moreno, Oswaldo. "Design of the step-feed activated sludge process." Thesis, McGill University, 1987. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=64054.
Full textMueller, Ralph. "Specification and Automatic Generation of Simulation Models with Applications in Semiconductor Manufacturing." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/16147.
Full textRadulovic, Luka. "Influence of advanced load simulation models on fatigue design of jackets for offshore wind turbines." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amslaurea.unibo.it/6369/.
Full textTonga, Melek Mehlika. "Uncertainty Evaluation Through Ranking Of Simulation Models For Bozova Oil Field." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613243/index.pdf.
Full textbuilding simulation models by using the most representative dynamic data
and doing sensitivity analysis around a best case in order to get a history-matched simulation model. Each step deals with a great variety of uncertainty and changing one parameter at a time does not comprise the entire uncertainty space. Not only knowing the impact of uncertainty related to each individual parameter but also their combined effects can help better understanding of the reservoir and better reservoir management. In this study, uncertainties associated only to fluid properties, rock physics functions and water oil contact (WOC) depth are examined thoroughly. Since sensitivity analysis around a best case will cover only a part of uncertainty, a full factorial experimental design technique is used. Without pursuing the goal of a history matched case, simulation runs are conducted for all possible combinations of: 19 sets of capillary pressure/relative permeability (Pc/krel) curves taken from special core analysis (SCAL) data
2 sets of pressure, volume, temperature (PVT) analysis data
and 3 sets of WOC depths. As a result, historical production and pressure profiles from 114 (2 x 3 x 19) cases are presented for screening the impact of uncertainty related to aforementioned parameters in the history matching of Bozova field. The reservoir simulation models that give the best match with the history data are determined by the calculation of an objective function
and they are ranked according to their goodness of fit. It is found that the uncertainty of Pc/krel curves has the highest impact on the history match values
uncertainty of WOC depth comes next and the least effect arises from the uncertainty of PVT data. This study constitutes a solid basis for further studies which is to be done on the selection of the best matched models for history matching purposes.
Hu, Huafen. "Risk-conscious design of off-grid solar energy houses." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31814.
Full textCommittee Chair: Godfried Augenbroe; Committee Member: Ellis Johnson; Committee Member: Pieter De Wilde; Committee Member: Ruchi Choudhary; Committee Member: Russell Gentry. Part of the SMARTech Electronic Thesis and Dissertation Collection.
Ley-Chavez, Adriana. "Quantitative Models to Design and Evaluate Risk-Specific Screening Strategies for Cervical Cancer Prevention." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1324545286.
Full textBa, Shan. "Multi-layer designs and composite gaussian process models with engineering applications." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44751.
Full textMachchhar, Raj Jiten. "Automated Model Generation and Pre-Processing to Aid Simulation-Driven Design : An implementation of Design Automation in the Product Development process." Thesis, Linköpings universitet, Maskinkonstruktion, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-168738.
Full textTaylor, Richard E. "A design tool for use in simulation and training of sinus surgery." Thesis, Loughborough University, 2010. https://dspace.lboro.ac.uk/2134/7294.
Full textStilkerich, Stephan C. "Probabilistic image models and their massively parallel architectures a seamless simulation- and VLSI design framework approach /." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=984791892.
Full textHarth, Tobias [Verfasser]. "Identification of Material Parameters for Inelastic Constitutive Models : Stochastic Simulation and Design of Experiments / Tobias Harth." Aachen : Shaker, 2003. http://d-nb.info/1179036204/34.
Full textWu, Sichao. "Computational Framework for Uncertainty Quantification, Sensitivity Analysis and Experimental Design of Network-based Computer Simulation Models." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/78764.
Full textPh. D.
Montero, Juan Esteban S. M. Massachusetts Institute of Technology. "Implication of the Jensen's inequality for system dynamic simulations : application to a plug & play integrated refinery supply chain model." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/100363.
Full textPage 113 blank. Cataloged from PDF version of thesis.
Includes bibliographical references (pages 60-65).
This investigation studies how critical is the effect of considering uncertainty to a dynamic model because of Jensen's Inequality. This is done using as an example the supply chain of a refinery, which illustrates that the difference between probable and expected results can be significant, arguing that the distributions and probabilities can be dramatically different from the expected-planned value. Moreover, this research discusses that, from the perspective of the dynamics of the system, the mode of behavior can vary considerably as well, leading managers to dissimilar situations and contexts that will inevitably produce different decisions or strategies. Supply chain management is a critical aspect of any business. The energy industry is a particularly relevant example of a global supply chain, representing a crucial challenge the management of complexity and relevance for the overall performance of the business. The complexity of managing the supply chain of an energy company is produced by the physical size, diversity of operations and products and dynamics of the system, among many others causes. On top of the intrinsic complexity of the business itself, the manager of a supply chain should also consider the complexity of the models and methodologies used to make decisions about it. These models and methodologies are diverse and they serve different purposes under certain assumptions. This study also discusses the complexity faced by supply chain managers, presenting a compilation of bibliographic research about different considerations and approaches. Managers often employ models and analytics to simplify the complexity and produce intuition by different means in order to form their decisions and strategies. The analysis of the effects of uncertainty on the results and behavior of a dynamic simulation model is done by stochastically simulating an already-developed -plug & play- dynamic model of a refinery. This approach permits the exploration of different configurations, considering different definitions of uncertainty, analyzing and comparing their particular results.
by Juan Esteban Montero.
S.M. in Engineering and Management
Razavi, Majarashin Asghar. "MARKOV STATE MODELS AND THEIR APPLICATIONS IN PROTEIN FOLDING SIMULATION, SMALL MOLECULE DESIGN, AND MEMBRANE PROTEIN MODELING." Diss., Temple University Libraries, 2015. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/362098.
Full textPh.D.
This dissertation is focused on the application of Markov State Models on protein folding and designing of small drug-like molecules, as well as application of computational tools on the study of biological processes. The central focus of protein folding is to understand how proteins obtain their unique three-dimensional structure from their aminoacid sequences. The function of protein critically depends on its three- dimensional structure; hence, any internal (such as mutations) or external (such as high temperature) perturbation that obstructs three-dimensional structure of a protein will also interfere with its function. Many diseases are associated with inability of protein to form its unique structure. For example, sickle cell anemia is caused by a single mutation that changes glutamic acid to valine. Molecular dynamics (MD) simulations could be utilized to study protein folding and effects of perturbations on protein energy landscape; however, due to its inherent atomic resolution, MD simulations usually provide enormous amount of data even for small proteins. A thorough analysis and extraction of desired information from MD provided data could be extremely challenging and is well beyond human comprehension. Markov state models (MSMs) are proved to be apt for the analysis of large scale random processes and equilibrium conditions, hence it could be applied for protein folding studies. MSMs can be used to obtain long timescale information from short timescale simulations. In other words, the combination of many short simulations and MSMs is a powerful technique to study the folding mechanism of many proteins, even the ones with folding times over millisecond. This dissertation is centered on the use of MSMs and MD simulation in understanding protein folding and biological processes and is constructed as the following. The first chapter provides a brief introduction into MD simulation and the different techniques that could be used to facilitate simulations. Protein folding and its challenges are also discussed in chapter one. Finally, chapter one ends with describing MSMs and technical aspects of building them for protein folding studies. Chapter two is focused on using MD simulations and MSMs to design small protein like molecules to prevent biofilm propagation by disrupting its lifecycle. The biofilm lifecycle and strategy for its interruption is described first. Then, the designed molecules and their conformational sampling by MD simulations are explained. Next, the application of MSMs in obtaining and comparing equilibrium population of all designs are discussed. At the end of chapter two, the molecular descriptions of best designs are explained. Chapter three is focused on the effects of mutations on the energy landscape of a sixteen residue protein from c-terminal hairpin of protein G, GB1. Three mutations, tz4, tz5, and tz6 are discussed, and their folding rates and folding mechanisms are compared with wild-type GB1 using MSMs built from a significantly large MD simulation data set (aggregating over 9 millisecond). Finally, chapter four is focused on the application of MD simulations on understanding the selectivity of Na,K-ATPase, a biologically critical protein that transports sodium ions outside and potassium ions inside against their concentration gradient in almost all eukaryotic cells. Multiple MD approaches, including metadynamics and free energy perturbation methods are used to describe the origins of selectivity for Na,K-ATPase.
Temple University--Theses
Yuce, Bilgiday. "Fault Attacks on Embedded Software: New Directions in Modeling, Design, and Mitigation." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/81824.
Full textPh. D.
Badal, Soler Andreu. "Development of advanced geometric models and acceleration techniques for Monte Carlo simulation in Medical Physics." Doctoral thesis, Universitat Politècnica de Catalunya, 2008. http://hdl.handle.net/10803/6615.
Full textTot i això, els models geomètrics implementats en la majoria de programes imposen certes limitacions a la forma dels objectes que es poden definir. Aquests models no són adequats per descriure les superfícies arbitràries que es troben en estructures anatòmiques o en certs aparells mèdics i, conseqüentment, algunes aplicacions que requereixen l'ús de models geomètrics molt detallats no poden ser acuradament estudiades amb aquests programes.
L'objectiu d'aquesta tesi doctoral és el desenvolupament de models geomètrics i computacionals que facilitin la descripció dels objectes complexes que es troben en aplicacions de física mèdica. Concretament, dos nous programes de simulació Monte Carlo basats en PENELOPE han sigut desenvolupats. El primer programa, penEasy, utilitza un algoritme de caràcter general estructurat i inclou diversos models de fonts de radiació i detectors que permeten simular fàcilment un gran nombre d'aplicacions. Les noves rutines geomètriques utilitzades per aquest programa, penVox, extenen el model geomètric estàndard de PENELOPE, basat en superfícices quàdriques, per permetre la utilització d'objectes voxelitzats. Aquests objectes poden ser creats utilitzant la informació anatòmica obtinguda amb una tomografia computeritzada i, per tant, aquest model geomètric és útil per simular aplicacions que requereixen l'ús de l'anatomia de pacients reals (per exemple, la planificació radioterapèutica). El segon programa, penMesh, utilitza malles de triangles per definir la forma dels objectes simulats. Aquesta tècnica, que s'utilitza freqüentment en el camp del disseny per ordinador, permet representar superfícies arbitràries i és útil per simulacions que requereixen un gran detall en la descripció de la geometria, com per exemple l'obtenció d'imatges de raig x del cos humà.
Per reduir els inconvenients causats pels llargs temps d'execució, els algoritmes implementats en els nous programes s'han accelerat utilitzant tècniques sofisticades, com per exemple una estructura octree. També s'ha desenvolupat un paquet de programari per a la paral·lelització de simulacions Monte Carlo, anomentat clonEasy, que redueix el temps real de càlcul de forma proporcional al nombre de processadors que s'utilitzen.
Els programes de simulació que es presenten en aquesta tesi són gratuïts i de codi lliures. Aquests programes s'han provat en aplicacions realistes de física mèdica i s'han comparat amb altres programes i amb mesures experimentals.
Per tant, actualment ja estan llestos per la seva distribució pública i per la seva aplicació a problemes reals.
Monte Carlo simulation of radiation transport is currently applied in a large variety of areas. However, the geometric models implemented in most general-purpose codes impose limitations on the shape of the objects that can be defined. These models are not well suited to represent the free-form (i.e., arbitrary) shapes found in anatomic structures or complex medical devices. As a result, some clinical applications that require the use of highly detailed phantoms can not be properly addressed.
This thesis is devoted to the development of advanced geometric models and accelration techniques that facilitate the use of state-of-the-art Monte Carlo simulation in medical physics applications involving detailed anatomical phantoms. To this end, two new codes, based on the PENELOPE package, have been developed. The first code, penEasy, implements a modular, general-purpose main program and provides various source models and tallies that can be readily used to simulate a wide spectrum of problems. Its associated geometry routines, penVox, extend the standard PENELOPE geometry, based on quadric surfaces, to allow the definition of voxelised phantoms. This kind of phantoms can be generated using the information provided by a computed tomography and, therefore, penVox is convenient for simulating problems that require the use of the anatomy of real patients (e.g., radiotherapy treatment planning). The second code, penMesh, utilises closed triangle meshes to define the boundary of each simulated object. This approach, which is frequently used in computer graphics and computer-aided design, makes it possible to represent arbitrary surfaces and it is suitable for simulations requiring a high anatomical detail (e.g., medical imaging).
A set of software tools for the parallelisation of Monte Carlo simulations, clonEasy, has also been developed. These tools can reduce the simulation time by a factor that is roughly proportional to the number of processors available and, therefore, facilitate the study of complex settings that may require unaffordable execution times in a sequential simulation.
The computer codes presented in this thesis have been tested in realistic medical physics applications and compared with other Monte Carlo codes and experimental data. Therefore, these codes are ready to be publicly distributed as free and open software and applied to real-life problems.
Heap, Ryan C. "Real-Time Visualization of Finite Element Models Using Surrogate Modeling Methods." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/6536.
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