Dissertations / Theses on the topic 'Biological simulation'
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1
Miller, Thomas F. "Quantum simulation of biological molecules." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414234.
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Hoyles, Matthew, and Matthew Hoyles@anu edu au. "Computer Simulation of Biological Ion Channels." The Australian National University. Theoretical Physics, 2000. http://thesis.anu.edu.au./public/adt-ANU20010702.135814.
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This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research.
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Corry, Ben Alexander, and ben corry@anu edu au. "Simulation Studies of Biological Ion Channels." The Australian National University. Research School of Physical Sciences and Engineering, 2003. http://thesis.anu.edu.au./public/adt-ANU20030423.162927.
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Biological ion channels are responsible for, and regulate the
communication system in the body. In this thesis I develop, test and
apply theoretical models of ion channels, that can relate their
structure to their functional properties. Brownian dynamics
simulations are introduced, in which the motions of individual ions
are simulated as they move through the channel and in baths attached
to each end. The techniques for setting boundary conditions which
maintain ion concentrations in the baths and provide a driving
potential are tested. Provided the bath size is large enough, all
boundary conditions studied yield the same results.
¶
Continuum theories of electrolytes have previously been used to study
ion permeation. However, I show that these continuum models do not
accurately reproduce the physics taking place inside ion channels by
directly comparing the results of both equilibrium Poisson-Boltzmann
theory, and non-equilibrium Poisson-Nernst-Planck theory to
simulations. In both cases spurious shielding effects are found to
cancel out forces that play an important role in ion permeation. In
particular, the `reaction field' created by the ion entering the
narrow channel is underestimated. Attempts to correct these problems
by adding extra force terms to account for this reaction field also
fail.
¶
A model of the L-type calcium channel is presented and studied using
Brownian dynamics simulations and electrostatic calculations. The
mechanisms of permeation and selectivity are explained as the result
of simple electrostatic interactions between ions and the fixed
charges in the protein. The complex conductance properties of the
channel, including the current-voltage and current-concentration
relationships, the anomalous mole fraction behaviour between sodium
and calcium ions, the attenuation of calcium currents by monovalent
ions and the effects of mutating glutamate residues, are all
reproduced.
¶
Finally, the simulation and electrostatic calculation methods are used
to study the gramicidin A channel. It is found that the continuum
electrostatic calculations break down in this narrow channel, as the
concept of applying a uniform dielectric constant is not accurate in
this situation. Thus, the permeation properties of the channel are
examined using Brownian dynamics simulations without electrostatic
calculations. Future applications and improvements of the Brownian
dynamics simulation technique are also described.
4
Rackauckas, Christopher Vincent. "Simulation and Control of Biological Stochasticity." Thesis, University of California, Irvine, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10827971.
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Stochastic models of biochemical interactions elucidate essential properties of the network which are not accessible to deterministic modeling. In this thesis it is described how a network motif, the proportional-reversibility interaction with active intermediate states, gives rise to the ability for the variance of biochemical signals to be controlled without changing the mean, a property designated as mean-independent noise control (MINC). This noise control is demonstrated to be essential for macro-scale biological processes via spatial models of the zebrafish hindbrain boundary sharpening. Additionally, the ability to deduce noise origin from the aggregate noise properties is shown.
However, these large-scale stochastic models of developmental processes required significant advances in the methodology and tooling for solving stochastic differential equations. Two improvements to stochastic integration methods, an efficient method for time stepping adaptivity on high order stochastic Runge-Kutta methods termed Rejection Sampling with Memory (RSwM) and optimal-stability stochastic Runge-Kutta methods, are combined to give over 1000 times speedups on biological models over previously used methodologies. In addition, a new software for solving differential equations in the Julia programming language is detailed. Its unique features for handling complex biological models, along with its high performance (routinely benchmarking as faster than classic C++ and Fortran integrators of similar implementations) and new methods, give rise to an accessible tool for simulation of large-scale stochastic biological models.
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Corry, Ben Alexander. "Simulation studies of biological ion channels." View thesis entry in Australian Digital Theses Program, 2002. http://thesis.anu.edu.au/public/adt-ANU20030423.162927/index.html.
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Yngve, Gary. "Visualization for biological models, simulation, and ontologies /." Thesis, Connect to this title online; UW restricted, 2008. http://hdl.handle.net/1773/6912.
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Wang, Eric Yiqing. "Comparison Between Deterministic and Stochastic Biological Simulation." Thesis, Uppsala universitet, Analys och sannolikhetsteori, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-230732.
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Millar, Campbell. "3D simulation techniques for biological ion channels." Thesis, University of Glasgow, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.401999.
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Mishra, Shikta. "Modeling and Simulation of Cutting in Soft Biological Tissues for Surgical Simulation." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1352994028.
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Topkaya, Pinar. "Computer Simulation Of A Complete Biological Treatment Plant." Master's thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/12609708/index.pdf.
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Nitrogen and phosphorus removal is often required before discharge of treated wastewater to sensitive water bodies. Kayseri Wastewater Treatment Plant (KWWTP) is a biological wastewater treatment plant that includes nitrogen and phosphorus removal along with carbon removal. The KWWTP receives both municipal wastewater and industrial wastewaters. In this study, KWWTP was modeled by using a software called GPS-X, which is developed for modeling municipal and industrial wastewaters. The Activated Sludge Model No.2d (ASM2d) developed by the International Association on Water Quality (IAWQ) was used for the simulation of the treatment plant. In this model, carbon oxidation, nitrification, denitrification and biological phosphorus removal are simulated at the same time.
During the calibration of the model, initially, sensitivities of the model parameters were analyzed. After sensitivity analysis, dynamic parameter estimation (DPE) was carried out for the optimization of the sensitive parameters. Real plant data obtained from KWWTP were used for DPE. The calibrated model was validated by using different sets of data taken from various seasons after necessary temperature adjustments made on the model.
Considerably good fits were obtained for removal of chemical oxygen demand (COD), total suspended solids (TSS) and nitrogen related compounds. However, the results for phosphorus removal were not satisfactory, probably due to lack of information on volatile fatty acids concentration and alkalinity of the influent wastewater.
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Lantin, Maria Louise. "An environment for the simulation of biological models." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0028/NQ51886.pdf.
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Phillips, Stephen Christopher. "Computer simulation of conformational change in biological molecules." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/373628/.
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A new method for modifying the course of a molecular dynamics computer simulation is presented. Digitally Filtered Molecular Dynamics (DFMD) applies the well-established theory of digital filters to molecular dynamics simulations, enabling atomic motion to be enhanced or suppressed in a selective manner solely on the basis of frequency. The basic theory of digital filters and its application to molecular dynamics simulations is presented, together with the application of DFMD to the simple systems of single molecules of water and butane. The extension of the basic theory to the condensed phase is then described followed by its application to liquid phase butane and the Syrian hamster prion protein. The high degree of selectivity and control offered by DFMD, and its ability to enhance the rate of conformational change in butane and in the prion protein, is demonstrated. The DFMD method is then modified and extended to become Reversible Digitally Filtered Molecular Dynamics (RDFMD). The RDFMD method improves the degree of control possible over that of DFMD. DFMD is applied to gas-phase pentane, alanine dipeptide, solvated alanine dipeptide and the pentapeptide YPGDV. In all four systems, RDFMD was able to enhance the rate of conformational change via reasonable transition paths. Finally, the new method of the Hilbert-Huang Transform (HHT) is described and applied to the analysis of conformational transitions. The HHT is shown to provide clear indications of the changes in energy and frequency during conformational transitions.
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Das, Anusuya. "Capillary characteristics in microfluidic experiments and computational simulation." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/62720.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, February 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 119-128).
Angiogenesis is crucial during many physiological processes, and is influenced by various biochemical and biomechanical factors. Models have proven useful in understanding the mechanisms of angiogenesis and the characteristics of the capillaries formed as part of the process. We have developed a 3D hybrid, agent-field model where individual cells are modeled as sprout-forming agents in a matrix field. Cell independence, cell-cell communication and stochastic cell response are integral parts of the model. The model simulations incorporate probabilities of an individual cell to transition into one of four states - quiescence, proliferation, migration and apoptosis. We demonstrate that several features such as continuous sprouts, cell clustering and branching that are observed in microfluidic experiments conducted under controlled conditions using few angiogenic factors can be reproduced by this model. We also identify the transition probabilities that result in specific sprout characteristics such as the length and number of continuous sprouts. We have used microfluidics to study cell migration and capillary morphogenesis. The experiments were conducted under different concentrations of VEGF and Ang I. We demonstrated that capillaries with distinct characteristics can be grown under different media conditions and that characteristics can be altered by changing these conditions. A two-channel microfluidic device fabricated in PDMS was used for all experiments. The rationale underlying the design of the experiments was twofold: the first goal was to generate reproducible and physiologically relevant results in a microfluidic device, and the second goal was to quantify the capillary characteristics and use them to estimate the transition parameters of the model. We developed stable, well-maintained sprouts by using human microvascular endothelial cells in 2.5 mg/ml dense collagen I gel and by using media supplemented with 40 ng/ml VEGF and 500 ng/ml Ang 1 for two days. It has been shown in many studies that VEGF acts as an angiogenic factor and Ang 1 acts as stabilizing factor. Here we showed that their roles are maintained in the 3D microenvironment, and the sprout characteristics obtained by using this baseline condition could be altered by changing the concentrations of these two growth factors in a systematic way. Sprout and cell characteristics obtained in the experiments and simulations were analyzed by adapting Decision Tree Analysis. This methodology provides us with a useful tool for discerning the impact of different growth factors on the process of cell migration or proliferation as they alter general sprout morphology. The imprints obtained via experiments and simulations were compared; by choosing appropriate values of the transition probabilities, the model generates capillary characteristics similar to those seen in experiments (R2 ~ 0.82- 0.99). Thus, this model can be used to cluster sprout morphology as a function of various influencing factors and, within bounds, predict if a certain growth factor will affect migration or proliferation as it impacts sprout morphology. This was demonstrated in the case of anti-angiogenic agent, PF4. We showed that at high concentration of PF4 (- 1000 ng/ ml), the transition to migration is more profoundly affected while at low concentrations of - 10 ng/ ml, PF4 does not have much of an effect on either migration or proliferation.
by Anusuya Das.
Ph.D.
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Eriksson, Emil. "Simulation of Biological Tissue using Mass-Spring-Damper Models." Thesis, Örebro universitet, Institutionen för naturvetenskap och teknik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-27663.
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The goal of this project was to evaluate the viability of a mass-spring-damper based model for modeling of biological tissue. A method for automatically generating such a model from data taken from 3D medical imaging equipment including both the generation of point masses and an algorithm for generating the spring-damper links between these points is presented. Furthermore, an implementation of a simulation of this model running in real-time by utilizing the parallel computational power of modern GPU hardware through OpenCL is described. This implementation uses the fourth order Runge-Kutta method to improve stability over similar implementations. The difficulty of maintaining stability while still providing rigidness to the simulated tissue is thoroughly discussed. Several observations on the influence of the structure of the model on the consistency of the simulated tissue are also presented. This implementation also includes two manipulation tools, a move tool and a cut tool for interaction with the simulation. From the results, it is clear that the mass-springdamper model is a viable model that is possible to simulate in real-time on modern but commoditized hardware. With further development, this can be of great benefit to areas such as medical visualization and surgical simulation.Målet med detta projekt var att utvärdera huruvida en modell baserad på massa-fjäderdämpare är meningsfull för att modellera biologisk vävnad. En metod för att automatiskt generera en sådan modell utifrån data tagen från medicinsk 3D-skanningsutrustning presenteras. Denna metod inkluderar både generering av punktmassor samt en algoritm för generering av länkar mellan dessa. Vidare beskrivs en implementation av en simulering av denna modell som körs i realtid genom att utnyttja den parallella beräkningskraften hos modern GPU-hårdvara via OpenCL. Denna implementation använder sig av fjärde ordningens Runge-Kutta-metod för förbättrad stabilitet jämfört med liknande implementationer. Svårigheten att bibehålla stabiliteten samtidigt som den simulerade vävnaden ges tillräcklig styvhet diskuteras genomgående. Flera observationer om modellstrukturens inverkan på den simulerade vävnadens konsistens presenteras också. Denna implementation inkluderar två manipuleringsverktyg, ett flytta-verktyg och ett skärverktyg för att interagera med simuleringen. Resultaten visar tydligt att en modell baserad på massa-fjäder-dämpare är en rimlig modell som är möjlig att simulera i realtid på modern men lättillgänglig hårdvara. Med vidareutveckling kan detta bli betydelsefullt för områden så som medicinsk bildvetenskap och kirurgisk simulering.
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Robinson, Alan Jonathan. "The computer simulation of lipid bilayers and biological membranes." Thesis, University of Oxford, 1996. https://ora.ox.ac.uk/objects/uuid:787e13b4-4a3e-44ce-bd2d-9bb847631a5d.
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Computer simulations of lipid bilayers and biological membranes using molecular mechanics calculations have been undertaken in order to study these complex systems which are so vital in the control and functioning of many biological processes. The preliminary research involved the development of a model that recreates experimentally observed properties. This is not a trivial task since structural data on lipids in the biologically relevant liquid crystalline phase are unavailable precisely because of their fluid nature. The starting configuration designed for simulation of lipids in the fluid phase contained four different lipid conformations. These reflected the most probable head group and glycerol moiety conformations plus gauche dihedrals were introduced into the hydrocarbon chains so that they resembled chains in the fluid phase and reduced the time required for equilibration molecular dynamics. The bilayer model was then used to study cholesterol-lipid and peptide-lipid interactions. The cholesterol simulations illustrated how this molecule orders lipid chains by virtue of its rigid skeleton while the peptide simulations showed how cooperative the interactions between proteins and lipids are. Finally simulations of ion channels of gramicidin and melittin in membranes were accomplished and conclusions drawn on the nature and mechanism of the toxicity of melittin and of how water and ion translocation occurs along gramicidin channels.
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Whitehead, L. "Computer simulation of biological membranes and membrane bound proteins." Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297412.
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Bemporad, Daniele. "Computer simulation of biological membranes and small molecule permeation." Thesis, University of Southampton, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273747.
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Karunaweera, Sadish. "Theory and simulation of molecular interactions in biological systems." Diss., Kansas State University, 2016. http://hdl.handle.net/2097/34631.
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Doctor of PhilosophyDepartment of Chemistry
Paul E. Smith
The impact of computer simulations has become quite significant especially with the development of supercomputers during the last couple of decades. They are used in a wide range of purposes such as exploring experimentally inaccessible phenomena and providing an alternative when experiments are expensive, dangerous, time consuming, difficult and controversial. In terms of applications in biological systems molecular modeling techniques can be used in rational drug design, predicting structures of proteins and circumstances where the atomic level descriptions provided by them are valuable for the understanding of the systems of interest. Hence, the potential of computer simulations of biomolecular systems is undeniable. Irrespective of the promising uses of computer simulations, it cannot be guaranteed that the results will be realistic. The precision of a molecular simulation depends on the degree of sampling achieved during the simulation while the accuracy of the results depends on the satisfactory description of intramolecular and intermolecular interactions in the system, i.e. the force field. Recently, we have been developing a force field for molecular dynamics simulations of biological systems based on the Kirkwood Buff (KB) theory of solutions, not only with an emphasis on the accurate description of intermolecular interactions, but also by reproducing several physical properties such as partial molar volume, compressibility and composition dependent chemical potential derivatives to match with respective experimental values. In this approach simulation results in terms of KB integrals can be directly compared with experimental data through a KB analysis of the solution properties and therefore it provides a simple and clear method to test the capability of the KB derived force field. Initially, we have provided a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the KB theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly₂ and Gly₃ in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. Then, we have attempted to quantify the interactions between amino acids in aqueous solutions using the KB theory of solutions. The results are illustrated using computer simulations for various concentrations of the twenty zwitterionic amino acids at ambient temperature and pressure. Next, several amino acids were also studied at higher temperatures and pressures and the results are discussed in terms of the preferential (solute over solvent) interactions between the amino acids. Finally, we have described our most recent efforts towards a complete force field for peptides and proteins. The results are illustrated using molecular dynamics simulations of several tripeptides, selected peptides and selected globular proteins at ambient temperature and pressure followed by replica exchange molecular dynamics simulations of a few selected peptides.
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Zhang, Wei. "Computer simulation of secondary structure of biological and synthetic macromolecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29729.
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Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009.Committee Chair: Ludovice, Pete; Committee Member: Chen, Rachel; Committee Member: Harvey, Steve; Committee Member: Sambanis, Athanassios; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Kosuri, Sriram. "Simulation, models, and refactoring of bacteriophage T7 gene expression." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/39912.
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Thesis (Sc. D.)--Massachusetts Institute of Technology, Biological Engineering Division, February 2007.Includes bibliographical references (leaves 108-124).
Our understanding of why biological systems are designed in a particular way would benefit from biophysically-realistic models that can make accurate predictions on the time-evolution of molecular events given arbitrary arrangements of genetic components. This thesis is focused on constructing such models for gene expression during bacteriophage T7 infection. T7 gene expression is a particularly well suited model system because knowledge of how the phage functions is thought to be relatively complete. My work focuses on two questions in particular. First, can we address deficiencies in past simulations and measurements of bacteriophage T7 to improve models of gene expression? Second, can we design and build refactored surrogates of T7 that are easier to understand and model? To address deficiencies in past simulations and measurements, I developed a new single-molecule, base-pair-resolved gene expression simulator named Tabasco that can faithfully represent mechanisms thought to govern phage gene expression. I used Tabasco to construct a model of T7 gene expression that encodes our mechanistic understanding. The model displayed significant discrepancies from new system-wide measurements of absolute T7 mRNA levels during infection.
(cont.) I fit transcript-specific degradation rates to match the measured RNA levels and as a result corrected discrepancies in protein synthesis rates that confounded previous models. I also developed and used a fitting procedure to the data that let us evaluate assumptions related to promoter strengths, mRNA degradation, and polymerase interactions. To construct surrogates of T7 that are easier to understand and model, I began the process of refactoring the T7 genome to construct an organism that is a more direct representation of the models that we build. In other words, instead of making our models evermore detailed to explain wild-type T7, we started to construct new phage that are more direct representations of our models. The goal of our original design, T7. 1, was to physically define, separate, and enable unique manipulation of primary genetic elements. To test our initial design, we replaced the left 11,515 bp of the wild-type genome with 12,179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. I also present a second generation design, T7.2, that extends the original goals of T7.1 by constructing a more direct physical representation of the T7 model.
by Sriram Kosuri.
Sc.D.
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McHarg, Amy Marie. "Optimisation of municipal wastewater biological nutrient removal using computer simulation." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/10479.
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Due to more stringent regulations for secondary municipal wastewater treatment, municipalities are beginning to implement tertiary treatment in their wastewater treatment plants. Tertiary treatment would be the removal of either phosphorous or nitrogen or both from the wastewater before it is discarded from the plant. Biological treatment is becoming an increasingly popular process used to accomplish this extra removal. There are several processes available that will provide acceptable levels of biological nutrient and BOD removal from wastewater. Three well-known processes were considered in this study - the Modified Bardenpho Process, the Modified UCT Process and the A2/O Process. For each of these processes, 2 1evel fractional factorial designs along with least squares analysis were performed in order to determine the optimal operating variables (recycle rates and anaerobic, anoxic and aerobic zone retention times), with respect to the final nitrogen concentration, the final phosphorous concentration and a combination of the final nitrogen and phosphorous concentrations. The analyses were performed at 10°C and 20°C with low, medium and high primary effluent concentrations. Due to the complexity of the processes, lab scale experiments were not feasible. Therefore, a widely accepted calibrated biokinetic model (Activated Sludge Model No 2d) was used in a computer simulation program (GPS-X) to gather the necessary data for analysis. Actual plant data were used to test the validity of the simulation model with respect to organic and nitrogen removal. Using the published kinetic and stoichiometric parameters for both temperature levels, the Activated Sludge Model provided a good estimation of outlet concentration levels. It was found that all three biological nutrient removal (BNR) process were capable of achieving an effluent soluble phosphorous concentration below the required limit of 1 mgP/L at 10 and 20°C with low, medium and high primary effluent concentration when the effluent nitrogen concentration was neglected. Neither the Modified Bardenpho, the Modified UCT nor the A 2/O process were capable of producing an effluent with nitrogen concentrations below the required limit of 5 mgN/L at high primary effluent concentrations. The Modified Bardenpho and the Modified UCT processes were both successful in achieving a combined nitrogen and phosphorous removal below their regulatory limits for low primary effluent concentrations at 10 and 20°C. The Modified Bardenpho process, at 20°C with medium primary effluent concentrations, was found to achieve an effluent with nitrogen and phosphorous concentrations below 5 mgN/L and 1 mgP/L, respectively. After analyzing the effects of individual operating variables, it was found that the anoxic recycle for the Modified UCT process had an insignificant effect on total nitrogen (TN) and soluble phosphorous (sP) removals and did not need to be included in future experimental studies. All of the input variables to the MB and A2/O process proved to be somewhat significant and it is recommended that they be kept within future experimental designs. From this study it was found that both the MB and MUCT process are capable of achieving the TN, sP and cBOD5 removals that ROPEC requires. However only the MB process proved to be a robust system when subjected to storm conditions (i.e., peaks in influent flow rate) with respect to sP and cBOD5 removal. Neither the MB nor the MUCT process provided acceptable TN removals when subjected to storm conditions. It is recommended that ROPEC further evaluate the MB process as a possible means to achieve simultaneous cBOD5, TN and sP removal.
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Goler, Jonathan Ari 1980. "BioJADE : a design and simulation tool for synthetic biological systems." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28408.
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Thesis (M. Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (p. 83-85).
The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.
by Jonathan Ari Goler.
M.Eng.and S.B.
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Van, Belle Daniel. "Computer studies of electronic polarization effects in biological systems." Doctoral thesis, Universite Libre de Bruxelles, 1992. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/212930.
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Molenaar, Robert. "Design and implementation of biosystem control and tools for biosystem simulation." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape11/PQDD_0017/NQ44519.pdf.
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Adiwijaya, Bambang Senoaji. "Simulation and optimization tools to study design principles of biological networks." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37973.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006.Includes bibliographical references.
Recent studies have developed preliminary wiring diagrams for a number of important biological networks. However, the design principles governing the construction and operation of these networks remain mostly unknown. To discover design principles in these networks, we investigated and developed a set of computational tools described below. First, we looked into the application of optimization techniques to explore network topology, parameterization, or both, and to evaluate relative fitness of networks operational strategies. In particular, we studied the ability of an enzymatic cycle to produce dynamic properties such as responsiveness and transient noise filtering. We discovered that non-linearity of the enzymatic cycle allows more effective filtering of transient noise. Furthermore, we found that networks with multiple activation steps, despite being less responsive, are better in filtering transient noise. Second, we explored a method to construct compact models of signal transduction networks based on a protein-domain network representation. This method generates models whose number of species, in the worst case, scales quadratically to the number of protein-domain sites and modification states, a tremendous saving over the combinatorial scaling in the more standard mass-action model was estimated to consist of more that 10⁷ species and was too large to simulate; however, a simplified model consists of only 132 state variables and produced intuitive behavior. The resulting models were utilized to study the roles of a scaffold protein and of a shared binding domain to pathway functions.
by Bambang Senoaji Adiwijaya.
Ph.D.
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Norman, Will. "BioAnalyze a tool for the simulation and analysis of biological systems /." Connect to this title online, 2007. http://etd.lib.clemson.edu/documents/1193079000/.
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Chan, Yue-ping, and 陳裕萍. "Simulation and analysis of biological wastewater treatment processes using GPS-X." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B31255437.
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Geiser, Kyle. "Computational modeling and simulation for projectile impact and indentation of biological tissues and polymers." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/112507.
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Thesis: S.M., Massachusetts Institute of Technology, Department of Biological Engineering, 2017.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 89-95).
Understanding the elastic and viscoelastic responses of biological soft tissues and engineered polymer simulants is of great interest to predicting and preventing penetrative injuries. Detailed understanding of the mechanical processes at work could aid in the development and evaluation of protective strategies such as armor and helmets, and repair strategies including robotic surgery or needle-based drug delivery. However, due to the mechanical complexity of so-called "soft tissues," including nonlinear viscoelastic behavior, surface adhesion, material failures and shock effects, the experimental characterization of various soft tissues is challenging and individual mechanical processes are often impossible to decouple without computational models and simulations. This thesis presents two finite element models designed to provide both replicate the results of indentation and impact experiments on synthetic polymers, aimed to decouple competing mechanical characteristics of contact based deformation. The first of these models describes the indentation on polydimethylsiloxane bilayer composites, with the aim of describing the relative effects of a adhesion and viscoelastic properties on the measured deformation response. That model expands on this objective via the analysis of the effects of surface adhesion commonly associated with highly compliant polymers and tissues. The second model attempts to replicate impact of a high velocity projectile on a relatively stiff material, polyurethane urea, and on a comparatively compliant polymer, gelatin hydrogel. These models provide means to simulate, predict and characterize material response, validated by comparison with available experiments. Such validated models can be used to simulate and design new materials as tissue simulants or as protective media that predictably dissipate concentrated mechanical impact.
by Kyle Geiser.
S.M.
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Alkhairy, Samiya Ashraf. "A modeling framework and toolset for simulation and characterization of the cochlea within the auditory system." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/67201.
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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 50-53).
Purpose: This research develops a modeling approach and an implementation toolset to simulate reticular lamina displacement in response to excitation at the ear canal and to characterize the cochlear system in the frequency domain. Scope The study develops existing physical models covering the outer, middle, and inner ears. The range of models are passive linear, active linear, and active nonlinear. These models are formulated as differential algebraic equations, and solved for impulse and tone excitations to determine responses. The solutions are mapped into tuning characteristics as a function of position within the cochlear partition. Objectives The central objective of simulation is to determine the characteristic frequency (CF)-space map, equivalent rectangular bandwidth (ERB), and sharpness of tuning (QERB) of the cochlea. The focus of this research is on getting accurate characteristics, with high time and space resolution. The study compares the simulation results to empirical measurements and to predictions of a model that utilizes filter theory and coherent reflection theory. Method We develop lumped and distributed physical models based on mechanical, acoustic, and electrical phenomena. The models are structured in the form of differential-algebraic equations (DAE), discretized in the space domain. This is in contrast to existing methods that solve a set of algebraic equations discretized in both space and time. The DAEs are solved using numerical differentiation formulas (NDFs) to compute the displacement of the reticular lamina and intermediate variables such as displacement of stapes in response to impulse and tone excitations at the ear canal. The inputs and outputs of the cochlear partition are utilized in determining its resonances and tuning characteristics. Transfer functions of the cochlear system with impulse excitation are calculated for passive and active linear models to determine resonance and tuning of the cochlear partition. Output characteristics are utilized for linear systems with tone excitation and for nonlinear models with stimuli of various amplitudes. Stability of the system is determined using generalized eigenvalues and the individual subsystems are stabilized based on their poles and zeros. Results The passive system has CF map ranging from 20 kHz at the base to 10 Hz at the apex of the cochlear partition, and has the strongest resonant frequency corresponding to that of the middle ear. The ERB is on the order of the CF, and the QERB is on the order of 1. The group delay decreases with CF which is in contradiction with findings from Stimulus Frequency Otoacoustic Emissions (SFOAE) experiments. The tuning characteristics of the middle ear correspond well to experimental observations. The stability of the system varies greatly with the choice of parameters, and number of space sections used for both the passive and active implementations. Implication Estimates of cochlear partition tuning based on solution of differential algebraic equations have better time and space resolution compared to existing methods that solve discretized set of equations. Domination of the resonance frequency of the reticular lamina by that of the middle ear rather than the resonant frequency of the cochlea at that position for the passive model is in contradiction with Bekesys measurements on human cadavers. Conclusion The methodology used in the thesis demonstrate the benefits of developing models and formulating the problem as differential-algebraic equations and solving it using the NDFs. Such an approach facilitates computation of responses and transfer functions simultaneously, studying stability of the system, and has good accuracy (controlled directly by error tolerance) and resolution.
by Samiya Ashraf Alkhairy.
M.Eng.
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Gambi, Naimj <1980>. "Experimental Studies on Electromagnetic Fields Effects on Biological Targets: Simulation and Dosimetry." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2010. http://amsdottorato.unibo.it/2472/.
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Ali, Yasmine. "Biological dose estimation in hadrontherapy using the GATE Monte Carlo simulation platform." Thesis, Lyon, 2021. http://www.theses.fr/2021LYSE1329.
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Un des challenges en hadronthérapie est l'estimation de la dose biologique. Les systèmes de planification de traitement (TPS) doivent optimiser les faisceaux de traitement en prenant en compte la prédiction de la dose biologique en plus de la prédiction de la dose physique. Pour estimer la dose biologique, des modèles biophysiques ont été développés tels que les modèles mMKM et NanOx. Les paramètres d'entrée de ces modèles peuvent être estimés grâce à des codes de calculs Monte Carlo en structure de trace. Nous utilisons les codes Geant4-DNA et LPCHEM et les comparons pour évaluer leurs différences. Les deux codes peuvent simuler les radiations ionisantes jusqu'à l'eV ainsi que la production d'espèces radiolytiques suite à la radiolyse de l'eau entre la picoseconde et la microseconde. Les modèles biophysiques permettent des calculs de dose complexes à l'échelle du voxel en les couplant à des codes de calcul Monte Carlo. Nous avons développé un outil pour la plateforme de calcul Monte Carlo GATE, le "Biodose actor", dans le but d'estimer la dose biologique pour des pics de Bragg étalés issus de lignes cliniques et précliniques, irradiant avec des faisceaux de protons, d'ions hélium et d'ions carbone. Nous avons comparé les codes Geant4-DNA et LPCHEM pout la simulation de spectres nanodosimétriques dans le cœur de trace d’ion et la production d'espèce radiolytiques dans l’eau par des particules chargées (10 MeV protons). Les spectres totaux d’énergie spécifique dans des cibles nanométriques ainsi que les rendements d’espèces radiolytiques pour les deux codes sont en bon accord. En plus de l’implémentation du BioDose actor dans GATE, l’outil a été testé et validé avec des données expérimentales de survie cellulaire obtenues grâce à différents pics de Bragg étalés. Cet outil facilitera les comparaisons et évaluation des diffèrents modèles biophysiquesOne of the current challenges in hadrontherapy is the evaluation of the biological effects due to microscopic pattern of energy deposition of ions. Treatment Planning Systems (TPS) should optimize beam parameters taking into account their predictions through the calculation of the biological dose in addition to the physical dose. To estimate the biological dose, biophysics models have been developed such as the mMKM and NanOx models. Some input parameters of the models are generally estimated with Monte Carlo Track Structure Codes such as Geant4-DNA and LPCHEM codes. Both codes are able to perform the simulation of ion and electron transport in water down to some eV as well as the evaluation of the chemical species generated during water radiolysis between 10-12 and 10-6 s. In this work, we first compared the outcome of LPCHEM and Geant4-DNA in terms of specific energy in nano and micro targets as well as yields of chemical species (input of the biophysical models). Then, we enhanced the GATE Monte Carlo simulation platform by creating a “Biodose actor” in order to estimate the biological dose for different clinical Spread-out Bragg Peaks (SOBP) with hydrogen, helium and carbon ion beams. We performed the first comparison between the LPCHEM and Geant4-DNA codes for the simulation of nanodosimetry spectra in the track core and the production of chemical species yields for water irradiations with charged particles (10 MeV protons). The total specific energy spectra in nanometric targets and the chemical yields predicted by the two codes are in good agreement. Besides the implementation of the BioDose actor in GATE has been tested and validated with comparison against experimental cell survival obtained in several SOBP. This tool paves the way of facilitated benchmarking between different models and evaluation approaches
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Tsafnat, Guy Computer Science & Engineering Faculty of Engineering UNSW. "Abstraction and representation of fields and their applications in biomedical modelling." Awarded by:University of New South Wales. School of Computer Science and Engineering, 2006. http://handle.unsw.edu.au/1959.4/24207.
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Computer models are used extensively to investigate biological systems. Many of these systems can be described in terms of fields???spatially- and temporally- varying scalar, vector and tensor properties defined over domains. For example, the spatial variation of muscle fibers is a vector field, the spatial and temporal variation in temperature of an organ is a scalar field, and the distribution of stress across muscle tissue is a tensor field. In this thesis I present my research on how to represent fields in a format that allows researchers to store and distribute them independently of models and to investigate and manipulate them intuitively. I also demonstrate how the work can be applied to solving and analysing biomedical models. To represent fields I created a two-layer system. One layer, called the Field Representation Language (FRL), represents fields by storing numeric, analytic and meta data for storage and distribution. The focus of this layer is efficiency rather than usability. The second layer, called the Abstract Field Layer (AFL), provides an abstraction of fields so that they are easier for researchers to work with. This layer also provides common operations for manipulating fields as well as transparent conversion to and from FRL representations. The applications that I used to demonstrate the use of AFL and FRL are (a) a fields visualisation toolkit, (b) integration of models from different scales and solvers, and (c) a solver that uses AFL internally. The layered architecture facilitated the development of tools that use fields. A similar architecture may also prove useful for representations of other modelled entities.
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Manyonge, Lawrence. "Autonomous finite capacity scheduling using biological control principles." Thesis, De Montfort University, 2012. http://hdl.handle.net/2086/7986.
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The vast majority of the research efforts in finite capacity scheduling over the past several years has focused on the generation of precise and almost exact measures for the working schedule presupposing complete information and a deterministic environment. During execution, however, production may be the subject of considerable variability, which may lead to frequent schedule interruptions. Production scheduling mechanisms are developed based on centralised control architecture in which all of the knowledge base and databases are modelled at the same location. This control architecture has difficulty in handling complex manufacturing systems that require knowledge and data at different locations. Adopting biological control principles refers to the process where a schedule is developed prior to the start of the processing after considering all the parameters involved at a resource involved and updated accordingly as the process executes. This research reviews the best practices in gene transcription and translation control methods and adopts these principles in the development of an autonomous finite capacity scheduling control logic aimed at reducing excessive use of manual input in planning tasks. With autonomous decision-making functionality, finite capacity scheduling will as much as practicably possible be able to respond autonomously to schedule disruptions by deployment of proactive scheduling procedures that may be used to revise or re-optimize the schedule when unexpected events occur. The novelty of this work is the ability of production resources to autonomously take decisions and the same way decisions are taken by autonomous entities in the process of gene transcription and translation. The idea has been implemented by the integration of simulation and modelling techniques with Taguchi analysis to investigate the contributions of finite capacity scheduling factors, and determination of the ‘what if’ scenarios encountered due to the existence of variability in production processes. The control logic adopts the induction rules as used in gene expression control mechanisms, studied in biological systems. Scheduling factors are identified to that effect and are investigated to find their effects on selected performance measurements for each resource in used. How they are used to deal with variability in the process is one major objective for this research as it is because of the variability that autonomous decision making becomes of interest. Although different scheduling techniques have been applied and are successful in production planning and control, the results obtained from the inclusion of the autonomous finite capacity scheduling control logic has proved that significant improvement can still be achieved.
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Ding, Wei. "Molecular dynamics simulation of biomembrane systems." Thesis, Queen Mary, University of London, 2018. http://qmro.qmul.ac.uk/xmlui/handle/123456789/36217.
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The fundamental structure of all biological membranes is the lipid bilayer. At- tributed to the multifaceted features of lipids and its dynamical interaction with other membrane-integrated molecules, the lipid bilayer is involved in a variety of physiological phenomena such as transmembrane transportation, cellular signalling transduction, energy storage, etc. Due to the nanoscale but high complexity of the lipid bilayer system, experimental investigation into many important processes at the molecular level is still challenging. Molecular dynamics (MD) simulation has been emerging as a powerful tool to study the lipid membrane at the nanoscale. Utilizing atomistic MD, we have quantitatively investigated the effect of lamellar and nonlamellar lipid composition changes on a series of important bilayer properties, and how membranes behave when exposed to a high-pressure environment. A series of membrane properties such as lateral pressure and dipole potential pro les are quanti ed. Results suggest the hypothesis that compositional changes, involving both lipid heads and tails, modulate crucial mechanical and electrical features of the lipid bilayer, so that a range of biological phenomena, such as the permeation through the membrane and conformational equilibria of membrane proteins, may be regulated. Furthermore, water also plays an essential role in the biomembrane system. To balance accuracy and efficiency in simulations, a coarse-grained ELBA water model was developed. Here, the ELBA water model is stress tested in terms of temperature- and pressure-related properties, as well as hydrating properties. Results show that the accuracy of the ELBA model is almost as good as conventional atomistic water models, while the computational efficiency is increased substantially.
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Leitner, Zachary Robert. "Soil Biological Temporal Variability as Functions of Physiochemical States and Soil Disturbance." Thesis, North Dakota State University, 2019. https://hdl.handle.net/10365/31620.
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Within our ecosystems, soil biota control an array of functions, such as nutrient cycling and decomposition, and have been pursued as a soil quality indicator. Though microbial communities are known to be a reflection of their environment, small scales dynamics within an agricultural system have been overlooked for many years leading to gaps when inferring on relative microbial values. To further asses our current microbial knowledge, two experiments analyzing microbial phospholipid fatty acid (PLFA) structures and enzyme activities sought out to determine temporal fluctuations, cycles, and driving force behind simulated daily microbial parameter outputs. Across both studies, temporal effects, cyclical structures, and common driving forces were recorded, but further validation and characterization is needed to solidify the temporal dynamics of the microbial community. Overall, this information serves as a valuable step towards determining the most viable tillage systems based on environmental conditions, and physical proof of small scale microbial fluctuations.
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Zhang, Wei. "Computational simulation of biological systems studies on protein folding and protein structure prediction /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.84Mb, 184 p, 2005. http://wwwlib.umi.com/dissertations/fullcit/3181881.
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Kästner, Johannes. "Biological nitrogen fixation simulation of the reaction mechanism of nitrogenase from first principles /." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971535701.
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Maladen, Ryan Dominic. "Biological, simulation, and robotic studies to discover principles of swimming within granular media." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/42852.
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The locomotion of organisms whether by running, flying, or swimming is the result of multiple degree-of-freedom nervous and musculoskeletal systems interacting with an environment that often flows and deforms in response to movement. A major challenge in biology is to understand the locomotion of organisms that crawl or burrow within terrestrial substrates like sand, soil, and muddy sediments that display both solid and fluid-like behavior. In such materials, validated theories such as the Navier-Stokes equations for fluids do not exist, and visualization techniques (such as particle image velocimetry in fluids) are nearly nonexistent.
In this dissertation we integrated biological experiment, numerical simulation, and a physical robot model to reveal principles of undulatory locomotion in granular media. First, we used high speed x-ray imaging techniques to reveal how a desert dwelling lizard, the sandfish, swims within dry granular media without limb use by propagating a single period sinusoidal traveling wave along its body, resulting in a wave efficiency, the ratio of its average forward speed to wave speed, of approximately 0.5. The wave efficiency was independent of the media preparation (loosely and tightly packed). We compared this observation against two complementary modeling approaches: a numerical model of the sandfish coupled to a discrete particle simulation of the granular medium, and an undulatory robot which was designed to swim within granular media. We used these mechanical models to vary the ratio of undulation amplitude (A) to wavelength (λ) and demonstrated that an optimal condition for sand-swimming exists which results from competition between A and λ. The animal simulation and robot model, predicted that for a single period sinusoidal wave, maximal speed occurs for A/ λ = 0.2, the same kinematics used by the sandfish. Inspired by the tapered head shape of the sandfish lizard, we showed that the lift forces and hence vertical position of the robot as it moves forward within granular media can be varied by designing an appropriate head shape and controlling its angle of attack, in a similar way to flaps or wings moving in fluids. These results support the biological hypotheses which propose that morphological adaptations of desert dwelling organisms aid in their subsurface locomotion. This work also demonstrates that the discovery of biological principles of high performance locomotion within sand can help create the next generation of biophysically inspired robots that could explore potentially hazardous complex flowing environments.
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Chen, Helen Hong. "Finite element-based computer simulation of motility, sorting, and deformation in biological cells." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0012/NQ30595.pdf.
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Chowdhury, Indranil. "Potential based multi-physics modeling and simulation for integrated electronic and biological systems /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/5977.
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Wierling, Christoph [Verfasser]. "Theoretical biology : Modeling and simulation of biological systems and laboratory methods / Christoph Wierling." Berlin : Freie Universität Berlin, 2010. http://d-nb.info/1024007383/34.
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Shen, Wensheng. "Computer Simulation and Modeling of Physical and Biological Processes using Partial Differential Equations." UKnowledge, 2007. http://uknowledge.uky.edu/gradschool_diss/501.
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Scientific research in areas of physics, chemistry, and biology traditionally depends purely on experimental and theoretical methods. Recently numerical simulation is emerging as the third way of science discovery beyond the experimental and theoretical approaches. This work describes some general procedures in numerical computation, and presents several applications of numerical modeling in bioheat transfer and biomechanics, jet diffusion flame, and bio-molecular interactions of proteins in blood circulation.
A three-dimensional (3D) multilayer model based on the skin physical structure is developed to investigate the transient thermal response of human skin subject to external heating. The temperature distribution of the skin is modeled by a bioheat transfer equation. Different from existing models, the current model includes water evaporation and diffusion, where the rate of water evaporation is determined based on the theory of laminar boundary layer. The time-dependent equation is discretized using the Crank-Nicolson scheme. The large sparse linear system resulted from discretizing the governing partial differential equation is solved by GMRES solver.
The jet diffusion flame is simulated by fluid flow and chemical reaction. The second-order backward Euler scheme is applied for the time dependent Navier-Stokes equation. Central difference is used for diffusion terms to achieve better accuracy, and a monotonicity-preserving upwind difference is used for convective ones. The coupled nonlinear system is solved via the damped Newton's method. The Newton Jacobian matrix is formed numerically, and resulting linear system is ill-conditioned and is solved by Bi-CGSTAB with the Gauss-Seidel preconditioner.
A novel convection-diffusion-reaction model is introduced to simulate fibroblast growth factor (FGF-2) binding to cell surface molecules of receptor and heparan sulfate proteoglycan and MAP kinase signaling under flow condition. The model includes three parts: the flow of media using compressible Navier-Stokes equation, the transport of FGF-2 using convection-diffusion transport equation, and the local binding and signaling by chemical kinetics. The whole model consists of a set of coupled nonlinear partial differential equations (PDEs) and a set of coupled nonlinear ordinary differential equations (ODEs). To solve the time-dependent PDE system we use second order implicit Euler method by finite volume discretization. The ODE system is stiff and is solved by an ODE solver VODE using backward differencing formulation (BDF). Findings from this study have implications with regard to regulation of heparin-binding growth factors in circulation.
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Campos, Luiza Cintra. "Modelling and simulation of the biological and physical processes of slow sand filtration." Thesis, University College London (University of London), 2002. http://discovery.ucl.ac.uk/43778/.
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Slow sand filtration (SSF) is the earliest form of engineered potable water treatment and remains one of the most efficient processes for improving the physical, biological and chemical quality of water. However, whilst widely used throughout the world, knowledge of the filtration mechanisms remains limited. This is important in understanding and managing the processes that are responsible for gradually blocking the filter reducing its operational life and filtration efficiency. The objective of this thesis was to develop a mechanistic simulation model of the fundamental physico-chemical and biological processes responsible for the filtration mechanisms operating in slow sand filters. The model solves a set of equations describing schmutzdecke development above the sand and microbial biomass growth within the sand. The model assumes that the schmutzdecke layer contributes to the water purification process and its growth is described as linear function in relation to time. The dynamic interactions between the principal groups of microorganisms including: algae, bacteria and protozoa, were modelled using Monod-type kinetic equations. The filtration performance of the filter media was defined in the model by the removal of particulate material from water and was represented by a combination of headloss and filtration coefficient functions. The model was calibrated and verified using data from full and pilot plant-scale SSF operated by Thames Water Utilities Ltd. Simulation results showed that interstitial biomass was the smallest part of the bulk specific deposit in both covered and uncovered filters. However, microbial dynamics played an important role in the filtration performance. Schmutzdecke development had a major influence on the operation of uncovered filters and was responsible for the significant increase of headloss observed during operation. The model provides a representation of the fundamental nature of SSF processes and could form the basis of an operational management system to optimise SSF.
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Vera-Licona, Martha Paola. "Algorithms for modeling and simulation of biological systems; applications to gene regulatory networks." Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/28073.
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Systems biology is an emergent field focused on developing a system-level understanding of biological systems. In the last decade advances in genomics, transcriptomics and proteomics have gathered a remarkable amount data enabling the possibility of a system-level analysis to be grounded at a molecular level. The reverse-engineering of biochemical networks from experimental data has become a central focus in systems biology. A variety of methods have been proposed for the study and identification of the systemâ s structure and/or dynamics.
The objective of this dissertation is to introduce and propose solutions to some of the challenges inherent in reverse-engineering of biological systems.
First, previously developed reverse engineering algorithms are studied and compared using data from a simulated network. This study draws attention to the necessity for a uniform benchmark that enables an ob jective comparison and performance evaluation of reverse engineering methods.
Since several reverse-engineering algorithms require discrete data as input (e.g. dynamic Bayesian network methods, Boolean networks), discretization methods are being used for this purpose. Through a comparison of the performance of two network inference algorithms that use discrete data (from several different discretization methods) in this work, it has been shown that data discretization is an important step in applying network inference methods to experimental data.
Next, a reverse-engineering algorithm is proposed within the framework of polynomial dynamical systems over finite fields. This algorithm is built for the identification of the underlying network structure and dynamics; it uses as input gene expression data and, when available, a priori knowledge of the system. An evolutionary algorithm is used as the heuristic search method for an exploration of the solution space. Computational algebra tools delimit the search space, enabling also a description of model complexity. The performance and robustness of the algorithm are explored via an artificial network of the segment polarity genes in the D. melanogaster.
Once a mathematical model has been built, it can be used to run simulations of the biological system under study. Comparison of simulated dynamics with experimental measurements can help refine the model or provide insight into qualitative properties of the systems dynamical behavior. Within this work, we propose an efficient algorithm to describe the phase space, in particular to compute the number and length of all limit cycles of linear systems over a general finite field.
This research has been partially supported by NIH Grant Nr. RO1GM068947-01.Ph. D.
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Xanthopoulos, Georgios. "Simulation of heat and mass transfer and biological changes in a grain store." Thesis, University of Newcastle upon Tyne, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394568.
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Ochoa, Cesar G. "Using arena simulation software to predict hospital capabilities during CBRNE events." To access this resource online via ProQuest Dissertations and Theses @ UTEP, 2007. http://0-proquest.umi.com.lib.utep.edu/login?COPT=REJTPTU0YmImSU5UPTAmVkVSPTI=&clientId=2515.
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Lee, Erik Ryan. "SET-WET: A Wetland Simulation Model to Optimize NPS Pollution Control." Thesis, Virginia Tech, 1999. http://hdl.handle.net/10919/35222.
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A dynamic, compartmental, continuously stirred tank reactor, simulation model (SET-WET) was developed for design and evaluation of constructed wetlands in order to optimize non-point source (NPS) pollution control measures. The model simulates the hydrologic, nitrogen, carbon, dissolved oxygen, bacteria, vegetative, phosphorous and sediment cycles of a wetland system. Written in Fortran 77, SET-WET models both free water surface (FWS) and sub-surface flow (SSF) wetlands and is designed in a modular manner which gives the user the flexibility to decide which cycles and processes to model. SET-WET differs from many existing wetland models in that it uses a system's approach, and limits the assumptions made concerning the interactions of the various nutrient cycles in a wetland system. It accounts for carbon and nitrogen interactions, as well as effect of oxygen levels upon microbial growth. It also directly links microbial growth and death to the consumption and transformations of nutrients in the wetland system. Many previous models have accounted for these interactions with zero and first order rate equations that assume rates are dependent only on initial concentrations. The SET-WET model is intended to be utilized with an existing NPS hydrologic simulation model, such as ANSWERS or BASINS, but may also be used in situations where measured input data to the wetland are available.
The model was calibrated and validated using limited data collected at Benton, Kentucky. A non-parametric statistical analysis of the model's output indicated eight out of nine examined outflow predictions were not statistically different from the measured observations. Linear regression analysis showed that six out of nine examined parameters were statistically similar, and that within the expected operating range, all of the examined outflow parameters (9) were within the 95% confidence intervals of the regression lines. A sensitivity analysis showed the most significant input parameters to the model were those which directly affect bacterial growth and oxygen uptake and movement. The model was applied to a subwatershed in the Nomini Creek watershed located in Virginia. Two year simulations were completed for five separate wetland designs, with reductions in percentage of BOD5 (4%-45%), TSS (85%-100%), total nitrogen (42%-56%), and total phosphorous (38%-57%) comparable to levels reported by previous research.Master of Science
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Wu, Chih-Sung. "Designing tangible tabletop interactions to support the fitting process in modeling biological systems." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/50128.
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This thesis aims to explore how to physically interact with computational models on an interactive tabletop display. The research began with the design and implementation of several prototype systems. The research of the prototype systems showed that tangible interactions on interactive tabletops have the potential to be more effective on some tasks than traditional interfaces that use screen displays, keyboards and mice. The prototype work shaped the research to focus on the effectiveness of adopting tangible interactions on interactive tabletops. To substantiate the thesis claims, this thesis develops an interactive tabletop application, Pathways, to support the fitting process in modeling biological systems. Pathways supports the concepts of Tangible User Interfaces (TUIs) and tabletop visualizations. It realizes real-time simulation of models and provides comparisons of simulation results with experimental data on the tabletop. It also visualizes the simulation of the model with animations. In addition to that, Pathways introduces a new visualization to help systems biologists quickly compare the simulation results. This thesis provides the quantitative and qualitative evaluation results of Pathways. The evidence showed that using tangible interactions to control numerical values is practical. The results also showed that in experimental conditions users achieved better fitting results and faster fitting results on Pathways than the control group, which used the systems biologists' current tools. The results further suggested that it is possible to recruit non-experts to perform the fitting tasks that are usually done by professional systems biologists.
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You, Tao. "Modelling and simulation of amino acid starvation responses in yeast Saccharomyces cerevisiae." Thesis, Available from the University of Aberdeen Library and Historic Collections Digital Resources. Restricted: no access until June 2, 2014, 2009. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?application=DIGITOOL-3&owner=resourcediscovery&custom_att_2=simple_viewer&pid=25979.
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Adil-Smith, Iran. "Structural analysis of thyroid hormones by EXAFS and molecular simulation : biological effects of '1'2'5I." Thesis, Brunel University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362488.
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