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Relevant bibliographies by topics / Protein simulation / Dissertations / Theses

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Dissertations / Theses on the topic 'Protein simulation'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Park, Changmoon Goddard William A. "Protein design and simulation Part I. Protein design. Part II. Protein simulation /." Diss., Pasadena, Calif. : California Institute of Technology, 1993. http://resolver.caltech.edu/CaltechTHESIS:11112009-114142428.

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Thesis (Ph. D.)--California Institute of Technology, 1993. UM #93-25,374.<br>Advisor names found in the Acknowledgements pages of the thesis. Title from home page. Viewed 01/15/2010. Includes bibliographical references.

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2

Flöck, Dagmar. "Protein-protein docking and Brownian dynamics simulation of electron transfer proteins." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969418736.

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3

Baskaran, Preetisri. "Computer simulation of protein superabsorbents." Thesis, Högskolan i Borås, Institutionen Ingenjörshögskolan, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:hb:diva-20927.

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The aim of this project is to develop superabsorbents from proteins in our case it is azygomycetes fungus, where the process of this fungus is studied experimentally in Universityof Borås. As a result of this experiment by-products of protein are produced and this project isabout the study to make use of such proteins as superabsorbing materials.The water absorbing capacity is computationally studied using Gibbs ensemble Monte Carlo(GEMC) simulations to determine the absorbing properties and to effectively improve theabsorbing capacity by using specific treatments, where this project focuses i

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4

Mellor, Brett Lee. "Liquid Dielectric Spectroscopy and Protein Simulation." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3661.

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Protein electrical properties have been studied using dielectric relaxation measurements throughout the past century. These measurements have advanced both the theory and practice of liquid dielectric spectroscopy and have contributed to understanding of protein structure and function. In this dissertation, the relationship between permittivity measurements and underlying molecular mechanisms is explored. Also presented is a method to take molecular structures from the Protein Data Bank and subsequently estimate the charge distribution and dielectric relaxation properties of the proteins in so

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5

Naser, Md Abu. "Molecular dynamics simulation of protein adsorption." Thesis, Heriot-Watt University, 2008. http://hdl.handle.net/10399/2187.

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6

Mitchell, Felicity. "Modelling protein flexibility using molecular simulation methods." Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525167.

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7

Dantas, Gautam. "In silico protein evolution by intelligent design : creating new and improved protein structures /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9236.

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8

Badcoe, Ian Geoffrey. "Computer studies of protein folding." Thesis, University of Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385585.

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9

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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10

Carpenter, Timothy S. "Simulation studies of the influenza M2 channel protein." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504314.

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11

Fischer, Bernhard Karl. "High throughput simulation methods for protein ligand docking." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/985070374/34.

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12

Wei, Shuai. "Protein-Surface Interactions with Coarse-Grain Simulation Methods." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3943.

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The interaction of proteins with surfaces is a major process involved in protein microarrays. Understanding protein-surface interactions is key to improving the performance of protein microarrays, but current understanding of the behavior of proteins on surfaces is lacking. Prevailing theories on the subject, which suggest that proteins should be stabilized when tethered to surfaces, do not explain the experimentally observed fact that proteins are often denatured on surfaces. This document outlines several studies done to develop a model which is capable of predicting the stabilization and de

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13

Richter, Barbara. "Combining simulation and experiment to extract protein dynamics." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612301.

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14

Bruce, Neil John. "Investigating protein conformational change via molecular dynamics simulation." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/investigating-protein-conformational-change-via-molecular-dynamics-simulation(17145939-f643-4b23-bbb9-029cf5489c15).html.

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Accumulation and aggregation of the 42-residue amyloid-[beta] (A[beta]) protein fragment, which originates from the cleavage of amyloid precursor protein by beta and gamma secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the A[beta] sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of A[beta] and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LP

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15

Ho, Sylvanna Sze Wan. "Molecular dynamics simulation studies of membrane protein biosensor components." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442469.

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16

Jiao, Yuanfang. "The development of accurate force fields for protein simulation." Diss., Kansas State University, 2012. http://hdl.handle.net/2097/13946.

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Doctor of Philosophy<br>Department of Chemistry<br>Paul E. Smith<br>Computer simulations have provided a wealth of information concerning a wide range of systems. The precision of computer simulation results depends on the degree of sampling (time scales) achieved, while the accuracy of the results (given sufficient sampling) depends on the quality of force field used. A force field provides a description of the energy for a system of interest. Recently, we have been developing a Kirkwood Buff (KB) force field for molecular dynamics simulations of biological systems. This force field is based

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17

Taylor, Richard David. "Novel simulation methods for flexible docking." Thesis, University of Southampton, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368873.

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18

Vagedes, Peter. "Simulation of enzyme reactions the influence of protonation on catalysis and on protein protein association /." [S.l. : s.n.], 2001. http://www.diss.fu-berlin.de/2001/49/index.html.

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19

Soni, Ravi. "Computer-aided modeling and simulation of molecular systems and protein secondary structure prediction." Ohio : Ohio University, 1993. http://www.ohiolink.edu/etd/view.cgi?ohiou1176235817.

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20

Huang, Zheng. "Computer-aided modeling and simulation of molecular systems and protein (WT-bGH) structure minimization." Ohio : Ohio University, 1995. http://www.ohiolink.edu/etd/view.cgi?ohiou1179347691.

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21

Rabenstein, Björn. "Monte Carlo methods for simulation of protein folding and titration." [S.l. : s.n.], 2000. http://www.diss.fu-berlin.de/2000/124/index.html.

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22

Marchut, Alexander Joseph. "Simulation of Polyglutamine Aggregation With An Intermediate Resolution Protein Model." NCSU, 2006. http://www.lib.ncsu.edu/theses/available/etd-01062006-142134/.

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The pathological manifestation of nine hereditary neurodegenerative diseases including Huntington's disease is the presence within the brain of aggregates of disease-specific proteins that contain polyglutamine tracts longer than a critical length. The molecular level mechanisms by which these proteins aggregate are still unclear. In an effort to shed light on this important phenomenon, we are investigating the aggregation of model fibril-forming peptides using molecular-level computer simulation. A simplified model of polyglutamine, the protein that is known to form fibrils (ordered aggregate

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23

Hopkins, Sawyer S. "Examination of nonlocal screening effects on protein crystallization." Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35376.

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Master of Science<br>Department of Physics<br>Jeremy Schmit<br>Over twenty percent of amino acids are ionized under biological conditions, and the subsequent electrostatic interactions have substantial effect on protein crystallization, binding, catalyzation, and recognition. These electrostatics along with other intermolecular forces create a delicate balancing act of repulsive and attractive forces. This thesis explores the effects of electrostatics on the formation of dense ordered structures. In dense protein aggregates the repulsive electrostatics are dominated by the entropic cost of co

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24

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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25

Pinska, Adrianna. "Addition of flexible linkers to GPU-accelerated coarse-grained simulations of protein-protein docking." Thesis, Faculty of Science, 2019. http://pubs.cs.uct.ac.za/archive/00001307/.

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Multiprotein complexes are responsible for many vital cellular functions, and understanding their formation has many applications in medical research. Computer simulation has become a valuable tool in the study of biochemical processes, but simulation of large molecular structures such as proteins on a useful scale is computationally expensive. A compromise must be made between the level of detail at which a simulation can be performed, the size of the structures which can be modelled and the time scale of the simulation. Techniques which can be used to reduce the cost of such simulations incl

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26

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.

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Chemistry<br>Ph.D.<br>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 structur

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27

Fischer, Bernhard Karl [Verfasser]. "High throughput simulation methods for protein ligand docking / Bernhard Karl Fischer." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/985070374/34.

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28

Duan, Jianxin. "Protein folding, stability and recognition /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-098-2/.

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29

Gunnerson, Kim Noreen. "Computer simulation studies of molecular interactions by application of classical molecular dynamics /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/8668.

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30

Engström, Mathias, and Erik Olby. "Evaluating Response Images From Protein Quantification." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416108.

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Gyros Protein Technologies develops instruments for automated immunoassays. Fluorescent antibodies are added to samples and excited with a laser. This results in a 16-bit image where the intensity is correlated to concentration of bound antibody. Artefacts may appear on the images due to dust, fibers or other problems, which affect the quantification. This project seeks to automatically detect such artifacts by classifying the images as good or bad using Deep Convolutional Neural Networks (DCNNs). To augment the dataset a simulation approach is used and a simulation program is developed that g

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31

Kolmodin, Karin. "Computer Simulation of Protein Tyrosine Phosphatase Reaction Mechanisms and Dihydrofolate Reductase Inhibition." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : [Univ.-bibl. [distributör]], 2001. http://publications.uu.se/theses/91-554-5148-9/.

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32

Mistry, Shailesh Lallubhai. "Mathematical modelling and computer simulation of aqueous two-phase continuous protein extraction." Thesis, University of Reading, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327153.

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33

Loganathan, Narasimhan. "Adsorption of protein bound uremic toxins in zeolites : a molecular simulation study." Aix-Marseille 1, 2010. http://www.theses.fr/2010AIX11120.

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Le paracrésol sous sa forme libre est une toxine urémique causant des dommages cellulaires très importants qui peuvent conduire E1 des arrêts cardiaques. Le traitement de l'insuffisance rénale repose principalement sur l‘utilisation de la dialyse. Il s'avère cependant que ce procédé ne permet pas une élimination efficace de la toxine. Une alternative serait d'utiliser des zéolithes afin de piéger la molécule pour ensuite l'éliminer. Ce travail de thèse présente une étude théorique de l‘adsorption du paracrésol et de l'eau dans les zéolithes silicalite-1 et faujasites NaY. Les simulations ont é

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34

Madeleine, Noelly. "Recherche d'inhibiteurs de l'interaction Lutheran-Laminine par des techniques de modélisation et de simulation moléculaires." Thesis, La Réunion, 2017. http://www.theses.fr/2017LARE0054/document.

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La drépanocytose est une maladie génétique qui se caractérise par des globules rouges en forme de faucille. Chez les personnes atteintes de drépanocytose, ces globules rouges (GR) adhèrent à l’endothélium vasculaire et provoquent ainsi une vaso-occlusion. Ce phénomène s’explique par la surexpression de la protéine Lutheran (Lu) à la surface des globules rouges falciformes qui se lie fortement à la Laminine (Ln) 511/521 exprimée par l’endothélium vasculaire enflammé. Le but de cette étude est d’identifier un inhibiteur d’interaction protéine-protéine (PPI) qui possède une forte probabilité de l

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35

Chen, Wei. "Molecular dynamics simulations of binding, unfolding, and global conformational changes of signaling and adhesion molecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28118.

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Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.

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36

Sawada, Ryusuke, Runcong Ke, Toshiyuki Tsuji, Masashi Sonoyama, and Shigeki Mitaku. "Ratio of membrane proteins in total proteomes of prokaryota." THE BIOPHYSICAL SOCIETY OF JAPAN, 2007. http://hdl.handle.net/2237/9298.

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37

Hirst-Dunton, Thomas Alexander. "Using molecular simulations to parameterize discrete models of protein movement in the membrane." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:893568e9-696f-47e7-8495-59ecfb810459.

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The work presented in this thesis centres on the development of a work-flow in which coarse-grained molecular dynamics (MD) simulations of a planar phospholipid bilayer, containing membrane proteins, is used to parameterize a larger-scale simplified bilayer model. Using this work-flow, repeat simulations and simulations of larger systems are possible, better enabling the calculation of bulk statistics for the system. The larger-scale simulations can be run on commercial hardware, once the initial parameterization has been performed. In the simplified representation, each protein was initially

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38

Wei, Aoran. "Adsorption of protein on a au surface studied by all-atom atomistic simulations." The Journal of Physical Chemistry C, 2016. http://hdl.handle.net/1993/31807.

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In this work, the adsorption of protein on Au surface coated by self-assembled monolayers (SAMs) of alkanethiol chains is studied by molecular dynamics simulations with an all-atom model. Particularly, a more realistic embedded-atom method potential has been used to characterize the Au-Au interactions in the system as compared to previous studies. With this all-atom model, many experimental observations have been reproduced from the simulations. It is found that the SAMs have the lowest adsorption energy on Au (111) surface where the alkanethiol chains form a well-ordered (√3x√3) R30° triangul

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39

Ullmann, G. Matthias. "Simulation and analysis of docking and molecular dynamics of electron transfer protein complexes." [S.l. : s.n.], 1998. http://darwin.inf.fu-berlin.de/1998/23/index.html.

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40

Javidialesaadi, Abdolreza. "Computer Simulations of Titin I27 and Knotted Protein Remodeling by Clp Biological Nanomachines." University of Cincinnati / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1523628577990709.

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41

Budi, Bunarta Hendra (Akin), and akin budi@rmit edu au. "On the effects of external stresses on protein conformation." RMIT University. School of Applied Sciences, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20061116.123431.

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The use of electromagnetic devices such as microwave ovens and mobile phones has certainly brought convenience to our lives. At the same time, the proliferation of said devices has increased public awareness of the potential health hazards. It is generally assumed that there is little or no risk associated with the use of electromagnetic devices, based on the small amount of power associated with those devices. However, case studies on animals indicate that the risk cannot be entirely ruled out. It has long been known that proteins are sensitive to stress, arising from various sources suc

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42

Beugelsdijk, Alex. "Understanding amyloid fibril growth through theory and simulation." Thesis, Kansas State University, 2014. http://hdl.handle.net/2097/18117.

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Master of Science<br>Biochemistry and Molecular Biophysics<br>Jianhan Chen<br>Proteins are fundamental building blocks of life in an organism, and to function properly, they must adopt an appropriate three-dimensional conformation or conformational ensemble. In protein aggregation diseases, proteins misfold to incorrect structures that allow them to join together and form aggregates. A wide variety of proteins are involved in these aggregation diseases and there are multiple theories of their disease mechanism. However, a common theme is that they aggregate into filamentous structures. Therapi

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43

Karjalainen, Eeva-Liisa. "The choreography of protein vibrations : Improved methods of observing and simulating the infrared absorption of proteins." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-60415.

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The work presented in this thesis has striven toward improving the capability to study proteins using infrared (IR) spectroscopy. This includes development of new and improved experimental and theoretical methods to selectively observe and simulate protein vibrations. A new experimental method of utilising adenylate kinase and apyrase as helper enzymes to alter the nucleotide composition and to perform isotope exchange in IR samples was developed. This method enhances the capability of IR spectroscopy by enabling increased duration of measurement time, making experiments more repeatable and al

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44

Merz, Dale R. Jr. "Molecular simulations uncover the nanomechanics of heat shock protein (70 kDa) & Indentation simulations of microtubules reveal katanin severing insights." University of Cincinnati / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1583154342504106.

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45

Druart, Karen. "Défis algorithmiques pour les simulations biomoléculaires et la conception de protéines." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLX080/document.

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Le dessin computationnel de protéine, ou CPD, est une technique qui permet de modifier les protéines pour leur conférer de nouvelles propriétés, en exploitant leurs structures 3D et une modélisation moléculaire. Pour rendre la méthode de plus en plus prédictive, les modèles employés doivent constamment progresser. Dans cette thèse, nous avons abordé le problème de la représentation explicite de la flexibilité du squelette protéique. Nous avons développé une méthode de dessin "multi-états", qui se base sur une bibliothèque discrète de conformations du squelette, établie à l'avance. Dans un cont

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46

Danielsson, Emma. "Towards a better understanding of protein structures : assessing the sulfur bridge in Cystine through photofragmentation." Thesis, Uppsala universitet, Materialteori, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416437.

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This work aims to investigate the fragmentation of an ionized Cystine molecule, as simulated in the framework of molecular dynamics and quantum mechanics. Cystine is viewed as a model system for larger sets of peptides -- ultimately contributing to the understanding of protein photofragmentation, which is crucial for determining the structure of a protein using new methods. The analysis software was written in Python, partly in conjunction with another student. The photofragmentation of the molecule is analyzed in terms of bond integrity versus time and mass-to-charge ratios for the resulting

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47

Mauk, Andrew W. "A new modeling protocol for G-protein coupled receptors : molecular simulation of phospholipid assemblies." Thesis, Georgia Institute of Technology, 1996. http://hdl.handle.net/1853/11033.

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48

Hosseini, Seyed Ali. "Modeling protein dynamics and protein-drug interactions with Monte Carlo based techniques." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/294730.

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A complete understanding of complex formation between proteins and ligands, a crucial matter for pharmacology and, more in general, in biomedicine, requires a detailed knowledge of their static and dynamic atomic interactions. The main objective of this thesis is to test recent developments in conformational sampling techniques in providing such a dynamical view. We aim at developing new protocols and methods for such a study. Moreover, we want to show how its application can aid in addressing existing problems in the biophysics of protein ligand interactions. Moreover, we apply and refine nov

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49

Dibenedetto, Domenica [Verfasser]. "Predicting conformational ensembles of the intrinsically disordered protein alpha-synuclein via molecular simulation / Domenica Dibenedetto." Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2014. http://d-nb.info/1052303420/34.

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50

Weber, Jeffrey. "Coarse Grained Monte Carlo Simulation of the Self-Assembly of the HIV-1 Capsid Protein." Honors in the Major Thesis, University of Central Florida, 2014. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1654.

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In this study, a Monte Carlo simulation was designed to observe the self-assembly of the HIV-1 capsid protein. The simulation allowed a coarse grained model of the capsid protein with defined interaction sites to move freely in three dimensions using the Metropolis criterion. Observations were made as to which parameters affected the assembly the process. The ways in which the assembly were affected were also noted. It was found that proper dimerization of the capsid protein was necessary in order for the lattice to form properly. It was also found that a strong trimeric interface could be res

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