Дисертації з теми "Biomolecular systems"
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Brampton, Christopher. "Forces in biomolecular systems." Thesis, University of Nottingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.429077.
Повний текст джерелаShah, Rushina(Rushina Jaidip). "Input-output biomolecular systems." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/129016.
Повний текст джерелаCataloged from student-submitted PDF of thesis.
Includes bibliographical references (pages 194-206).
The ability of cells to sense and respond to their environment is encoded in biomolecular reaction networks, in which information travels through processes such as production, modification, and removal of biomolecules. These reaction networks can be modeled as input-output systems, where the input, state and output variables are concentrations of the biomolecules involved in these reactions. Tools from non-linear dynamics and control theory can be leveraged to analyze and control these systems. In this thesis, we study two key biomolecular networks. In part 1 of this thesis, we study the input-output behavior of signaling systems, which are responsible for the transmission of information both from outside and from within the cells, and are ubiquitous, playing a role in cell cycle progression, survival, growth, differentiation and apoptosis. A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion.
A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. In this work, we identify signaling architectures that can overcome retroactivity, allowing unidirectional transmission of signals. These findings can be used to decompose natural signal transduction networks into modules, and at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design. In part 2 of this thesis, we design inputs to trigger a transition of cell-fate from one cell type to another. The process of cell-fate decision-making is often modeled by means of multistable gene regulatory networks, where different stable steady states represent distinct cell phenotypes. In this thesis, we provide theoretical results that guide the selection of inputs that trigger a transition, i.e., reprogram the network, to a desired stable steady state.
Our results depend uniquely on the structure of the network and are independent of specific parameter values. We demonstrate these results by means of several examples, including models of the extended network controlling stem-cell maintenance and differentiation.
by Rushina Shah.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Mechanical Engineering
Xin, W. (Weidong). "Continuum electrostatics of biomolecular systems." Doctoral thesis, University of Oulu, 2008. http://urn.fi/urn:isbn:9789514287602.
Повний текст джерелаJanosi, Lorant. "Multiscale modeling of biomolecular systems." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4801.
Повний текст джерелаThe entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on February 14, 2008) Vita. Includes bibliographical references.
Desai, Amruta. "Design support for biomolecular systems." Cincinnati, Ohio : University of Cincinnati, 2010. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1265986863.
Повний текст джерелаAdvisor: Carla Purdy. Title from electronic thesis title page (viewed Apr. 19, 2010). Includes abstract. Keywords: Biological pathways; weighted gate; BMDL; pyrimidine. Includes bibliographical references.
Diez, Stefan, and Jonathon Howard. "Nanotechnological applications of biomolecular motor systems." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1223724473713-41365.
Повний текст джерелаRecent advances in understanding how biomolecular motors work have raised the possibility that they might find applications as nanomachines. For example, they could be used as molecule- sized robots that work in molecular factories where small, but intricate structures are made on tiny assembly lines, that construct networks of molecular conductors and transistors for use as electrical circuits, or that continually patrol inside “adaptive” materials and repair them when necessary. Thus biomolecular motors could form the basis of bottom-up approaches for constructing, active structuring and maintenance at the nanometer scale
Dey, Abhishek. "Modeling and identification of biomolecular systems." Thesis, IIT Delhi, 2019. http://eprint.iitd.ac.in:80//handle/2074/8121.
Повний текст джерелаTyka, Michael. "Absolute free energy calculations for biomolecular systems." Thesis, University of Bristol, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439666.
Повний текст джерелаShu, Wenmiao. "Biomolecular sensing and actuation using microcantilever systems." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612828.
Повний текст джерелаLickert, Benjamin [Verfasser], and Gerhard [Akademischer Betreuer] Stock. "Data-based Langevin modeling of biomolecular systems." Freiburg : Universität, 2021. http://d-nb.info/1241962669/34.
Повний текст джерелаBaker, Nathan Andrew. "Mathematical and computational modeling of biomolecular systems /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3007138.
Повний текст джерелаvon, Hansen Yann [Verfasser]. "Stochastic Dynamics in Biomolecular Systems / Yann von Hansen." Berlin : Freie Universität Berlin, 2014. http://d-nb.info/1069165948/34.
Повний текст джерелаClark, Kendal W. "STM Study of Molecular and Biomolecular Electronic Systems." Ohio University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1282363151.
Повний текст джерелаO'Reilly, E. J. "Quantum traits in the dynamics of biomolecular systems." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1451070/.
Повний текст джерелаMertiri, Alket. "Mid-infrared photothermal hyperspectral imaging of biomolecular systems." Thesis, Boston University, 2014. https://hdl.handle.net/2144/12952.
Повний текст джерелаThe development of novel techniques in spectroscopy and microscopy that are label-free, contactless and accessible is useful among many scientific disciplines, ranging from Materials Science to Biomedical Engineering. Hyperspectral photothermal imaging using vibrational spectroscopy promises to be a new tool in the arsenal for analysis and characterization of materials. This technique can be used for understanding structural composition of a material that is advantageous to the materials scientist. A combination of microscopy and spectroscopy is also beneficial to the biologist or pathologist that analyzes a complex sample with rich morphology. Photothermal hyperspectral microscopy is a label-free nondestructive method that utilizes specific vibrational bands of a molecule giving spectral information to an image. The method is based on changes in the thermal state, and the associated change in the refractive index of the sample as it is irradiated with mid-infrared light. Photothermal microscopy has rapidly emerged as one of the most sensitive label-free optical spectroscopic methods, rivaling current well-established methods based on fluorescence. The method has been used to image single non-fluorescent molecules in room temperature and to directly characterize biological features such as mitochondria and red blood cells. Despite great breakthroughs in the visible regime, the method has not been explored in the mid-infrared regime where most of the biological molecules have characteristic vibrational modes that constitute an intrinsic molecular "fingerprint" . This thesis presents the development of a new technique to measure the linear and nonlinear mid-infrared photothermal response induced by tunable high power lasers such as Quantum Cascade Lasers (QCLs). Photothermal response can be measured in pump-probe heterodyne detection, using short wavelength visible lasers and compact fiber lasers as a probe. This allows for direct detection of the fingerprint mid-infrared vibrational modes through ultrasensitive photodetectors. Integrated into a mid-infrared microscope, the system facilitates the acquisition of spectra and images on condensed phase samples. Photothermal heterodyne mid-infrared hyperspectral vibrational technique is used to image biological samples such as bird brain and other biomolecules First photothermal images on specially designed plasmonic metamaterials, designed to either enhance or suppress a selected mid-infrared vibrational normal mode, are demonstrated. Plasmonic metamaterials can be engineered using electron beam lithography for functional studies on biomolecules enhancing selected vibrational infrared resonances. This study takes advantage of the strong interaction between light and matter and investigates properties of the material that are difficult to detect through conventional spectroscopic methods. The new technique has the ability to advance studies in many fields, as it is applicable to different types of materials, non-destructive, accessible and inexpensive.
Viveca, Lindahl. "Optimizing sampling of important events in complex biomolecular systems." Doctoral thesis, KTH, Fysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-217837.
Повний текст джерелаQC 20171117
Prévot, Martine. "Biomolecular simulations: structure, thermodynamics and dynamics of biological systems." Doctoral thesis, Universite Libre de Bruxelles, 2002. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/211440.
Повний текст джерелаAlapan, Yunus. "MICROFABRICATED SYSTEMS INTEGRATED WITH BIOMOLECULAR PROBES FOR CELL MECHANICS." Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1466014738.
Повний текст джерелаVanMetre, Holly Sue Morris. "Individual submicrometer particles and biomolecular systems studied on the nanoscale." Diss., University of Iowa, 2016. https://ir.uiowa.edu/etd/3207.
Повний текст джерелаMelli, Mauro. "Mechanical resonating devices and their applications in biomolecular studies." Doctoral thesis, SISSA, 2010. http://hdl.handle.net/20.500.11767/4646.
Повний текст джерелаTorun, Hamdi. "Micromachined membrane-based active probes for biomolecular force spectroscopy." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/39638.
Повний текст джерелаKummer, Kurt. "Investigation of structural properties in biomolecular systems using synchrotron-based spectroscopies." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-39506.
Повний текст джерелаKlassische Festkörpertechniken zur Strukturuntersuchung, wie Streu- oder Mikroskopiemethoden, können häufig nicht auf Biomolekülsysteme angewandt werden, zumindest nicht ohne spezielle Postpräparation, die die ursprünglichen Eigenschaften dieser Systeme oft verfälscht. In dieser Arbeit soll untersucht werden, inwieweit Röntgenspektroskopien basierend auf Synchrotronstrahlung einen alternativen Zugang zu Struktureigenschaften solcher Systeme bieten. Dazu wurden drei Systeme exemplarisch untersucht, jeweils mit Schwerpunkt auf einen anderen Aspekt und charakteristischen Längenbereich. Für selbstorganisierende DNA-Alkanthiol-Schichten, sogenannte DNA-Chips, wurde nach eine Weg gesucht, ihre strukturelle Zusammensetzung auf der mesoskopischen Ebene vieler tausend Moleküle zu bestimmen und kontrolliert zu modifizieren. Metallisierte Proteinstrukturen wurden auf Einzelmolekül- bzw. submolekularer Ebene untersucht, mit dem Ziel, die Orte der Metallanlagerung innerhalb des Proteins und die zugrundeliegenden Wechselwirkungsmechanismen zu identifizieren. Die unterste strukturelle Ebene, der Bereich einzelne Bindungen und Molekülorbitale, wurde adressiert am Beispiel der pi*peptide Orbitale des Proteinrückrats. Dafür wurde eine Methode zur Kartographierung einzelner Orbitale anhand von Röntgenabsorptionseigentschaften herausgearbeitet und praktisch getestet. In allen drei Fällen konnten Röntgenspektroskopien die nötigen Informationen liefern und damit ihr Potential für Strukturuntersuchungen in weicher Materie unter Beweis stellen
Nakajima, Nobuyuki. "A multicanonical molecular dynamics method and its applications to biomolecular systems." 京都大学 (Kyoto University), 2000. http://hdl.handle.net/2433/181460.
Повний текст джерелаSchaudinnus, Norbert [Verfasser], and Gerhard [Akademischer Betreuer] Stock. "Stochastic modeling of biomolecular systems using the data-driven Langevin equation." Freiburg : Universität, 2015. http://d-nb.info/1122646887/34.
Повний текст джерелаSmart, Jason. "The application of contimuum electrostatics and diffusional models to biomolecular systems /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9906489.
Повний текст джерелаBörjesson, Ulf Börjesson Ulf Erik. "Electrostatic interactions in computer simulations of biomolecular systems : influence of system size, solvation, and titration /." [S.l.] : [s.n.], 2004. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=15454.
Повний текст джерелаWeggler, Sophie [Verfasser], and Andreas [Akademischer Betreuer] Hildebrandt. "Correlation induced electrostatic effects in biomolecular systems / Sophie Weggler. Betreuer: Andreas Hildebrandt." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2011. http://d-nb.info/105109514X/34.
Повний текст джерелаSeibert, Johann Jakob [Verfasser]. "Computation of Electronic Excitation Spectra of Large Biomolecular Systems / Johann Jakob Seibert." Bonn : Universitäts- und Landesbibliothek Bonn, 2020. http://d-nb.info/1224270584/34.
Повний текст джерелаHerath, Narmada Kumari. "Model order reduction for stochastic models of biomolecular systems with time-scale separation." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118083.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references (pages 177-183).
Biomolecular systems often involve reactions that take place on different time-scales, giving rise to 'slow' and 'fast' system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In deterministic systems, methods to obtain such reduced-order models are well defined by the singular perturbation or averaging techniques. However, model reduction of stochastic systems remains an ongoing area of research. In particular, existing model reduction methods for stochastic models of biomolecular systems lack rigorous error quantifications between the full and reduced dynamics. Furthermore, they only provide approximations for the slow variable dynamics, making the application of such methods to biomolecular systems difficult since the variables of interest are typically mixed (i.e., they encompass both fast and slow variables). In this thesis, we consider biomolecular systems modeled using the chemical Langevin equation (CLE) and the Linear Noise Approximation (LNA). Specifically, we consider biomolecular systems with linear propensity functions modeled by the CLE and systems with arbitrary propensity functions modeled by the LNA. For these systems, we obtain reduced-order models that approximate both the slow and fast variables under time-scale separation conditions. In particular, with suitable assumptions, we prove that the moments of the reduced-order models converge to those of the full systems as the time-scale separation becomes large. Our results further provide a rigorous justification for the accuracy of the stochastic total quasi-steady state approximation (tQSSA). We then consider two applications of these reduced-order models. In the first application, we analyze the trade-offs between modularity and signal noise in biomolecular networks. In the second application, we consider the application of the reduced-order LNA developed in this work to obtain reduced-order stochastic models for gene-regulatory networks.
by Narmada Kumari Herath.
Ph. D.
Zanoli, Laura Maria. "Ultrasensitive methods for the detection of biomolecular systems at the micro/nano scale." Doctoral thesis, Università di Catania, 2012. http://hdl.handle.net/10761/976.
Повний текст джерелаDoro, F. "COMPUTATIONAL MODELLING OF BIOMOLECULAR SYSTEMS: APPLICATIONS TO THE STUDY OF MOLECULAR RECOGNITION PROCESSES." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/229385.
Повний текст джерелаBörjesson, Ulf [Verfasser]. "Electrostatic interactions in computer simulations of biomolecular systems: influence of system size, solvation, and titration / Ulf Börjesson." Aachen : Shaker, 2004. http://d-nb.info/1170529933/34.
Повний текст джерелаQuantrill, Nigel Stuart Michael. "Optical fluoroassays based on substrate induced quenching." Thesis, Cranfield University, 1995. http://dspace.lib.cranfield.ac.uk/handle/1826/10428.
Повний текст джерелаMarkthaler, Daniel [Verfasser], and Niels [Akademischer Betreuer] Hansen. "Disentangling force field and sampling issues in biomolecular systems / Daniel Markthaler ; Betreuer: Niels Hansen." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2020. http://d-nb.info/1233737767/34.
Повний текст джерелаLenive, Oleg. "The role of extrinsic noise in biomolecular information processing systems : an in silico analysis." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/31575.
Повний текст джерелаTauer, Anthony Philip. "Theoretical Investigations of Pi-Pi and Sulfur-Pi Interactions and their Roles in Biomolecular Systems." Thesis, Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/7573.
Повний текст джерелаFowler, Philip William. "Qualitative and quantitative aspects of biomolecular systems revealed by large scale and grid computing methods." Thesis, University College London (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.430877.
Повний текст джерелаMonti, Susanna. "Molecular Dynamics Studies of the Adsorption of Biomolecular Systems on Metal and Metal Oxide Surfaces." Doctoral thesis, KTH, Teoretisk kemi och biologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-198489.
Повний текст джерелаKenning, Nicole Lynn. "Spatial and temporal evolution of the photoinitiation rate in thick polymer systems." Diss., University of Iowa, 2006. http://ir.uiowa.edu/etd/76.
Повний текст джерелаBeutler, Thomas Christian. "Thermodynamic properties derived from molecular dynamics computer simulations : improved methods for the application to biomolecular systems /." [S.l.] : [s.n.], 1994. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10915.
Повний текст джерелаSchneider, Violetta Franziska Roswitha [Verfasser], and M. [Akademischer Betreuer] Elstner. "Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations / Violetta Franziska Roswitha Schneider ; Betreuer: M. Elstner." Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1168325587/34.
Повний текст джерелаCrompton, D. L. "Decoding the picosecond dynamics of aqueous biomolecular systems : through novel terahertz instrumentation and molecular dynamic simulations." Thesis, University of Essex, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.617016.
Повний текст джерелаSchneider, Violetta [Verfasser], and M. [Akademischer Betreuer] Elstner. "Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations / Violetta Franziska Roswitha Schneider ; Betreuer: M. Elstner." Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1168325587/34.
Повний текст джерелаHahn, Jaeseung. "Programmable biomolecular integration and dynamic behavior of DNA-based systems for development of biomedical nano-devices." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122213.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references.
Departing from the traditional role as a carrier of genetic information, DNA has emerged as an engineering material for construction of nano-devices. The advances in the field of DNA nanotechnology have enabled design and synthesis of DNA nanostructures of arbitrary shapes and manipulation of the nanostructures' conformations in a programmable way. DNA-based systems offer potential applications in medicine by manipulating the biological components and processes that occur at the nanometer scale. To accelerate the translation of DNA-based systems for medical applications, we identified some of the challenges that are hindering our ability to construct biomedical nano-devices and addressed these challenges through advances in both structural and dynamic DNA nanotechnology. First, we tested the stability of DNA nanostructures in biological environments to highlight the necessity of and path towards protection strategies for prolonged integrity of biomedical nano-devices. Then, we constructed a platform for robust 3D molecular integration using DNA origami technique and implemented the platform for a nanofactory capable of production of therapeutic RNA to overcome the challenges in RNA delivery. Moreover, we established a mechanism to drive DNA devices by changing temperature with prolonged dynamic behavior that was previously challenging to accomplish without special modification of DNA and/or equipment not readily available in a typical lab setting. Together, the progress made in this thesis bring us another step closer to realization of medical applications of DNA nanotechnology by focusing on the challenges in both structural and dynamic aspects of the technology.
by Jaeseung Hahn.
Ph. D. in Medical Engineering and Medical Physics
Ph.D.inMedicalEngineeringandMedicalPhysics Harvard-MIT Program in Health Sciences and Technology
FARROTTI, ANDREA. "Molecular dynamics approaches in the study of biomolecular systems of increasing complexity: peptides, proteins and membranes." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2013. http://hdl.handle.net/2108/203357.
Повний текст джерелаMujica, Martinez Cesar Augusto [Verfasser], and Michael [Akademischer Betreuer] Thorwart. "Quantum dissipative dynamics of electrons in tailored molecular systems and of excitons in biomolecular systems / Cesar Augusto Mujica Martinez. Betreuer: Michael Thorwart." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2014. http://d-nb.info/1059238004/34.
Повний текст джерелаLemke, Oliver [Verfasser]. "Theoretical Analysis of Biomolecular Systems: Computational Simulations, Core-set Markov State Models, Clustering, Molecular Docking / Oliver Lemke." Berlin : Freie Universität Berlin, 2020. http://d-nb.info/1205735461/34.
Повний текст джерелаAndrejić, Milica. "Development of Hybrid QM/QM Local Correlation Methods for the Study of Metal Sites in Biomolecular Catalysis." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://hdl.handle.net/11858/00-1735-0000-0022-6011-C.
Повний текст джерелаBenson, Sven P. [Verfasser], and Jürgen [Akademischer Betreuer] Pleiss. "Molecular modeling of hydrophobic effects in complex biomolecular systems : from simple mixtures to protein-interface aggregation / Sven P. Benson. Betreuer: Jürgen Pleiss." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1066646015/34.
Повний текст джерелаNydén, Magnus. "NMR diffusion studies of microheterogeneous systems surfactant solutions, polymers solutions and gels /." Lund : University of Lund, 1998. http://catalog.hathitrust.org/api/volumes/oclc/68945132.html.
Повний текст джерела