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Dissertations / Theses on the topic 'Molecular computer'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.

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2

Hodgkin, E. E. "Molecular similarity in computer-aided molecular design." Thesis, University of Oxford, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379971.

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3

Parsons, Jeremy David. "Computer analysis of molecular sequences." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282922.

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4

Lee, Devin. "Computer aided design for molecular inhibitors." Thesis, McGill University, 2010. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=86881.

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In-silico methods used to aid the development of therapeutic drugs have gained utility in the recent past and continue to grow in importance. Small molecule drugs for the use in the treatment of type 2 diabetes were designed using computational methods to probe the active site of Dipeptidyl Peptidase IV (DPP-IV) and were subsequently synthesized and tested in-vitro. A number of pseudodipeptides formed from derivatives of tryptophan and proline were synthesized. The effects of a tetrazole group on the pyrrolidine of proline were studied, as well as the effect of protecting groups on the activit

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5

Gallegos, Saliner Ana. "Molecular quantum similarity in QSAR: applications in computer-aided molecular design." Doctoral thesis, Universitat de Girona, 2004. http://hdl.handle.net/10803/7937.

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La present tesi està centrada en l'ús de la Teoria de Semblança Quàntica per a calcular descriptors moleculars. Aquests descriptors s'utilitzen com a paràmetres estructurals per a derivar correlacions entre l'estructura i la funció o activitat experimental per a un conjunt de compostos. Els estudis de Relacions Quantitatives Estructura-Activitat són d'especial interès per al disseny racional de molècules assistit per ordinador i, en particular, per al disseny de fàrmacs. <br/>Aquesta memòria consta de quatre parts diferenciades. En els dos primers blocs es revisen els fonaments de la teoria de

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6

Dean, Delphine Marguerite Denise 1978. "Molecular electromechanics : modeling electrostatic forces between GAG molecules." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/86649.

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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.<br>Includes bibliographical references (p. 81-83).<br>by Delphine Marguerite Denise Dean.<br>M.Eng.and S.B.

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7

Dourado, Eduardo Manuel de Azevedo. "Computer simulations of adsorption and molecular recognition phenomena in molecularly imprinted polymers." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5680.

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Molecularly imprinted polymers (MIPs) are a novel, promising family of porous materials with potential applications ranging from separations, chemical sensing and catalysis to drug delivery and artificial immunoassays. The unique feature of these materials is their biomimetic molecular recognition functionality. Molecular recognition is the biological phenomenon of specific, selective and strong association between a substrate and a ligand. In man made MIPs this functionality is implemented via templated synthesis protocol. MIPs are synthesized in the presence of additional template molecules

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8

Lion, Thomas. "Osmosis : a molecular dynamics computer simulation study." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7877.

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Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gra

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9

Calmiano, Mark Daniel. "Computer simulation of molecular sorption in zeolites." Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249244.

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10

OLIVA, FRANCESCO. "A COMPUTER AIDED EXCURSUS INTO MOLECULAR BIOSYSTEMS." Doctoral thesis, Università degli Studi di Milano, 2020. http://hdl.handle.net/2434/761132.

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The application of computational methods to study biological and biochemical processes is a growing field in both industrial and academical environment. They can be used to explore condition that would be extremely expensive or flat out impossible to reproduce in a laboratory; to filter out molecules that would be unlikely to react with the designed target, thus reducing the price needed to produce a new drug; to understand experimental data by looking at the behaviour of molecules and proteins at an atomistic level. In this PhD thesis, molecular modeling, molecular dynamics and differe

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11

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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12

Yang, Steve Wuter. "Display of molecular models with interactive computer graphics /." Online version of thesis, 1987. http://hdl.handle.net/1850/10347.

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13

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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14

Carlsson, Peter. "Nuclear receptors studied by molecular dynamics computer simulations /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-823-8.

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15

Phippen, R. W. "A computer simulation study of anisotropic molecular models." Thesis, University of Southampton, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383559.

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16

Emerson, Andrew Peter John. "Molecular theories and computer simulations of liquid crystals." Thesis, University of Southampton, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.293355.

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17

Forester, Timothy Ronald. "Computer simulations of condensed phases of molecular systems." Thesis, University of Cambridge, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279657.

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18

Austin, Nick Donnelly. "Tools for Computer-Aided Molecular and Mixture Design." Research Showcase @ CMU, 2017. http://repository.cmu.edu/dissertations/894.

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This thesis explores mathematical optimization techniques to address the computeraided molecular and mixture design problems (CAMD/CAMxD). In particular, we leverage the power of mixed-integer linear programs (MILPs) to quickly and efficiently design over the massive chemical search space. These MILPs, when coupled with state-ofthe- art derivative-free optimization (DFO) methods, make for an efficient optimization strategy when designing mixtures of molecules or when considering a single molecule design problem that involves difficult thermodynamics or process models. In the first chapter, we

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19

Yin, Hao. "Computer Simulations of Water in Nonpolar Cavities and Proteins." Fogler Library, University of Maine, 2007. http://www.library.umaine.edu/theses/pdf/YinH2007.pdf.

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20

McBride, Carl. "Computer simulation of liquid crystals." Thesis, Durham University, 1999. http://etheses.dur.ac.uk/4588/.

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Molecular dynamics simulation performed on modern computer workstations provides a powerful tool for the investigation of the static and dynamic characteristics of liquid crystal phases. In this thesis molecular dynamics computer simulations have been performed for two model systems. Simulations of 4,4'-di-n-pentyl-bibicyclo[2.2.2]octane demonstrate the growth of a structurally ordered phase directly from an isotropic fluid. This is the first time that this has been achieved for an atomistic model. The results demonstrate a strong coupling between orientational ordering and molecular shape, bu

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21

Bates, Martin Alexander. "Computer simulation of liquid crystals." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243183.

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22

Kapla, Jon. "Computer Simulations of Membrane–Sugar Interactions." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-127402.

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Carbohydrate molecules are essential parts of living cells. They are used as energy storage and signal substances, and they can be found incorporated in the cell membranes as attachments to glycoproteins and glycolipids, but also as free molecules. In this thesis the effect of carbohydrate molecules on phospholipid model membranes have been investigated by the means of Molecular Dynamics (MD) computer simulations. The most abundant glycolipid in nature is the non-bilayer forming monogalactosyldiacylglycerol (MGDG). It is known to be important for the membrane stacking typical for the thylakoid

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23

Ricketts, D. M. "Computer aided molecular design using a single user workstation." Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.375319.

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24

Long, Fei. "Computer simulation techniques of pseudopotential theory and molecular dynamics." Thesis, University of Hull, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343701.

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25

Sahota, Parminda. "Evolving cellular automata molecular computer models using genetic algorithms." Thesis, University of Nottingham, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362898.

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26

Zhang, Zhancheng Berkowitz Max L. "Molecular dynamics computer simulations of lipid bilayers containing cholesterol." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2195.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2009.<br>Title from electronic title page (viewed Jun. 26, 2009). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.

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27

Pinches, Mark Robert Smythe. "Computer simulation of small molecules adsorbed on graphite." Thesis, University of Southampton, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239678.

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28

Landaverde, Raphael J. "GPU optimizations for a production molecular docking code." Thesis, Boston University, 2014. https://hdl.handle.net/2144/21199.

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Thesis (M.Sc.Eng.) -- Boston University<br>Scientists have always felt the desire to perform computationally intensive tasks that surpass the capabilities of conventional single core computers. As a result of this trend, Graphics Processing Units (GPUs) have come to be increasingly used for general computation in scientific research. This field of GPU acceleration is now a vast and mature discipline. Molecular docking, the modeling of the interactions between two molecules, is a particularly computationally intensive task that has been the subject of research for many years. It is a critica

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29

Fowler, R. F. "Computer simulation of microscopic liquid drops." Thesis, University of Kent, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371212.

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30

Whatling, Shaun Gary. "Computer simulation studies of liquid crystals." Thesis, University of Southampton, 1997. https://eprints.soton.ac.uk/421720/.

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31

Warren, Mark Alistair. "The computer simulation of liquid crystals." Thesis, University of Bristol, 1997. http://hdl.handle.net/1983/57728402-9ded-466a-a1ca-13f6e02a5446.

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32

Pakka, Vijayanarasimha Hindupur. "Dynamics of molecular fluctuations in gene regulatory networks." Thesis, University of Southampton, 2009. https://eprints.soton.ac.uk/71823/.

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The components that are central to cellular processing are proteins, whose production is regulated by other proteins known as transcription factors. Proteins are products of genes that regulate the expression of one another, thereby forming large gene regulatory networks that perform specific cellular functions. The complex connectivity between genes of a network could result in various behaviours that are interesting. The assumption then is that tracking subnetwork behaviour helps understand the characteristics of the larger networks they are embedded in. For example, the structure of a subne

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33

Caves, L. S. D. "Computer simulation studies of native and modified insulins." Thesis, University of York, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234931.

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34

Zhang, Junfang, and junfang zhang@csiro au. "Computer simulation of nanorheology for inhomogeneous fluids." Swinburne University of Technology. Centre for Molecular Simulation, 2005. http://adt.lib.swin.edu.au./public/adt-VSWT20050620.095154.

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In this thesis, we use nonequilibrium molecular dynamics (NEMD) methods to investigate the structural and dynamic properties of highly confined atomic and polymeric fluids undergoing planar Poiseuille flow. We derive 'method of planes' expressions for pressure tensor and heat flux vector for confined inhomogeneous atomic fluids under the influence of three-body forces. Our derivation is validated against NEMD simulations of a confined atomic fluid acted upon by a two-body Barker-Fisher-Watts force coupled with the Axilrod-Teller three-body force. Our method of planes calculations are in excell

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35

Archer, Emory Scott. "Development of graphical software tools for molecular biology." Thesis, Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19974218.

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36

Law, Timothy R. "An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/111980/.

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We develop the projection sorting algorithm, used to compute pairwise short-range interaction forces between particles in molecular dynamics simulations. We contrast this algorithm to the state of the art and discuss situations where it may be particularly effective. We then explore the efficient implementation of the projection sorting algorithm in both on-node (shared memory parallel) and off-node (distributed memory parallel) environments. We provide AVX, AVX2, KNC and AVX-512 intrinsic implementations of the force calculation kernel. We use the modern multi- and many-core architectures: In

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37

Du, Qishi. "Heuristic molecular lipophilicity potential for computer-aided rational drug design." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ27402.pdf.

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38

Firanescu, George. "Computer simulation of infrared spectra and structures of molecular nanoparticles." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/22485.

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Molecular nanoparticles, i.e. molecular aggregates held together by weak intermolecular interactions, are ubiquitous in planetary atmospheres and the interstellar space. Although they play a crucial role for radiative energy transfer and chemical processes, the understanding of their properties — which can differ significantly from those of the bulk — is still in its infancy. The present thesis is devoted to a better understanding of the influence of intrinsic properties of these particles on their infrared spectra. The influence of shape, size, architecture and phase on infrared spectra is mo

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39

Lukinov, Tymofiy. "Computer simulation of materialsunder extreme conditions." Doctoral thesis, KTH, Kondenserade materiens teori, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-188146.

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Extreme conditions allow us to reveal unusual material properties. At the same time an experimental approach is di-cult under such conditions. Capabilities of a theoretical approach based on simplied models are limited. This explainsa wide application of computer simulations at extreme conditions. My thesis is concerned with computer simulations undersuch a conditions. I address such problems as melting, solidsolid phase transitions, shockwave impact on material properties and chemical reactions under extreme conditions. We addressed these problems to facilitate simulations of phase transition

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40

Goldstein, Alexandra Susan. "Computer simulations of amorphous copper-zirconium /." Thesis, Connect to this title online; UW restricted, 1995. http://hdl.handle.net/1773/8629.

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41

Hennessey, Anthony. "Statistical shape analysis of large molecular data sets." Thesis, University of Nottingham, 2018. http://eprints.nottingham.ac.uk/52088/.

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Protein classification databases are widely used in the prediction of protein structure and function, and amongst these databases the manually-curated Structural Classification of Proteins database (SCOP) is considered to be a gold standard. In SCOP, functional relationships are described by hyperfamily and superfamily categories and structural relationships are described by family, species and protein categories. We present a method to calculate a difference measure between pairs of proteins that can be used to reproduce SCOP2 structural relationship classifications, and that can also be used

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42

Mason, Carl Peter. "The computer simulation of the hard ellipsoid fluid." Thesis, University of Bristol, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259472.

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43

Smale, Jonathan Ross. "Fitting and using model Hamiltonian in non-adiabatic molecular dynamics simulations." Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/3764/.

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In order to study computationally increasingly complex systems using theoretical methods model Hamiltonians are required to accurately describe the potential energy surface they represent. Also ab-initio methods improve the calculation of the excited states of these complex systems becomes increasingly feasible. One such model Hamiltonian described herein, the Vibronic Coupling Hamiltonian, has previously shown its versitility and ability to describe a variety of non-adiabatic problems. This thesis describes a new method, a genetic algorithm, for the parameterisation of the Vibronic Coupling H

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44

Dasari, Vivek. "Platform for spatial molecular data." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/107103.

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Thesis: M. Eng. in Computer Science and Molecular Biology, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 49-50).<br>I designed and implemented a comprehensive platform for storing, analyzing, visualizing, and interacting with spatial molecular data. With the advent of high throughput in situ sequencing methods, such as fluorescent in situ sequencing (FISSEQ), the need for a platform to organize spatial molecular data has become paramount. The platform

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45

Paydavosi, Sarah. "Organic molecular floating gate memories." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/64591.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 42-45).<br>Flash memory devices dominate the non-volatile memory market, with device structures that utilize charge storage in polysilicon floating gates imbedded in insulating silicon oxide films'. As demands for high storage density, high chip memory capacity, and decreasing process costs continue to mount, conventional flash memory has found it challenging to continue scaling and it may reach fun

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46

Trobro, Stefan. "Computer simulations of ribosome reactions." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8429.

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<p>Peptide bond formation and translational termination on the ribosome have been simulated by molecular mechanics, free energy perturbation, empirical valence bond (MD/FEP/EVB) and automated docking methods. Recent X-ray crystallographic data is used here to calculate the entire free energy surface for the system complete with substrates, ribosomal groups, solvent molecules and ions. A reaction mechanism for peptide bond formation emerges that is found to be catalyzed by the ribosome, in agreement with kinetic data and activation entropy measurements. The results show a water mediated network

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47

Zhang, Junfang. "Computer simulation of nanorheology for inhomogenous fluids." Australasian Digital Thesis Program, 2005. http://adt.lib.swin.edu.au/public/adt-VSWT20050620.095154.

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Thesis (PhD) - Swinburne University of Technology, School of Information Technology, Centre for Molecular Simulation - 2005.<br>A thesis submitted in fulfilment of requirements for the degree of Doctor of Philosophy, Centre for Molecular Simulation, School of Information Technology, Swinburne University of Technology - 2005. Typescript. Bibliography: p. 164-170.

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48

Spencer, Steven Charles. "Computer simulations of flux pinning in type II superconductors." Thesis, Imperial College London, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338422.

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49

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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50

Warne, Mark Robert. "Computer simulation of molecules at the kaolinite interface." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322604.

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