Дисертації з теми "Complex systems- Molecular dynamics study"
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Haughney, Michael Francis. "A molecular dynamics study of selected polar liquids and their aqueous mixtures." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.254062.
Повний текст джерелаMICELI, GIACOMO FRANCESCO LEONARDO. "Fist principles study of the LINH2/LI2NH hydrogen storage system." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19693.
Повний текст джерелаSingh, Vidisha. "Integrative analysis and modeling of molecular pathways dysregulated in rheumatoid arthritis Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis Automated inference of Boolean models from molecular interaction maps using CaSQ." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL039.
Повний текст джерелаRheumatoid arthritis (RA) is a complexautoimmune disease that results in synovial inflammationand hyperplasia leading to bone erosion and cartilagedestruction in the joints. The aetiology of RA remainspartially unknown, yet, it involves a variety of intertwinedsignalling cascades and the expression of pro-inflammatorymediators. In the first part of my PhD project, we present asystematic effort to construct a fully annotated, expertvalidated, state of the art knowledge-base for RA. The RAmap illustrates significant molecular and signallingpathways implicated in the disease. Signal transduction isdepicted from receptors to the nucleus systematically usingthe systems biology graphical notation (SBGN) standardrepresentation. Manual curation based on strict criteria andrestricted to only human-specific studies limits theoccurrence of false positives in the map. The RA map canserve as an interactive knowledge base for the disease butalso as a template for omic data visualization and as anexcellent base for the development of a computationalmodel. The static nature of the RA map could provide arelatively limited understanding of the emerging behaviorof the system under different conditions. Computationalmodeling can reveal dynamic network properties throughin silico perturbations and can be used to test and predictassumptions.In the second part of the project, we present a pipelineallowing the automated construction of a large Booleanmodel, starting from a molecular interaction map. For thispurpose, we developed the tool CaSQ (CellDesigner asSBML-qual), which automates the conversion ofmolecular maps to executable Boolean models based ontopology and map semantics. The resulting Booleanmodel could be used for in silico simulations to reproduceknown biological behavior of the system and to furtherpredict novel therapeutic targets. For benchmarking, weused different disease maps and models with a focus onthe large molecular map for RA.In the third part of the project we present our efforts tocreate a large scale dynamical (Boolean) model forrheumatoid arthritis fibroblast-like synoviocytes (RAFLS).Among many cells of the joint and of the immunesystem involved in the pathogenesis of RA, RA FLS playa significant role in the initiation and perpetuation ofdestructive joint inflammation. RA-FLS are shown toexpress immuno-modulating cytokines, adhesionmolecules, and matrix-modelling enzymes. Moreover,RA-FLS display high proliferative rates and an apoptosisresistantphenotype. RA-FLS can also behave as primarydrivers of inflammation, and RA FLS-directed therapiescould become a complementary approach to immunedirectedtherapies. The challenge is to predict the optimalconditions that would favour RA FLS apoptosis, limitinflammation, slow down the proliferation rate andminimize bone erosion and cartilage destruction
Ouyang, Jian. "Molecular dynamics studies of interfacial properties of complex liquid systems." Diss., Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/30494.
Повний текст джерелаKenway, O. A. "Molecular dynamics simulations of complex systems including HIV-1 protease." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/19485/.
Повний текст джерелаDing, Xiaoyan. "Increasingly Complex Systems in Intense Laser Fields." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/38504.
Повний текст джерелаShim, Sangwoo. "Quantum Dynamics in Biological Systems." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10125.
Повний текст джерелаVanga, Amulya. "A Molecular Dynamics Study of Systems of Hard Ellipses." Kent State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=kent149849408801736.
Повний текст джерелаIuchi, Satoru. "Theoretical study on dynamics of molecular systems in solution." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/145101.
Повний текст джерелаMegerle, Uwe. "Photoinduced molecular dynamics in increasingly complex systems: From ultrafast transient absorption spectroscopy to nanoscopic models." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-130444.
Повний текст джерелаViveca, 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
Perez, Benito Laura. "Application of Molecular Dynamics methods to the study of biological systems." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/402258.
Повний текст джерелаApplication of Molecular Dynamics (MD) methods to the study of biological systems. This thesis is focused on the application of both classical MD and free energy perturbation (FEP) to study biological systems such as G protein-coupled receptors and BACE1 inhibitors. The thesis is divided into 5 sections, firstly an introduction where a timeline and evolution of MD methodology is explained, secondly a second section on Methods, the third section focuses on the use of MD simulation to study two different aspects of GPCRs, oligomerization of the tetramer formed by Adenosine receptors and the mechanism of activation by allosteric ligands targeting the metabotropic glutamate 2 receptor. The fourth section is focused on the application of FEP with the aim of designing new BACE1 inhibitors and to implement this methodology into a real drug discovery project performed in collaboration with Janssen Pharmaceutica. The final section summarizes the conclusions reached. Overall, it is shown that state of the art MD simulations, and hence modern computational methodology, can be of value to understand the described scenarios at the molecular level, and in particular the interactions and dynamic processes which occur. This in turn will help with more detailed understanding of basic biology and drug design. The work justifies future applications in these areas and continued deeper exploration of the limits of the impact which MD and FEP methods can reach.
Tsoo, Chia-Chin. "The study of finite size systems using simulated annealing molecular dynamics /." The Ohio State University, 1992. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487760357822546.
Повний текст джерелаKvasnikova, Ioulia. "A classical molecular dynamics study of thermodynamic variables for finite nuclear systems." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=24017.
Повний текст джерелаWe consider a system of 85 nucleons interacting through two-body nucleon-nucleon potential. The calculations are first carried out ignoring Coulomb interaction and then including it. Data on various thermodynamic quantities are obtained and the question of the existence of the phase transition is investigated.
To estimate the effect of a finite particle number on critical parameters we go to a system of 200 nucleons.
Del, Frate Gianluca. "Development, validation and application of accurate molecular force fields for complex soft matter systems." Doctoral thesis, Scuola Normale Superiore, 2018. http://hdl.handle.net/11384/85815.
Повний текст джерелаYeo, Narelle Fiona. "“THE INFALLIBLE PROTAGONIST” A STUDY OF COMPLEXITY THEORY AND REHEARSAL DYNAMICS IN MONODRAMA." Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/16418.
Повний текст джерелаSrivastava, Anand. "A MOLECULAR DYNAMICS BASED STUDY OF BULK AND FINITE POLYSTYRENE-CARBON DIOXIDE BINARY SYSTEMS." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1285029096.
Повний текст джерелаYoung, Alexander L., and Alexander L. Young. "Three Essays on Complex Systems: Self-Sorting in a One-Dimensional Gas, Collective Motion in a Two-Dimensional Ensemble of Disks, and Environment-Driven Seasonality of Mosquito Abundance." Diss., The University of Arizona, 2017. http://hdl.handle.net/10150/624567.
Повний текст джерелаLee, Seung Eun Ph D. Massachusetts Institute of Technology. "Mechanotransduction by talin : a molecular dynamics study of force-induced recruitment of vinculin to a focal adhesion complex." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42290.
Повний текст джерелаIncludes bibliographical references (p. 112-123).
It is now well established that cells can sense mechanical force, but the mechanisms by which force is transduced into a biochemical signal remain poorly understood. One example is the recruitment of vinculin to reinforce initial contacts between a cell and the extracellular matrix due to tensile force. Talin, an essential structural protein in the adhesion, contains the N-terminal five-helix bundle in the rod domain with a known cryptic vinculin binding site 1 (VBS1). The perturbation of this stable structure through elevated temperature or destabilizing mutation activates vinculin binding. Here, molecular dynamics (MD) is employed to demonstrate a force-induced conformational change that exposes the cryptic vinculin-binding-residues of VBS1 to solvent under applied forces along a realistic pulling direction. VBS 1 undergoes a rigid body rotation by an applied torque transmitted through hydrogen-bonds and salt bridges. Activation was observed with mean force of 13.2±8.0pN during constant velocity simulation and with steady force greater than 18.0pN. The crystal structure of vinculin head subdomain (Vhl) bound to the talin VBS1 implies that vinculin undergoes a large conformational change upon binding to talin, but the molecular basis for this, or the precise nature of the binding pathway remain elusive. In the second part of the thesis, MD is employed to investigate the binding mechanism of Vhl and VBS1 with minimal constraints to facilitate the binding. One simulation demonstrates binding of the two molecules in the complete absence of external force. VBS1 makes early hydrophobic contact with Vhl through an initial hydrophobic insertion. Then, other solvent-exposed hydrophobic residues of VBS1 gradually embed into the hydrophobic core of Vhl further displacing helix 1 from helix 2.
(cont.) These highly conserved critical residues are experimentally shown to be essential in Vhl-VBS1 binding, and are also the same residues that are shown to become exposed by applied tension to talin in the first part of the thesis. Similar mechanisms are demonstrated in separate MD simulations of Vhl binding to other VBSs both in talin and a-actinin. Together, these results provide molecular insights, for the first time, into the early force-induced recruitment of vinculin to the mechanosensitive mechanisms of cell-matrix adhesion complex, and establish the basis for further numerical and experimental studies to fully understand the force response of focal adhesions.
by Seung Eun Lee.
Ph.D.
Vladimirov, Egor. "Molecular dynamics study of solvent reorganization energies for electron transfer processes in DNA-related systems." kostenfrei, 2009. https://mediatum2.ub.tum.de/node?id=820913.
Повний текст джерелаSteinhauser, Martin Oliver. "A molecular dynamics study of the influence of chain branching on the properties of polymer systems." [S.l. : s.n.], 2001. http://ArchiMeD.uni-mainz.de/pub/2001/0115/diss.pdf.
Повний текст джерелаFARROTTI, 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 джерелаPowell, Sean K. "A quantitative study of diffusion in quasi-periodic fibre networks and complex porous media." Thesis, Queensland University of Technology, 2016. https://eprints.qut.edu.au/92506/12/92506%28thesis%29.pdf.
Повний текст джерелаFisher, Diana Marie. "Introducing Complex Systems Analysis in High School Mathematics Using System Dynamics Modeling: A Potential Game-Changer for Mathematics Instruction." PDXScholar, 2016. http://pdxscholar.library.pdx.edu/open_access_etds/2950.
Повний текст джерелаWang, Dongqing. "NMR Study of the Reorientational and Exchange Dynamics of Organometallic Complexes." Thesis, University of North Texas, 1996. https://digital.library.unt.edu/ark:/67531/metadc278073/.
Повний текст джерелаLindberg, Maria. "Computer simulations of electronic energy transfer and a molecular dynamics study of a decapeptide." Doctoral thesis, Umeå universitet, Kemiska institutionen, 1991. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-118929.
Повний текст джерелаDiss. (sammanfattning) Umeå : Umeå universitet, 1991, härtill 5 uppsatser
digitalisering@umu
Dunsing, Valentin [Verfasser], Salvatore [Akademischer Betreuer] Chiantia, Salvatore Gutachter] Chiantia, Carsten [Gutachter] [Beta, and Thorsten [Gutachter] Wohland. "Fluorescence fluctuation spectroscopy techniques to quantify molecular interactions and dynamics in complex biological systems / Valentin Dunsing ; Gutachter: Salvatore Chiantia, Carsten Beta, Thorsten Wohland ; Betreuer: Salvatore Chiantia." Potsdam : Universität Potsdam, 2020. http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-478494.
Повний текст джерелаDunsing, Valentin [Verfasser], Salvatore [Akademischer Betreuer] Chiantia, Salvatore [Gutachter] Chiantia, Carsten [Gutachter] Beta, and Thorsten [Gutachter] Wohland. "Fluorescence fluctuation spectroscopy techniques to quantify molecular interactions and dynamics in complex biological systems / Valentin Dunsing ; Gutachter: Salvatore Chiantia, Carsten Beta, Thorsten Wohland ; Betreuer: Salvatore Chiantia." Potsdam : Universität Potsdam, 2020. http://d-nb.info/1219911585/34.
Повний текст джерелаKriuchevskyi, Ivan. "Mechanical and viscoelastic properties of glass-forming polymers in the bulk and thin films : molecular dynamics study of model systems." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAE044/document.
Повний текст джерелаFocusing on the equilibrium shear modulus Geq of well-known glass-forming polymer model system (sampled by means of MD), we have addressed the general question of how the mechanical properties of the thin polymer films differs from the bulk. Using ”stress fluctuation” formalism we obtained Geq(T) for the bulk and films. It has been demonstrated that in both cases Geq unambiguously separates the fluid state (Geq = 0) from the glass (Geq > 0). We also stressed that Geq for the film does not only depend on film thickness h, but also on tangential pressure that is a consequence of the film preparation procedure
Martínez-Seara, Monné Hector. "Theoretical Study of Phospholipid Membranes: the Complex Role of Cholesterol and Lipid Unsaturation." Doctoral thesis, Universitat de Barcelona, 2010. http://hdl.handle.net/10803/35684.
Повний текст джерелаL'objectiu principal d'aquesta tesi és estudiar el paper dels fosfolípids insaturats i del colesterol en les propietats de les membranes cel·lulars animals mitjançant dinàmica molecular clàssica. En general, s'han estudiat els mecanismes moleculars subjacents responsables de la preferència, dictada genèticament, per composicions lipídiques determinades en aquestes membranes. Per exemple, la preferència general pels fosfolípids insaturats amb un doble enllaç al mig de la cadena sn-2. Entre els resultats obtinguts destaquen les evidències trobades que justifiquen la importància de la posició del doble enllaç en els fosfolípids que constitueixen les membranes. S'ha observat que els fosfolípids insaturats amb un doble enllaç al mig de la cua presenten una major capacitat d'induir desordre en la membrana. Aquesta capacitat d'induir desordre es maximitza quan la cadena insaturada és la sn-2, posició genèticament afavorida. Un altre resultat important obtingut en aquest treball és l'explicació del paper del colesterol com a promotor d'ordre en el pla de la membrana a causa de la seva acció col·lectiva sobre els fosfolípids circumdants. Hem constatat la preferència natural del colesterol per col·locar-se en la segona esfera de coordinació en relació amb els altres colesterols adjacents. En altres paraules, al colesterol no li agrada estar en contacte directe amb altres colesterols. Aquest resultat dóna suport a la teoria del paraigües. A més, s'ha trobat que els colesterols s'emplacen entre ells formant un patró dinàmic amb simetria trigonal. Aquest resultat no és gens intuïtiu tenint en compte la naturalesa fluïda del medi i que els colesterols no es troben en contacte directe. La combinació d'aquestes dues característiques justifica el conegut efecte de condensació dels colesterols: colesterols adjacents ordenen les cues fosfolipídiques aixafant-les entre ells. Aquests resultats, fins ara desconeguts, aclareixen algunes de les raons existents darrere de la selecció natural dels lípids i els mecanismes responsables dels coneguts efectes de condensació que indueix el colesterol, que fins ara eren en gran mesura controvertits. Per acabar, aquesta tesi doctoral dedica el seu darrer capítol a l'estudi de membranes que contenen cardiolípids en comptes de colesterol, com és el cas de la membrana mitocondrial.
Alharbi, Fahad. "The Dynamics of the L2 Motivational Self System among Saudi Study Abroad Students." Scholar Commons, 2017. http://scholarcommons.usf.edu/etd/6672.
Повний текст джерелаVilciauskas, Linas [Verfasser], and Joachim [Akademischer Betreuer] Maier. "Proton transport mechanisms of phosphoric acid and related phosphorus oxoacid systems : a first principles molecular dynamics study / Linas Vilciauskas. Betreuer: Joachim Maier." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2012. http://d-nb.info/1021923397/34.
Повний текст джерелаZiadat, Wael. "A meta-analysis study of project and programme management complexity in the oil and gas sector of the Middle East and North Africa region." Thesis, University of Manchester, 2018. https://www.research.manchester.ac.uk/portal/en/theses/a-metaanalysis-study-of-project-and-programme-management-complexity-in-the-oil-and-gas-sector-of-the-middle-east-and-north-africa-region(1fb607f9-b665-4dbd-9f10-9ef5f73d43e9).html.
Повний текст джерелаMillan, Cabrera Reisel. "Computational study of heterogeneous catalytic systems. Kinetic and structural insights from Density Functional Theory." Doctoral thesis, Universitat Politècnica de València, 2021. http://hdl.handle.net/10251/161934.
Повний текст джерела[CA] En aquest treball estudiem dues reaccions catalítiques rellevants per a la indústria i la localització de l'anió fluorur en la zeolita RTH, sintetitzada al mig fluorur. El capítol 3 és el primer capítol de resultats, on s'estudia la reducció quimioselectiva del nitroestireno en les superfícies Ni(111), Co(111), Cu(111) i Pd(111). El mecanisme generalment acceptat d'aquesta reacció està basat en l'esquema proposat per Haver-hi en 1898, en el qual la reacció pot transcórrer per dues rutes, la directa i la de condensació. En aquest capítol explorem totes dues rutes, i observem que la ruptura dels enllaços N-O i la conseqüent formació d'enllaços metall-O està més afavorida que la formació d'enllaços N-H en les superfícies Ni(111) i Co(111), a causa del caràcter oxofílico de tots dos metalls. Les etapes més lentes involucren la formació d'enllaços N-H. En les superfícies de metalls nobles com Pt(111) i Pd(111) s'observa el comportament contrari. La superfície Cu(111) és un cas intermedi comparat amb els metalls nobles i no nobles. A més, el nitroestireno interactua amb els àtoms de Cu de la superfície sol a través de grup nitre, amb la qual cosa és un candidat ideal per a aconseguir selectivitats prop del 100%. No obstant això, la superfície Cu(111) no és capaç d'activar la molècula d'H2. En aquest sentit, proposem un catalitzador bimetàl·lic basat en Cu, dopat amb un altre metall capaç d'activar a l'H2, com ara el Pd o el Ni. En els capítols 4 i 5 hem estudiat la reducció catalítica selectiva dels òxids de nitrogen (SCR, en anglés) amb amoníac. Usant mètodes de DFT, hem trobat rutes per a l'oxidació de NO a NO2, nitrits i nitrats amb energies d'activació relativament baixes. També, hem trobat que la reducció de Cu2+ a Cu+ requereix la participació simultània de NO i NH3. Posteriorment, hem estudiat la influència del NH3 en aquest sistema amb mètodes de dinàmica molecular. El NH3 interacciona fortament amb el Cu+ de manera que dues molècules d'aquest gas són suficients per a trencar la coordinació del catió Cu+ amb els oxígens de l'anell 6r, i formar el complex lineal [Cu(NH3)2]+. A més, els cations Cu2+ poden ser estabilitzats fora de la xarxa mitjançant la formació del complex tetraamincobre(II). A causa de la presència dels cations Cu+ i Cu2+ coordinats a la xarxa de la zeolita, apareixen bandes a la regió entre 800-1000 cm-1 de l'espectre infraroig. L'anàlisi de les freqüències IR de diversos models amb Cu+ i Cu2+ coordinats a l'anell 6r, o formant complexos amb amoníac indica que quan els cations Cu+ i Cu2+ estan coordinats als oxígens de l'anell 6r apareixen vibracions entre 830 i 960 cm-1. Freqüències en aquesta zona també s'obtenen en els casos en què NO, NO2, O2 i combinacions de dues d'ells estan adsorbidos en Cu+ i Cu2+. No obstant això, quan els cations Cu+ i Cu2+ estan fora de l'anell (no hi ha enllaços entre els cations de coure i els oxígens de l'anell 6r) no s'obtenen vibracions d'IR en aquesta regió de l'espectre. Aquests resultats indiquen que amb el seguiment de l'espectre IR durant la reacció SCR és possible determinar si els cations Cu+ i Cu2+ estan coordinats o no a l'anell de 6r en les etapes d'oxidació i reducció. Finalment, hem simulat el desplaçament químic de 19F, δiso, en la zeolita sintetitzada RTH. L'anàlisi del δiso dels diferents models utilitzats ens ha permés reconéixer la simetria del material sintetitzat, el qual pertany al grup espacial P1 i la nova cel·la unitat ha sigut confirmada experimentalment per difracció de raigs X. Finalment, hem assignat el senyal experimental que apareix en l'espectre de 19F a -67.2 ppm, al F- localitzat en un lloc T2, el qual és al seu torn la posició més estable. A més, el senyal a -71.8 ppm s'ha assignat a l'anió F- localitzat en un lloc T4.
[EN] In this work, we have studied two heterogeneous catalytic reactions and the localization of the fluoride anion in the as-made RTH framework, synthesized in fluoride medium. The first results, included in chapter 3, correspond to the chemoselective reduction of nitrostyrene on different metal surfaces, i.e, Ni(111), Co(111), Cu(111) and Pd(111). Until very recently, the reduction of the nitro group was explained on the basis of the general mechanism proposed by Haber in 1898 where the reaction can follow two routes, the direct and condensation route. We have explored the relevant elementary steps of both routes and found that because of the oxophilic nature of Ni and Co, the steps involving the dissociation of N-O bonds and formation of metal-O bonds are significantly favored compared with the other steps on both metal surfaces. In addition, the most demanding steps in terms of energy involve the formation of N-H bonds. These findings are in contrast to those of noble metals such as Pt and Pd, where the opposite behavior is observed. The behavior of Cu(111) lies in between the aforementioned cases, and also no chemical bonds between the carbon atoms of the aromatic ring of nitrostyrene and the Cu(111) surface is formed. For this reason, it might be an ideal candidate to achieve nearly 100 % selectivity. However, the Cu(111) surface does not seem to activate the H2 molecule. In this regard, we propose a bimetallic Cu-based catalyst whose surface is doped with atoms of a H2-activating metal, such as Ni or Pd. On another matter, we have also investigated the selective catalytic reduction of nitrogen oxides (SCR-NOx) and the main results are presented in the following two chapters, 4 and 5. By using static DFT methods, we found pathways for the oxidation of NO to NO2, nitrites and nitrates with relatively low activation energies. We also found, in agreement with experimental reports, that the reduction of Cu2+ to Cu+ requires the simultaneous participation of NO and NH3. Later, molecular dynamics simulations allowed us to assess the influence of NH3. The strong interaction of NH3 with the Cu+ cation is evidenced by its ability to detach Cu+ from the zeolite framework and form the mobile linear complex [Cu(NH3)2]+. Cu+ is no longer coordinated to the zeolite framework in the presence of two NH3 molecules. This observation and the fact that the T-O-T vibrations of the framework produce bands in the 800-1000 cm-1 region of the IR spectrum when perturbed by the coordination of Cu+ and Cu2+ cations, indicate that bands in the 800-1000 cm-1 regions should be observed when both copper cations are bonded to the framework oxygens. Finally, we have also studied NMR properties of the as-made pure silica RTH framework, aiming at locating the compensating fluoride anion. The calculation of the 19F chemical shift in different T sites and comparison with the experimental NMR spectra shows that the as-made RTH belongs to the P-1 space group with 16 Si, 32 O atoms, one fluoride anion and one OSDA cation. These results have been confirmed experimentally by XRD. In addition, we have assigned the experimental signal of 19F at -67.2 ppm to the fluoride anion in a T2 site, which in turn is the most stable location found, and the signal of -71.8 ppm to a fluoride anion sitting in a T4 site.
My acknowledgements to “La Caixa foundation” for the financial support through “La Caixa−Severo Ochoa” International PhD Fellowships (call 2015), to the Spanish Supercomputing Network (RES), to the Centre de Càlcul de la Universitat de València, to the Flemish Supercomputer Center (VSC) of Ghent University for the computational resources and technical support, and to the Spanish Government through the MAT2017-82288-C2-1-P programme
Millan Cabrera, R. (2021). Computational study of heterogeneous catalytic systems. Kinetic and structural insights from Density Functional Theory [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/161934
TESIS
Shrivastav, Gourav. "Molecular dynamics studies of complex systems : molecular chain and ionic liquids." Thesis, 2018. http://localhost:8080/iit/handle/2074/7624.
Повний текст джерелаLi, Chao. "Toward molecular dynamics simulation of complex molecular systems." 2006. http://etd.utk.edu/2006/LiChao.pdf.
Повний текст джерелаTitle from title page screen (viewed June 12, 2006). Thesis advisors: David J. Keffer, William V. Steele. Vita. Includes bibliographical references.
Lai, Yi-Sin, and 賴奕忻. "Study of hnps-PLA2 Complex Binding Interactions by Molecular Dynamics Simulation." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/26j8e9.
Повний текст джерелаTorres, Juan Andres. "Study of nano-scale systems using discontinuous molecular dynamics." 1999. http://catalog.hathitrust.org/api/volumes/oclc/44606109.html.
Повний текст джерелаTypescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 41-42).
Ing, Christopher. "Path integral Langevin dynamics of complex molecular systems: from low-temperature quantum clusters to biomolecules." Thesis, 2011. http://hdl.handle.net/10012/6202.
Повний текст джерелаZeiske, Tim. "Understanding complex biomolecular systems through the synergy of molecular dynamics simulations, NMR spectroscopy and X-Ray crystallography." Thesis, 2016. https://doi.org/10.7916/D8TX3F60.
Повний текст джерелаBalawi, Ahmed. "Photophysics of Organic Molecular Systems – A Study of Excited State Dynamics." Diss., 2019. http://hdl.handle.net/10754/660290.
Повний текст джерелаDORIA, SANDRA. "Energy flow in complex molecular systems: Spectroscopic study by static and time-resolved techniques". Doctoral thesis, 2017. http://hdl.handle.net/2158/1077394.
Повний текст джерелаMegerle, Uwe [Verfasser]. "Photoinduced molecular dynamics in increasingly complex systems : from ultrafast transient absorption spectroscopy to nanoscopic models / vorgelegt von Uwe Megerle." 2011. http://d-nb.info/1012207234/34.
Повний текст джерелаFennell, Christopher Joseph. "Development of molecular dynamics techniques for the study of water and biochemical systems." 2006. http://etd.nd.edu/ETD-db/theses/available/etd-10182006-144608/.
Повний текст джерелаThesis directed by J. Daniel Gezelter for the Department of Chemistry and Biochemistry. "October 2006." Includes bibliographical references (leaves 163-173).
Mukherjee, Saumyak. "Structure, Thermodynamics and Dynamics in Complex Systems: From Stability of Biomolecules to Phase Transitions in Polymorphic Ice." Thesis, 2020. https://etd.iisc.ac.in/handle/2005/4870.
Повний текст джерелаINSPIRE Fellowship, DST, India
Esai, Selvan Myvizhi. "Molecular-Level Modeling of Proton Transport in Aqueous Systems and Polymer Electrolyte Membranes: A Reactive Molecular Dynamics Study." 2010. http://trace.tennessee.edu/utk_graddiss/880.
Повний текст джерелаLiu, Junwu. "A Study of Polymer Electrolyte Membranes and Associated Interfacial Systems via Molecular Dynamics Simulations." 2009. http://trace.tennessee.edu/utk_graddiss/619.
Повний текст джерелаPereira, Joana de Freitas Salgado do Fundo. "A fundamental study on physical properties and stability in food systems : the relationship with molecular dynamics." Doctoral thesis, 2014. http://hdl.handle.net/10400.14/19347.
Повний текст джерелаO controlo das propriedades físicas e da estabilidade dos alimentos é requisito essencial para o fornecimento de produtos seguros e saudáveis aos consumidores. Por este motivo, desde há muito tempo que o tema tem despertado a atenção e a curiosidade dos cientistas que trabalham na área alimentar. A literatura tem vindo a sugerir que as propriedades físicas e a estabilidade só podem ser plenamente compreendidas se a dinâmica molecular e a estrutura dos alimentos for tida em consideração; ou seja, é necessário um conhecimento da composição, da estrutura e da dinâmica molecular dos sistemas alimentares, entendendo o arranjo tridimensional dos vários elementos estruturais e das suas interacções. No caso particular dos alimentos, a dinâmica molecular da água desempenha um papel fundamental no seu comportamento. A “disponibilidade” da água influencia profundamente a qualidade química, física e microbiológica dos sistemas alimentares. A compreensão das alterações na localização e mobilidade da água do sistema representa um passo significativo no conhecimento dos mecanismos que estão associados às reacções de degradação dos alimentos. A ressonância magnética nuclear (RMN), através da análise dos tempos de relaxação da magnetização nuclear, tem sido considerada uma poderosa técnica para investigar a dinâmica da água e avaliar estruturas físicas em sistemas complexos como os alimentos. A aplicação desta técnica pode ser muito útil na previsão de alterações físico-químicas como a textura, a viscosidade ou a migração da água na matriz. Esta tese considerou dois sistemas alimentares distintos: (i) filmes de origem biológica, pelo seu interesse como matrizes modelo e potencial para a indústria alimentar; e (ii) fruta minimamente processada, pela sua complexidade e reconhecida importância económica nos mercados de alimentos. Os filmes com origem biológica, neste caso específico provenientes do quitosano, possuem várias aplicações industriais como é o caso das embalagens ou revestimentos comestíveis, que têm como objectivo prolongar a vida útil dos produtos. Como modelo para sistemas alimentares mais complexos têm as vantagens de: serem facilmente reprodutíveis; e tal como os alimentos, de um ponto de vista fundamental podem ser considerados biopolímeros comestíveis parcialmente cristalinos, e parcialmente amorfos. Apesar da vasta informação que existe na literatura sobre as propriedades físicas dos filmes de quitosano, uma abordagem sistemática para a identificação da contribuição das soluções formadoras do filme, assim como a influência da dinâmica molecular nessas propriedades, revela-se ainda necessária. Nesta tese, a importância da composição das soluções formadoras nas propriedades dos filmes é realçada através da monitorização de soluções formadoras com diferentes proporções polímero/plasticizante. A importância destas soluções foi avaliada também nas alterações das propriedades termomecânicas dos filmes assim como a sua influência na dinâmica molecular dos mesmos (através de técnicas de RMN). Os resultados demonstram que a composição das soluções formadoras influenciou as propriedades mecânicas e térmicas dos filmes, bem como as propriedades relacionadas com a água (atividade, solubilidade, permeabilidade e a dinâmica molecular). A concentração de quitosano afetou o coeficiente de consistência das soluções formadoras, o que pode ser relacionado com diferenças na estrutura e na retenção de água dos filmes. Por outro lado, a quantidade de plasticizante usado na preparação das soluções formadoras é responsável pela composição dos filmes, enquanto a razão polímero/plasticizante determinou a espessura, logo a estrutura dos filmes. Através dos estudos de RMN foi possível compreender o rearranjo molecular dos filmes, demonstrando o papel importante que a água, como componente, desempenha neste tipo de matrizes, revelando diferenças de comportamento entre esta e o plasticizante. Estes resultados revelaram ainda que existe uma relação entre a dinâmica molecular quer da água quer do plasticizante nos filmes com as propriedades macroscópicas dos mesmos. As frutas são alimentos com uma estrutura celular muito complexa, ricos em água que pode estar presente quer nos espaços intracelulares, quer nos extracelulares. As frutas, minimamente processadas, devido ao ferimento a que são sujeitas, tem altas taxas metabólicas que provocam rápidas alterações fisiológicas, bioquímicas e de degradação microbianas, resultando, por exemplo, em perda de cor e textura. A segunda parte desta tese dedica-se ao estudo de pêra e melão minimamente processados. Estas frutas são muito diferentes no que diz respeito à estrutura. As amostras foram estudadas durante 7 dias de armazenamento em condições de refrigeração. Foram avaliados alguns dos parâmetros de qualidade mais relevantes, como é o caso da cor e da textura. A atividade da água (aw) e a dinâmica molecular da água (T2), analisada através de uma técnica de RMN, foram também monitorizadas durante o tempo de armazenamento. Os resultados mostram que quer o processamento quer o tempo de armazenamento afetaram os parâmetros de qualidade, bem como a dinâmica da água nos sistemas. Observou-se ainda uma relação entre os parâmetros de qualidade e os valores da dinâmica da água. Esta relação foi diferente para os dois frutos estudados, realçando o papel da estrutura na estabilidade dos alimentos. Nesta tese evidencia-se o interesse e a utilidade dos estudos de dinâmica molecular, utilizando a técnica de RMN como ferramenta na avaliação das propriedades físicas e da estabilidade de sistemas alimentares e complexos.
Wolff, David. "Molecular dynamics applications and techniques : a comparison study of silica potentials and techniques for accelerating computation." Thesis, 1999. http://hdl.handle.net/1957/33213.
Повний текст джерелаGraduation date: 1999
Yen, Cheng-Pin, and 顏正濱. "Theoretical study of ethanol decomposition on Pt(111) surface and electron transfer in push-pull molecular systems from ab initio molecular dynamics." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/57981305367727481606.
Повний текст джерела淡江大學
化學學系碩士班
97
Abstract: In part 1 , total energy calculation based on Density Function Theory (DFT) with Ultrasoft-pseudopotenital and generalized gradient spin-polarized approximation (GGSA) was used to investigate (1) O-H cleavage of ethanol and (2)C-H hydrogen elimination via four-membered ring and five-membered ring on Pt(111)-3x3 surface. By means of Partial Structure Constrain Path Minimization(PSCPM) method , our calculated energy barrier for O-H cleavage is 0.849eV and C-H hydrogen elimination via four-membered ring and five-membered ring are 0.319eV and 0.966eV , respectively. These results are in good agreement with TPD experimental result. Furthermore , we found that (1) less change in Pt-Pt dimmer bond length and (2) more H-Pt bond formation , less change in carbon hybrid orbital and π bonding in C=O by means of the partial density of state (PDOS) for the four-membered-ring hydrogen elimination to explain reaction selectivity. In part 2 , we performed first principle molecular dynamics based on Density Function Theory with norm-conversing pseudopotential and accurate LCAO basis set in SIESTA package on CN-CH=CH-NH2 , NO2-CH=CH-NH2 and BH2-CH=CH-NH2¬ push-pull molecule system and we collected dipole moment ,structure and charge trajectory in 3ps molecular dynamics. We used Fourier Transformed dipole moment AutoCorrelation Function to simulate IR spectra and analyzed characteristic vibration mode in molecule by using PaDAF and SCAF method. By comparison of Fourier Transformed charge AutoCorrelation Function (FT[charge-ACF]) and IR spectra , we found that main-chain vibration mode induced charge transfer. Furthermore , we calculated charge transfer rate by utilizing charge dynamics and explain charge transfer effect of these push-pull molecules.Finally , we also investigated temperature effect on charge transfer and calculated activation barrier of charge transfer.