subject:(MD simulation)

1. Zhang, Baofeng. Molecular Dynamics Simulation and Theoretical Studies of Vibrational Energy Relaxation: Vibrational Energy Relaxation of a Large Polyatomic Molecule in a Liquid.

Degree: PhD, Chemistry, 2012, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:297591/

► Our central goal in this thesis is to investigate the vibrational energy relaxation (VER) of perylene in solution. The size of a perylene molecule makes… (more)

▼ Our central goal in this thesis is to investigate the vibrational energy relaxation (VER) of perylene in solution. The size of a perylene molecule makes MD simulation of VER very challenging. By using a harmonic oscillator model and figuring out the centrifugal force expression for vibration-rotation coupling, we successfully simulate this lowest vibrational energy mode, the warping vibrational mode, in perylene under equilibrium and nonequilibrium conditions. Based on the simulation results, we discover that the VER of the warping vibrational mode is not straightforward, but proceeds through different intramolecular pathways, which we call intrinsic vibrational kinetic energy (VKE) and vibrational potential energy (VPE) pathways. We find out that during the VER process in liquid, the abilities of the solvent to relax VKE and VPE are different. At low vibrational frequency, VKE relaxation is very fast with nearly hard sphere-like initial energy transfer to the solvent molecules in the first solvation shell. At high vibrational frequency, VKE relaxation is very slow. we thoroughly study the equilibrium solvent mass effects and use an effective frequency concept and a harmonic triatomic model to successfully explain the simulation results. In addition, we use INM band theory [84-86] to study the perylene system and draw a much clear physical picture of the VER process. Our main work in studying nonequilibrium VER of perylene focuses on figuring out whether linear response theory is working and explaining the results by using Time Scale theory. Our final simulation results not only examine the power of TS theory, but also fundamentally confirm that linear response theory always works in the VER process. We use Time Scale theory to investigate the solvent structure origin and the time scale origins of linear response. Unlike the situation with the nonlinear rotational energy relaxation of the CN rotor [18-20], we find out that in the VER of perylene, the intrinsic characteristics of warping vibrational mode guarantee that one could never simultaneously induce significant solvent structure change and keep the time scale difference between solute and solvent large enough to trigger nonlinear response. Advisors/Committee Members: Stratt, Richard (Director), Doll, Jimmie (Reader), Wang, Lai-Sheng (Reader).

Subjects/Keywords: MD simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhang, B. (2012). Molecular Dynamics Simulation and Theoretical Studies of Vibrational Energy Relaxation: Vibrational Energy Relaxation of a Large Polyatomic Molecule in a Liquid. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:297591/

Chicago Manual of Style (16^th Edition):

Zhang, Baofeng. “Molecular Dynamics Simulation and Theoretical Studies of Vibrational Energy Relaxation: Vibrational Energy Relaxation of a Large Polyatomic Molecule in a Liquid.” 2012. Doctoral Dissertation, Brown University. Accessed April 12, 2021. https://repository.library.brown.edu/studio/item/bdr:297591/.

MLA Handbook (7^th Edition):

Zhang, Baofeng. “Molecular Dynamics Simulation and Theoretical Studies of Vibrational Energy Relaxation: Vibrational Energy Relaxation of a Large Polyatomic Molecule in a Liquid.” 2012. Web. 12 Apr 2021.

Vancouver:

Zhang B. Molecular Dynamics Simulation and Theoretical Studies of Vibrational Energy Relaxation: Vibrational Energy Relaxation of a Large Polyatomic Molecule in a Liquid. [Internet] [Doctoral dissertation]. Brown University; 2012. [cited 2021 Apr 12]. Available from: https://repository.library.brown.edu/studio/item/bdr:297591/.

Council of Science Editors:

Zhang B. Molecular Dynamics Simulation and Theoretical Studies of Vibrational Energy Relaxation: Vibrational Energy Relaxation of a Large Polyatomic Molecule in a Liquid. [Doctoral Dissertation]. Brown University; 2012. Available from: https://repository.library.brown.edu/studio/item/bdr:297591/

2. Creazzo, Fabrizio. Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics : Réaction d'évolution de l'oxygène aux interfaces d'oxides de cobalt/eau liquide : électrocatalyse hétérogène par simulations de DFT-MD et de metadynamique.

Degree: Docteur es, Chimie, 2020, université Paris-Saclay

URL: http://www.theses.fr/2020UPASE012

►

Dans cette thèse, des simulations DFT-MD couplées à des techniques inno-vantes de métadynamique, sont appliquées pour acquérir une compréhensionglobale des interfaces aqueuses d'oxyde de cobalt… (more)

▼

Dans cette thèse, des simulations DFT-MD couplées à des techniques inno-vantes de métadynamique, sont appliquées pour acquérir une compréhensionglobale des interfaces aqueuses d'oxyde de cobalt Co3O4 et CoO(OH) dansla catalyse de la réaction d'évolution de l'oxygène (OER), et ainsi éventuellement aider à la conception de nouveaux catalyseurs basés sur des matériaux non précieux, un domaine clé de la recherche scientifique et technologique, particulièrement important pour l'économie de l'hydrogène, pour les technologies vertes dans une période de temps avec une demande toujours plus croissanteen énergie verte. Dans cette thèse, nous révélons étape par étape les mécanismes de l'OER sur les électrocatalyseurs aqueux d'oxyde de cobalt Co3O4 etCoO(OH) via de nouvelles techniques de métadynamique.Jusqu'à présent, la littérature n'a jamais pris en compte les modificationsau niveau atomique de la structure des électrodes ainsi que de l'eau interfaciale dans leur modélisation des processus OER. Ce manque de connaissances représente clairement un obstacle important au développement de catalyseurs améliorés, qui pourrait être surmonté en utilisant des méthodes capables de suivre les caractéristiques catalytiques de l'OER à l'échelle atomique. Pour la première fois, nous montrons combien il est important de prendre en considération la présence de l'environnement aqueux dans la caractérisation structurale des surfaces du catalyseur, c'est-à-dire (110)-Co3O4 et (0001)-CoO(OH) dans ce travail. Une caractérisation détaillée des propriétés chimiques et physiques des interfaces aqueuses est fournie (la structure, la dynamique, la spectroscopie, le champ électrique), pour les surfaces (110)-Co3O4 et (0001)-CoO(OH) en contact avec l'eau liquide.Une étude détaillée de l'OER est présentée non seulement du point de vue descatalyseurs, mais aussi en abordant le rôle de l'environnement de l'eau dans leprocessus catalytique, ce qui n'a pas été fait auparavant dans la littérature. En conséquence, l'OER en phase gazeuse et en phase liquide sont étudiés ici auxinterfaces aqueuses (110)-Co3O4 et (0001)-CoO(OH) en adoptant une nouvelleapproche de métadynamique d'échantillonnage amélioré, capable d'identifieret caractériser les mécanismes de réaction chimique et d'intégrer pleinement lerôle des degrés de liberté du solvant, permettant ainsi de dévoiler des réactivités chimiques d'une complexité remarquable. L'énergétique, la cinétique et la thermodynamique derrière l'OER sont donc trouvées à ces surfaces d'oxyde de cobalt à l'interface avec l'eau.

In this thesis, DFT-MD simulations, coupled with state-of-the-art metadynamics techniques, are applied to gain a global understanding of Co3O4 and CoO(OH) cobalt oxide aqueous interfaces in catalyzing the oxygen evolution reaction (OER), and hence possibly help in the design of novel catalysts basedon non-precious materials, a current key field of research in science and technology, especially of importance for the hydrogen economy, for green technology in a period of time with an ever more growing…

Advisors/Committee Members: Gaigeot, Marie-Pierre (thesis director).

Subjects/Keywords: Simulation DFT-MD; Métadynamique; DFT-MD; Metadynamics

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Creazzo, F. (2020). Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics : Réaction d'évolution de l'oxygène aux interfaces d'oxides de cobalt/eau liquide : électrocatalyse hétérogène par simulations de DFT-MD et de metadynamique. (Doctoral Dissertation). université Paris-Saclay. Retrieved from http://www.theses.fr/2020UPASE012

Chicago Manual of Style (16^th Edition):

Creazzo, Fabrizio. “Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics : Réaction d'évolution de l'oxygène aux interfaces d'oxides de cobalt/eau liquide : électrocatalyse hétérogène par simulations de DFT-MD et de metadynamique.” 2020. Doctoral Dissertation, université Paris-Saclay. Accessed April 12, 2021. http://www.theses.fr/2020UPASE012.

MLA Handbook (7^th Edition):

Creazzo, Fabrizio. “Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics : Réaction d'évolution de l'oxygène aux interfaces d'oxides de cobalt/eau liquide : électrocatalyse hétérogène par simulations de DFT-MD et de metadynamique.” 2020. Web. 12 Apr 2021.

Vancouver:

Creazzo F. Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics : Réaction d'évolution de l'oxygène aux interfaces d'oxides de cobalt/eau liquide : électrocatalyse hétérogène par simulations de DFT-MD et de metadynamique. [Internet] [Doctoral dissertation]. université Paris-Saclay; 2020. [cited 2021 Apr 12]. Available from: http://www.theses.fr/2020UPASE012.

Council of Science Editors:

Creazzo F. Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics : Réaction d'évolution de l'oxygène aux interfaces d'oxides de cobalt/eau liquide : électrocatalyse hétérogène par simulations de DFT-MD et de metadynamique. [Doctoral Dissertation]. université Paris-Saclay; 2020. Available from: http://www.theses.fr/2020UPASE012

Universiteit Utrecht

3. Wolterink, J.M. Extending Time Scales for Molecular Simulations.

Degree: 2012, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/261054

► Molecular dynamics simulations and protein structure prediction are essential tools in the quest for better understanding of the behavior of complex proteins. Based on these… (more)

Subjects/Keywords: ARPS; MD; GPU; Simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wolterink, J. M. (2012). Extending Time Scales for Molecular Simulations. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/261054

Chicago Manual of Style (16^th Edition):

Wolterink, J M. “Extending Time Scales for Molecular Simulations.” 2012. Masters Thesis, Universiteit Utrecht. Accessed April 12, 2021. http://dspace.library.uu.nl:8080/handle/1874/261054.

MLA Handbook (7^th Edition):

Wolterink, J M. “Extending Time Scales for Molecular Simulations.” 2012. Web. 12 Apr 2021.

Vancouver:

Wolterink JM. Extending Time Scales for Molecular Simulations. [Internet] [Masters thesis]. Universiteit Utrecht; 2012. [cited 2021 Apr 12]. Available from: http://dspace.library.uu.nl:8080/handle/1874/261054.

Council of Science Editors:

Wolterink JM. Extending Time Scales for Molecular Simulations. [Masters Thesis]. Universiteit Utrecht; 2012. Available from: http://dspace.library.uu.nl:8080/handle/1874/261054

IUPUI

4. Leng, Xiaoling. Insights on PUFA-containing lipid membranes probed by MD simulations.

Degree: 2017, IUPUI

URL: http://hdl.handle.net/1805/12326

►

Indiana University-Purdue University Indianapolis (IUPUI)

The cell membrane serves as a barrier between the interior and exterior of a living cell. Its main structural component… (more)

▼

Indiana University-Purdue University Indianapolis (IUPUI)

The cell membrane serves as a barrier between the interior and exterior of a living cell. Its main structural component is the lipid bilayer, which is composed of various kinds of lipids that segregate into domains. These lipid domains, distinguished in composition and physical properties from the bulk lipids that surround them, are believed to modulate the function of resident proteins by providing an appropriate lipid environment. Polyunsaturated fatty acids (PUFA) are a type of fatty acid that contain multiple C=C double bonds. They have a lot of health benefits, which may originate in part due to their incorporation into lipids in the plasma membrane. Hypotheses that PUFA-containing lipids laterally separate into domains and/or modulate the structure of existing domains have been raised to explain the fundamental role played by PUFA. In our research, we use molecular dynamics (MD) simulations to simulate model membranes composed of PUFA-containing phospholipids and to investigate their interaction with cholesterol and vitamin E that are influential membrane constituents. The presumptive function for vitamin E in membranes is to protect PUFA against oxidation. Although the chemistry of the process is well established, the role played by the molecular structure that we address with atomistic molecular dynamics (MD) simulations remains controversial. We compared the behavior of vitamin E in lipid bilayers composed of 1-stearoyl-2-docosahexaenoylphosphatidylcholine (SDPC, 18:0-22-6PC) and 1-stearoyl-2-oleoylphosphatidylcholine (SOPC, 18:0-18:1PC) via all-atom MD simulations at 37° C. SDPC represents a PUFA-containing lipid, and SOPC serves as monounsaturated control. From the calculation of van der Waals energy of interaction between vitamin E and fatty acid (FA) chains, we found higher probability that the PUFA chains surround the chromanol head group on vitamin E. This is further demonstrated by probability density maps of acyl chains around vitamin E molecules. Also, an ability to more easily penetrate deep into the PUFA containing bilayer of vitamin E is detected by faster flip-flop rate of vitamin E observed in the SDPC bilayers. These results showed that the high disorder of polyunsaturated docosahexaenoic acid (DHA) chains allows vitamin E to easily tunnel down into the bilayer and often brings the PUFA chains up to the surface of the bilayer, improving the likelihood that the reactive (hydroxyl) group on vitamin E would encounter a lipid peroxyl radical and terminate the oxidation process. Thus, the simulations indicate that the molecular structure of vitamin E supports its role as an antioxidant in a PUFA-containing membrane. A subsequent study on the partitioning of vitamin E into PUFA-containing lipids was done by analyzing the binding energy of vitamin E in the corresponding lipid bilayer. The binding energy is obtained from the potential of mean force (PMF) profile of vitamin E alone the membrane normal direction (z), which is calculated…

Advisors/Committee Members: Wassall, Stephen.

Subjects/Keywords: PUFA; lipid membrane; MD simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Leng, X. (2017). Insights on PUFA-containing lipid membranes probed by MD simulations. (Thesis). IUPUI. Retrieved from http://hdl.handle.net/1805/12326

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Leng, Xiaoling. “Insights on PUFA-containing lipid membranes probed by MD simulations.” 2017. Thesis, IUPUI. Accessed April 12, 2021. http://hdl.handle.net/1805/12326.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Leng, Xiaoling. “Insights on PUFA-containing lipid membranes probed by MD simulations.” 2017. Web. 12 Apr 2021.

Vancouver:

Leng X. Insights on PUFA-containing lipid membranes probed by MD simulations. [Internet] [Thesis]. IUPUI; 2017. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1805/12326.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Leng X. Insights on PUFA-containing lipid membranes probed by MD simulations. [Thesis]. IUPUI; 2017. Available from: http://hdl.handle.net/1805/12326

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University

5. Zhang, Yu. Molecular Dynamics Study of Electric Double Layer Capacitors: Modifying Electrode and Electrolyte Composition.

Degree: PhD, Chemical Engineering, 2019, Vanderbilt University

URL: http://hdl.handle.net/1803/12289

► Electric double layer capacitors (EDLCs) are energy storage devices that are the subject of active research due to high power density, moderate energy density, broad… (more)

▼ Electric double layer capacitors (EDLCs) are energy storage devices that are the subject of active research due to high power density, moderate energy density, broad operating temperature windows, and long cycle lifetimes. Distinct from batteries, which convert external energy to charges through redox reactions, EDLCs store charge by electrosorption of ions from electrolyte onto an electrode surface, resulting in an electric double layer. This physical charge storage mechanism enables EDLCs to yield greater power densities over batteries, but also limits their energy density. The past few years has seen a huge increase in the performance of supercapacitors due to the discovery of novel electrode and electrolyte materials, better understanding of charging/discharging mechanisms, as well as more intelligent design of hybrid systems. In this work, molecular dynamics (MD) simulations were conducted to study the performance of carbon-based EDLCs. We applied different modifications to the carbon-based materials, including nitrogen doping, edge sites, and surface oxidization, and evaluated their corresponding influences on the performance. Nitrogen doping and edge sites were both found to be effective to increases the capacitance of graphene-based EDLCs, but both of these modifications needed careful selection of doping/edge configurations. While oxidizations on nonporous carbon electrodes decreased capacitance, oxidizations in porous confinements exhibited different influences on small pores (0.8 nm) and large pores (2.6 nm). In addition, we investigated the effects of electrolyte composition and concentration on the capacitance and ion dynamics on various carbon electrodes. It was found that the increase of cation size decreased the capacitance and ion dynamics. Moreover, solvation of ionic liquid electrolytes drastically enhanced ion dynamics, but its effects on capacitance depended on the specific carbon electrodes used. Advisors/Committee Members: Carglar Oskay (committee member), Clare McCabe (committee member), Rizia Bardhan (committee member), Peter T. Cummings (Committee Chair).

Subjects/Keywords: Supercapacitor; MD simulation; Ionic liquids; Carbon materials

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhang, Y. (2019). Molecular Dynamics Study of Electric Double Layer Capacitors: Modifying Electrode and Electrolyte Composition. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12289

Chicago Manual of Style (16^th Edition):

Zhang, Yu. “Molecular Dynamics Study of Electric Double Layer Capacitors: Modifying Electrode and Electrolyte Composition.” 2019. Doctoral Dissertation, Vanderbilt University. Accessed April 12, 2021. http://hdl.handle.net/1803/12289.

MLA Handbook (7^th Edition):

Zhang, Yu. “Molecular Dynamics Study of Electric Double Layer Capacitors: Modifying Electrode and Electrolyte Composition.” 2019. Web. 12 Apr 2021.

Vancouver:

Zhang Y. Molecular Dynamics Study of Electric Double Layer Capacitors: Modifying Electrode and Electrolyte Composition. [Internet] [Doctoral dissertation]. Vanderbilt University; 2019. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1803/12289.

Council of Science Editors:

Zhang Y. Molecular Dynamics Study of Electric Double Layer Capacitors: Modifying Electrode and Electrolyte Composition. [Doctoral Dissertation]. Vanderbilt University; 2019. Available from: http://hdl.handle.net/1803/12289

University of Rochester

6. Zhang, Xiaoju. Computational studies of yeast protein translational components.

Degree: PhD, 2016, University of Rochester

URL: http://hdl.handle.net/1802/30945

► In the past decades, RNA has been discovered to have new functional roles, and it is no longer considered simply intermediate molecule between DNA and… (more)

▼ In the past decades, RNA has been discovered to have new functional roles, and it is no longer considered simply intermediate molecule between DNA and protein as the Central Dogma described. Protein translation is one of the most crucial cellar activities in which RNA molecules are involved. In this thesis work, tRNA and mRNA, two major RNA components of protein synthesis, were computationally investigated. </br> Experimental studies reveal that covalent modifications play an important role in tuning tRNA function. The X-ray crystal structures of tRNA^Asp, tRNA^Phe, and tRNA^iMet, both with and without modifications, were used as initial structures for 333 ns explicit solvent MD simulations with AMBER. For each tRNA molecule, three independent trajectory calculations were performed in parallel. The root mean square deviations (RMSD) of the anticodon stem-loop (ASL) suggest that modified tRNA has a more rigid structure compared to the unmodified tRNA in this domain. Interestingly, the anticodon RMSDs of the modified tRNAs are higher than those of corresponding unmodified tRNAs. These findings suggest that the rigidity of the anticodon stem-loop is finely tuned by modifications, where rigidity in the anticodon arm is essential for tRNA translocation in the ribosome, and flexibility of the anticodon is important for codon recognition. </br> Similar to codon usage, codon pair usage is also biased in mRNA. Fourteen codon pairs were identified as inhibitory in S. cerevisiae from a previous study. In order to test the hypothesis that these inhibitory codon pairs (ICPs) are functional in yeast, a comparative genomic study was performed upon an open reading frame (ORF) sequence alignment dataset. The alignment includes five sensu stricto Saccharomyces species, bayanus var. uvarum, kudriavzevii, mikatae, cerevisiae and paradoxus. A whole ORF genome survey was conducted, suggesting that genes with ICPs are not significantly more conserved than the genes without ICPs. However, the conservation rate of a subset of the inhibitory codon pairs is higher than the product of conservation rate of its two composing codons. </br> Sequence variation in tRNA genes influences the tRNA’s structure, modification and stability, and hence affects tRNA activity and impacts translational fidelity. In order to define the effects of mutation on tRNA function, a high-throughput in vivo screen to quantify the activity of a model tRNA, SUP4oc of S. cerevisiae was developed and a library of 25,491 tRNA variants were scored for the activity. For the tRNA variants, quantified tRNA structure traits (ensemble defect and folding free energy) were tested for the correlations to tRNA activity, tRNA susceptibility to rapid tRNA decay and tRNA temperature sensitivity.

Subjects/Keywords: Conservation; Inhibitory codon pair; MD simulation; tRNA modification; Yeast

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhang, X. (2016). Computational studies of yeast protein translational components. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/30945

Chicago Manual of Style (16^th Edition):

Zhang, Xiaoju. “Computational studies of yeast protein translational components.” 2016. Doctoral Dissertation, University of Rochester. Accessed April 12, 2021. http://hdl.handle.net/1802/30945.

MLA Handbook (7^th Edition):

Zhang, Xiaoju. “Computational studies of yeast protein translational components.” 2016. Web. 12 Apr 2021.

Vancouver:

Zhang X. Computational studies of yeast protein translational components. [Internet] [Doctoral dissertation]. University of Rochester; 2016. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1802/30945.

Council of Science Editors:

Zhang X. Computational studies of yeast protein translational components. [Doctoral Dissertation]. University of Rochester; 2016. Available from: http://hdl.handle.net/1802/30945

University of Alberta

7. Ni, Xiao. Molecular simulation of the wetting of selected solvents on sand and clay surfaces.

Degree: MS, Chemical and Materials Engineering, 2009, University of Alberta

URL: https://era.library.ualberta.ca/files/nc580n98b

► Molecular dynamics simulation and density functional theory were applied to calculate heats of immersion (ΔHimm) of n-heptane, toluene, pyridine and water on two model sand… (more)

Subjects/Keywords: Wetting; Clay; Heat of Immersion; Sand; Oil Sands; MD Simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ni, X. (2009). Molecular simulation of the wetting of selected solvents on sand and clay surfaces. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/nc580n98b

Chicago Manual of Style (16^th Edition):

Ni, Xiao. “Molecular simulation of the wetting of selected solvents on sand and clay surfaces.” 2009. Masters Thesis, University of Alberta. Accessed April 12, 2021. https://era.library.ualberta.ca/files/nc580n98b.

MLA Handbook (7^th Edition):

Ni, Xiao. “Molecular simulation of the wetting of selected solvents on sand and clay surfaces.” 2009. Web. 12 Apr 2021.

Vancouver:

Ni X. Molecular simulation of the wetting of selected solvents on sand and clay surfaces. [Internet] [Masters thesis]. University of Alberta; 2009. [cited 2021 Apr 12]. Available from: https://era.library.ualberta.ca/files/nc580n98b.

Council of Science Editors:

Ni X. Molecular simulation of the wetting of selected solvents on sand and clay surfaces. [Masters Thesis]. University of Alberta; 2009. Available from: https://era.library.ualberta.ca/files/nc580n98b

Loyola University Chicago

8. Gao, Yi. Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations.

Degree: PhD, Chemistry, 2014, Loyola University Chicago

URL: https://ecommons.luc.edu/luc_diss/1262

► Molecular dynamics (MD) simulation has been widely used in understanding the physical basis of the structure and function of biological macromolecules. However, its application… (more)

▼ Molecular dynamics (MD) simulation has been widely used in understanding the physical basis of the structure and function of biological macromolecules. However, its application in pharmaceutical research is still at an early stage. This dissertation attempts to establish the use of MD simulation in studying several important pharmaceutical mass transfer processes. The three-series study included (1) the understanding of drug crystal dissolution at molecular level, (2) the elucidation of an unique mechanism for facile polymorphic transformation of crystalline drugs in solutions, and (3) the determination of drug-polymer interactions at water-crystal interface and the implications to crystallization inhibition. A drug crystal dissolution into aqueous solution was simulated successfully for the first time on acetaminophen crystal Form I. The results revealed distinct corner & edge effect and differentiated dissolution rate among the three crystal surfaces of (001), (101) and (100), which correlated strongly with total interaction energies among the drug molecules and between the drug and water molecules. This study helped us gain additional fundamental understanding in the relationship between dissolution rate and particle size and morphology. A series of MD simulations and experimental methods were utilized to evaluate the thermodynamic and kinetic forces that control the polymorphic transformation in solutions. Acetaminophen Form II, a metastable crystalline form which readily converts to the themodymically stable Form I when in contact with solution was studied. It was found that the facile polymorphic transformation is not attributed to the solubility differences; rather it is caused by a unique mechanism of surface facilitated phase transformation (SurFPT). This new mechanism is able to promote faster polymorphic transformation than the well-known mechanism of solution-mediated phase transformation (SMPT), thus it is more detrimental. In the third study, the molecular mechanism of crystal surface specific drug-polymer interaction was investigated by simulating tolazamide crystals in the presence of hydrated PEG-b-PLA, a diblock copolymer. The results from the simulations demonstrated the polymer's strong interaction with the (001) face, weaker interaction with the (010) face and minimal to no interaction with the (100) face, which matched remarkably well with the reported crystal habit alteration by the preferential interaction of PEG-b-PLA primarily with the (001) and partially with (010). Interestingly, van der Waals interactions were identified as the dominant forces (accounts for 77-93% of total interaction energies) that enabled such strong drug-polymer interactions. These findings suggest that polymers capable of forming strong hydrophobic interactions are more effective in inhibiting crystallization of poorly-water soluble and hydrophobic drugs in aqueous media than those with hydrogen bonding capacities. Such in-depth analysis and understanding facilitate the rational selection of…

Subjects/Keywords: dissolution; interaction; MD simulation; Pharmaceutical; polymer; polymorph; Pharmacy and Pharmaceutical Sciences

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gao, Y. (2014). Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations. (Doctoral Dissertation). Loyola University Chicago. Retrieved from https://ecommons.luc.edu/luc_diss/1262

Chicago Manual of Style (16^th Edition):

Gao, Yi. “Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations.” 2014. Doctoral Dissertation, Loyola University Chicago. Accessed April 12, 2021. https://ecommons.luc.edu/luc_diss/1262.

MLA Handbook (7^th Edition):

Gao, Yi. “Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations.” 2014. Web. 12 Apr 2021.

Vancouver:

Gao Y. Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations. [Internet] [Doctoral dissertation]. Loyola University Chicago; 2014. [cited 2021 Apr 12]. Available from: https://ecommons.luc.edu/luc_diss/1262.

Council of Science Editors:

Gao Y. Investigation of Pharmaceutical Mass Transfer Phenomena Using Molecular Dynamics Simulations. [Doctoral Dissertation]. Loyola University Chicago; 2014. Available from: https://ecommons.luc.edu/luc_diss/1262

Texas A&M University

9. Fu, Xuebing. How trehalose protects DNA in the dry state: a molecular dynamics simulation.

Degree: MS, Chemistry, 2008, Texas A&M University

URL: http://hdl.handle.net/1969.1/86002

► Molecular dynamics simulations were conducted on a system consisting of a decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a relatively… (more)

Subjects/Keywords: trehalose; DNA; MD simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fu, X. (2008). How trehalose protects DNA in the dry state: a molecular dynamics simulation. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/86002

Chicago Manual of Style (16^th Edition):

Fu, Xuebing. “How trehalose protects DNA in the dry state: a molecular dynamics simulation.” 2008. Masters Thesis, Texas A&M University. Accessed April 12, 2021. http://hdl.handle.net/1969.1/86002.

MLA Handbook (7^th Edition):

Fu, Xuebing. “How trehalose protects DNA in the dry state: a molecular dynamics simulation.” 2008. Web. 12 Apr 2021.

Vancouver:

Fu X. How trehalose protects DNA in the dry state: a molecular dynamics simulation. [Internet] [Masters thesis]. Texas A&M University; 2008. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1969.1/86002.

Council of Science Editors:

Fu X. How trehalose protects DNA in the dry state: a molecular dynamics simulation. [Masters Thesis]. Texas A&M University; 2008. Available from: http://hdl.handle.net/1969.1/86002

Texas A&M University

10. Hu, Yuzhu. Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance.

Degree: MS, Mechanical Engineering, 2014, Texas A&M University

URL: http://hdl.handle.net/1969.1/153304

► Concentrated Solar Power (CSP) systems are used widely as a stable and reliable renewable source of energy. However, intermittency of this power source and the… (more)

▼ Concentrated Solar Power (CSP) systems are used widely as a stable and reliable renewable source of energy. However, intermittency of this power source and the variability in demand for electrical power creates challenges that necessitate the integration with energy storage for reliable dispatch of power. Thermal Energy Storage (TES) systems provide a cheap, cost-effective and reliable option for energy storage in renewable power delivery systems. Due to their low vapor pressures at elevated temperatures, molten salts and their eutectics are used in conventional high temperature thermal energy storage (TES) systems and also as coolants for energy conversion, such as in power tower configurations that are typically used in CSP applications. A major drawback of the molten salts is their relatively poor thermo-physical properties, which may lead to lower systemic efficiencies in CSP/TES. Recent reports in the literature have shown that doping molten salts with nanoparticles at minute concentrations (typically less than 5% mass fraction and ideally at less than 1-2% mass fraction) can significantly enhance the thermo-physical properties of these nanomaterial (also termed as “nanocomposites” in solid state and “nanofluids” in liquid state). The dominant factor that controls the resultant thermo-physical properties of these nanomaterials is the interfacial thermal resistance (or Kapitza Resistance “R_(k)”) that impedes the heat transfer between the nanoparticle surface and the bulk solvent molecules. In this study, the interfacial thermal resistance between a carbon nanotube (CNT) and carbonate molten salt eutectics were calculated by using numerical models that were then implemented in Molecular Dynamics (MD) simulations. The estimates for “R_(k)” obtained from these simulations enabled the prediction of the optimum dimensions of the nanoparticles for maximizing the thermo-physical properties of the mixture, i.e. thermal conductivity and specific heat capacity values of these nanomaterial. The simulations were restricted to the carbonate salt eutectic, which is composed of a molar ratio of 62:38 for lithium carbonate (Li_(2)CO_(3)) and potassium carbonate (K_(2)CO_(3)). In this study, parametric simulations were performed to estimate the values of “R_(k)” by varying the chirality of a single walled CNT (i.e, for armchair, chiral, and zig-zag CNT). The results show that the Kapitza resistance of the CNT is significantly affected by the change in the chirality of the CNT. Advisors/Committee Members: Banerjee, Debjyoti (advisor), Morrison, Gerald (committee member), Chen, Hamn-Ching (committee member).

Subjects/Keywords: Interfacial Thermal Resistance; Carbon Nanotube; MD simulation; Chirality

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hu, Y. (2014). Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/153304

Chicago Manual of Style (16^th Edition):

Hu, Yuzhu. “Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance.” 2014. Masters Thesis, Texas A&M University. Accessed April 12, 2021. http://hdl.handle.net/1969.1/153304.

MLA Handbook (7^th Edition):

Hu, Yuzhu. “Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance.” 2014. Web. 12 Apr 2021.

Vancouver:

Hu Y. Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance. [Internet] [Masters thesis]. Texas A&M University; 2014. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1969.1/153304.

Council of Science Editors:

Hu Y. Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance. [Masters Thesis]. Texas A&M University; 2014. Available from: http://hdl.handle.net/1969.1/153304

Penn State University

11. Qi, Xin. Probing monocrystalline and multiply-twinned nanocrystal growth from thermodynamic and kinetic perspectives.

Degree: 2018, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/15413xzq103

► Metal nanocrystals are beautiful and powerful. While they attract great attentions for their exceptional structural-dependent performance in an array of modern technologies, how they are… (more)

▼ Metal nanocrystals are beautiful and powerful. While they attract great attentions for their exceptional structural-dependent performance in an array of modern technologies, how they are born and why they can grow into various shapes still largely remain mysterious. The lack of comprehensive fundamental understanding in their growth mechanism inevitably obstructs the perfection of the process, specifically in increasing the selectivity and yield of certain structures and sizes, as well as elevating the production capacity to a manufacturing level. In synthesizing metal nanocrystals, the solution-phase polyol syntheses outper- form other protocols and are applicable to a variety of metal species. Chemical additives are often added in these processes to prevent aggregation and, at the same time, to promote the selection of a specific shape. Considering the chemical complexity and the length/time scale of these systems, it is particularly challenging to unravel the formation and growth mechanisms via experimental means. Compu- tational methods, on the other hand, can be notably useful in this regard, as they are able to probe atomistic details, and by integrating theories, they can be used to calculate properties that are difficult to measure. This dissertation elucidates several important aspects in Ag nanocrystal growth using classical all-atom molecular dynamics (MD) simulation. The work included in this dissertation covers the thermodynamic and kinetic ramification from chemical additives in monocrystalline Ag nanocrystals, as well as the 1-dimensional (1D) growth origin of the five-fold-twinned Ag nanowire. To evaluate the thermodynamic influence, we develop a method that calculates the facet-specific interfacial free energy γsl for multi-component solid-liquid interface described by complex force fields. We use this method to assess how polyvinylpyrroli- done (PVP), an effective structure-directing agent (SDA) for Ag(100)-faceted shapes, alters the interfacial free energy for Ag surfaces solvated in ethylene glycol upon adsorption, and further extend the study to characterize a general impact from additives on Ag surfaces at a range of binding energies. We also examine the facet-selective solution-phase deposition on to crystal surfaces regulated by PVP and show how it influences the steady-state kinetic shapes. In contrast to monocrystalline, multiply-twinned nanocrystals bear stress and strain. Interestingly, we find that the stress and strain in a 5-fold-twinned Ag nanowire can alter the surface atomistic structure and affect adatom distribution, and such alternations can bring unique surface atom diffusion that triggers the 1D expansion. Altogether, we report on our progress in probing monocrystalline and multiply- twinned nanocrystal growth from thermodynamic and kinetic perspectives and outlook for future research directions. Advisors/Committee Members: Kristen Ann Fichthorn, Dissertation Advisor/Co-Advisor, Kristen Ann Fichthorn, Committee Chair/Co-Chair, Michael John Janik, Committee Member, Adrianus C Van Duin, Committee Member, Seong Han Kim, Outside Member.

Subjects/Keywords: Ag; nanocrystal growth; MD simulation; Theory; thermodynamics; kinetics

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Qi, X. (2018). Probing monocrystalline and multiply-twinned nanocrystal growth from thermodynamic and kinetic perspectives. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/15413xzq103

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Qi, Xin. “Probing monocrystalline and multiply-twinned nanocrystal growth from thermodynamic and kinetic perspectives.” 2018. Thesis, Penn State University. Accessed April 12, 2021. https://submit-etda.libraries.psu.edu/catalog/15413xzq103.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Qi, Xin. “Probing monocrystalline and multiply-twinned nanocrystal growth from thermodynamic and kinetic perspectives.” 2018. Web. 12 Apr 2021.

Vancouver:

Qi X. Probing monocrystalline and multiply-twinned nanocrystal growth from thermodynamic and kinetic perspectives. [Internet] [Thesis]. Penn State University; 2018. [cited 2021 Apr 12]. Available from: https://submit-etda.libraries.psu.edu/catalog/15413xzq103.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Qi X. Probing monocrystalline and multiply-twinned nanocrystal growth from thermodynamic and kinetic perspectives. [Thesis]. Penn State University; 2018. Available from: https://submit-etda.libraries.psu.edu/catalog/15413xzq103

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

12. Jo, Gunwoo. PROTON HOPPING IN A SINGLE LAYER WATER BETWEEN MXENE LAYERS USING REAXFF MD SIMULATION.

Degree: 2017, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/13879gzj5062

► The purpose of this thesis is to analyze proton migrations in single layer water which is located between two MXene layers with nine different temperatures… (more)

Subjects/Keywords: MXenes; ReaxFF; Proton hopping; Diffusion constant; MD simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Jo, G. (2017). PROTON HOPPING IN A SINGLE LAYER WATER BETWEEN MXENE LAYERS USING REAXFF MD SIMULATION. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/13879gzj5062

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Jo, Gunwoo. “PROTON HOPPING IN A SINGLE LAYER WATER BETWEEN MXENE LAYERS USING REAXFF MD SIMULATION.” 2017. Thesis, Penn State University. Accessed April 12, 2021. https://submit-etda.libraries.psu.edu/catalog/13879gzj5062.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Jo, Gunwoo. “PROTON HOPPING IN A SINGLE LAYER WATER BETWEEN MXENE LAYERS USING REAXFF MD SIMULATION.” 2017. Web. 12 Apr 2021.

Vancouver:

Jo G. PROTON HOPPING IN A SINGLE LAYER WATER BETWEEN MXENE LAYERS USING REAXFF MD SIMULATION. [Internet] [Thesis]. Penn State University; 2017. [cited 2021 Apr 12]. Available from: https://submit-etda.libraries.psu.edu/catalog/13879gzj5062.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Jo G. PROTON HOPPING IN A SINGLE LAYER WATER BETWEEN MXENE LAYERS USING REAXFF MD SIMULATION. [Thesis]. Penn State University; 2017. Available from: https://submit-etda.libraries.psu.edu/catalog/13879gzj5062

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

13. Mostofian, Barmak. The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study.

Degree: 2014, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_graddiss/3156

► The use of ionic liquids for the dissolution of cellulose promises an alternative method for the thermochemical pretreatment of biomass that may be more efficient… (more)

▼ The use of ionic liquids for the dissolution of cellulose promises an alternative method for the thermochemical pretreatment of biomass that may be more efficient and environmentally acceptable than conventional techniques in aqueous solution. Understanding how ionic liquids act on cellulose is essential for improving pretreatment conditions and thus detailed knowledge of the interactions between solute and solvent molecules is necessary. Here, results from the first all-atom molecular dynamics simulation of an entire cellulose microfibril in 1-butyl-3-methylimidazolium chloride (BmimCl) are presented and the interactions and orientations of solvent ions with respect to glucose units on the hydrophobic and hydrophilic surfaces of the fiber are analyzed in detail, shedding light on the initiation stages of cellulose dissolution. Moreover, replica-exchange simulations of a single cellulose chain fully solvated in BmimCl and in water are performed for a total of around 13 μs in order to study the dynamics and thermodynamics of the end state of the dissolution. The results indicate that chloride anions predominantly interact with cellulose hydroxyl groups and disrupt the intrachain O3H’···O5 hydrogen bonds, which are essential for the integrity of cellulose fibers. The cations stack preferentially on the hydrophobic cellulose surface, governed by non-polar interactions with cellulose, which can stabilize detached cellulose chains by compensating the interaction between stacked layers. Moreover, a frequently occurring intercalation of cations on the hydrophilic surface is observed, which by separating cellulose layers can also potentially facilitate the initiation of fiber disintegration. The single-chain simulations indicate that differences in cellulose solvation mechanisms between the two solvents exist. Although global size-related properties of the cellulose chain are comparable in the two solvents, local conformational properties of cellulose differ significantly between the BmimCl and water solutions. In general, the results indicate that solute-solvent interaction energies are more favorable and that the cellulose chain is more flexible in BmimCl than in water. Taken together, the simulations explain how ionic liquids can facilitate cellulose dissolution: the synergistic action of anions and cations helps to initiate fiber deconstruction through specific interactions on the fiber surface and to solvate single cellulose chains through favorable solvent interactions and conformational flexibility.

Subjects/Keywords: Biofuels; Cellulose; Ionic Liquids; Pretreatment; MD Simulation; Biophysics

10 more images…

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mostofian, B. (2014). The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study. (Doctoral Dissertation). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_graddiss/3156

Chicago Manual of Style (16^th Edition):

Mostofian, Barmak. “The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study.” 2014. Doctoral Dissertation, University of Tennessee – Knoxville. Accessed April 12, 2021. https://trace.tennessee.edu/utk_graddiss/3156.

MLA Handbook (7^th Edition):

Mostofian, Barmak. “The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study.” 2014. Web. 12 Apr 2021.

Vancouver:

Mostofian B. The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study. [Internet] [Doctoral dissertation]. University of Tennessee – Knoxville; 2014. [cited 2021 Apr 12]. Available from: https://trace.tennessee.edu/utk_graddiss/3156.

Council of Science Editors:

Mostofian B. The Dissolution of Cellulose in Ionic Liquids - A Molecular Dynamics Study. [Doctoral Dissertation]. University of Tennessee – Knoxville; 2014. Available from: https://trace.tennessee.edu/utk_graddiss/3156

Clemson University

14. Senanayake, Manjula. Solvent as a Tool to Tune the Association of Structured Ionic Block Co-Polymers: Neutron Scattering and Computational Study.

Degree: PhD, Chemistry, 2020, Clemson University

URL: https://tigerprints.clemson.edu/all_dissertations/2739

► The work probes the behavior of associating polymers including their assembly in different environments, using neutron scattering techniques coupled with molecular dynamics (MD) simulations.… (more)

▼ The work probes the behavior of associating polymers including their assembly in different environments, using neutron scattering techniques coupled with molecular dynamics (MD) simulations. Polymers interact with their surroundings through van der Waals forces and through stronger association groups such as ionizable groups and p-p stacking, as well as specific chemical binding, where assembly depends on the strength of the interactions of the associating groups as well as the interactions of the polymers with their solvent environment. The current effort centers on understanding the assembly of structured polymers that consists of multiple blocks or components, each with their distinct interactions with solvents. The main body of the work focuses on the assembly of a multi- functional ionic polymers of the form ABCBA in which the center block is a sulfonated polystyrene (C) that enables transport tethered to, B, a polyethylene propylene (PEP) block, terminated by A, a t-butyl polystyrene (t-BPS) block. These polymers find broad uses in transport-controlled applications such as clean energy, separation membranes, and biotechnology. The aggregation of this polymer is driven by segregation of the ionizable block from the rest of the polymer as well as the interactions of each bock with solvents. The first part introduces experimental studies of assembly of this polymer as the solvent polarity is changed, followed by atomistic MD simulations insight into the assembly process. A more general insight into the assembly process is obtained by coarse grained MD The structural SANS studies have shown that the polymer forms core-shell aggregates with the ionic blocks in the core of the micelles in non-polar solvents such as cyclohexane. These micelles become gradually elongated with the addition of propanol to a propanol fraction of about 0.4. This change in shape of the micelles is driven by increasing of core-corona interfacial energy while collapsing the non-polar segments. Further increase in propanol results in reentrance to spherical micelles but with a smaller number of polymer molecules and significantly higher portion of solvent in the core. Solvent tuning of assembly to pentablock copolymer was further probed by fully atomistic MD simulation in cyclohexane, THF and propanol, solvents with different polarity. We find that the structure of the assemblies is driven by the different binding affinities of the solvents with polar and non-polar segments as well as the ionic fraction. Cyclohexane predominantly resides in the non-polar segments that are swollen, while the ionic blocks remain segregated in the micellar core. In contrast to cyclohexane, propanol and THF, which have an affinity towards both the ionic and non-ionic segments, swell the ionic blocks. With increasing sulfonation, the ionic blocks form a more stable spherical ionic core with cyclohexane associating around the core while THF and propanol penetrate into the core. To further understand the interactions of this structured block co polymer… Advisors/Committee Members: Gary S Grest, Rhett C Smith, Steve Stuart.

Subjects/Keywords: MD simulation; neutron scattering; polymers; soft matter; synthesis

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Senanayake, M. (2020). Solvent as a Tool to Tune the Association of Structured Ionic Block Co-Polymers: Neutron Scattering and Computational Study. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/2739

Chicago Manual of Style (16^th Edition):

Senanayake, Manjula. “Solvent as a Tool to Tune the Association of Structured Ionic Block Co-Polymers: Neutron Scattering and Computational Study.” 2020. Doctoral Dissertation, Clemson University. Accessed April 12, 2021. https://tigerprints.clemson.edu/all_dissertations/2739.

MLA Handbook (7^th Edition):

Senanayake, Manjula. “Solvent as a Tool to Tune the Association of Structured Ionic Block Co-Polymers: Neutron Scattering and Computational Study.” 2020. Web. 12 Apr 2021.

Vancouver:

Senanayake M. Solvent as a Tool to Tune the Association of Structured Ionic Block Co-Polymers: Neutron Scattering and Computational Study. [Internet] [Doctoral dissertation]. Clemson University; 2020. [cited 2021 Apr 12]. Available from: https://tigerprints.clemson.edu/all_dissertations/2739.

Council of Science Editors:

Senanayake M. Solvent as a Tool to Tune the Association of Structured Ionic Block Co-Polymers: Neutron Scattering and Computational Study. [Doctoral Dissertation]. Clemson University; 2020. Available from: https://tigerprints.clemson.edu/all_dissertations/2739

15. Schmelter, Ralf. Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran.

Degree: 2002, Universität Dortmund

URL: http://hdl.handle.net/2003/2514

► Phospholipide sind einer der Hauptbestandteile biologischer Membranen,welche neben der Kompartimentierung der Zellen für die Kontrolle vonStoffaustauschvorgängen verantwortlich sind. Weiterhin finden vielebedeutende biochemische Reaktionen in der… (more)

▼ Phospholipide sind einer der Hauptbestandteile biologischer Membranen,welche neben der Kompartimentierung der Zellen für die Kontrolle vonStoffaustauschvorgängen verantwortlich sind. Weiterhin finden vielebedeutende biochemische Reaktionen in der Zelle an Membran-gebundenenReaktionszentren statt. Aus diesem Grund ist ein tiefer gehendesVerständnis der physikalischen und chemischen Eigenschaftenbiologischer Membranen von entscheidender Bedeutung. So muß z.B. beider Entwicklung von Arzneimitteln gewährleistet werden, daß diese dieZellmembranen durchdringen können, falls sie ihre Wirkung in der Zelleselbst entfalten.In dieser Arbeit wurde eine voll hydratisierte DPPC-Membran in einerall-atom-Darstellung für 6 ns im mit Hilfe der SPME-Methode simuliert.Da die elektrostatischen Wechselwirkungen einen bedeutenden Einflußauf die Struktur und Dynamik des simulierten Systems ausüben wird,wurden die Partialladungen des DPPC-Moleküls quantenmechanischermittelt.Auf Grund der Anisotropie des Systems mußten viele strukturelle Größendurch mehrdimensionale Funktionen beschrieben werden, welche eine derwesentlichen in dieser Arbeit vorgestellten Neuerungen im Vergleich zuälteren Simulationen darstellen.Die ermittelten strukturellen Größen zeigen dabei eine in den meistenFällen zufriedenstellende Übereinstimmung mit experimentellen Daten,soweit diese vorhanden sind. So werden die CD-Ordnungsparameter unddie Anteile verschiedener Konformationen in der Alkylkette recht gutwiedergegeben. Dagegen zeigen sich für die Glyceringruppenregiondeutliche Abweichungen von experimentellen Daten. Dies läßt sich ausder langsamen Dynamik in der Glyceringruppenregion ableiten, welche zueiner vollständigen Equilibrierung deutlich längere Simulationszeitenerfordern würde. Die Struktur der Kopfgruppenregion, mit dem zurBilayernormalen deutlich gekippten PN-Vektor, entspricht wieder demexperimentell erhaltenen Bild. Die DPPC-Moleküle scheinen sich aufeinem annähernd hexagonalen Gitter anzuordnen. Eine genauereUntersuchung, welche die Artefakte der periodischen Randbedingungenweitgehend ausschließen sollte, ist jedoch nur mit einem deutlichgrößeren System zu erhalten. Die strukturellen Eigenschaften derWassermoleküle werden im wesentlichen von dem DPPC-Bilayeraufgeprägt. Dies ist gut aus derOrientierungswahrscheinlichkeitsdichte des Dipolmoments des Wassers zuentnehmen. Bis zur Alkylkettenregion liegt das Wasser überwiegend ineinem Netzwerk mit anderen Wassermolekülen gebunden vor, auch wenn derVerknüpfungsgrad dieses Netzwerks mit der Eindringtiefe des Wassers indie Membran deutlich abnimmt. Auch die dynamischen Eigenschaften derWasserphase werden durch die elektrostatischen Wechselwirkungen mitden DPPC-Molekülen entscheidend beeinflußt. So verlangsamt sich sowohldie Reorientierungsdynamik als auch die Diffusionsdynamik derWassermoleküle mit steigender Eindringtiefe in den Bilayerdeutlich. Die Dynamik des Wassers in der Alkylkettenregion konntejedoch auf Grund der geringen Wasserdichte in diesem Bereich nichtbzw. nur ansatzweise ermittelt werden. Die… Advisors/Committee Members: Geiger, A..

Subjects/Keywords: DPPC Phospholipid; MD-Simulation; Membran; 540

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schmelter, R. (2002). Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran. (Thesis). Universität Dortmund. Retrieved from http://hdl.handle.net/2003/2514

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Schmelter, Ralf. “Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran.” 2002. Thesis, Universität Dortmund. Accessed April 12, 2021. http://hdl.handle.net/2003/2514.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Schmelter, Ralf. “Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran.” 2002. Web. 12 Apr 2021.

Vancouver:

Schmelter R. Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran. [Internet] [Thesis]. Universität Dortmund; 2002. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/2003/2514.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Schmelter R. Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran. [Thesis]. Universität Dortmund; 2002. Available from: http://hdl.handle.net/2003/2514

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

16. Schmelter, Ralf. Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran.

Degree: 2002, Technische Universität Dortmund

URL: http://dx.doi.org/10.17877/DE290R-12161

► Phospholipide sind einer der Hauptbestandteile biologischer Membranen,welche neben der Kompartimentierung der Zellen für die Kontrolle vonStoffaustauschvorgängen verantwortlich sind. Weiterhin finden vielebedeutende biochemische Reaktionen in der… (more)

▼ Phospholipide sind einer der Hauptbestandteile biologischer Membranen,welche neben der Kompartimentierung der Zellen für die Kontrolle vonStoffaustauschvorgängen verantwortlich sind. Weiterhin finden vielebedeutende biochemische Reaktionen in der Zelle an Membran-gebundenenReaktionszentren statt. Aus diesem Grund ist ein tiefer gehendesVerständnis der physikalischen und chemischen Eigenschaftenbiologischer Membranen von entscheidender Bedeutung. So muß z.B. beider Entwicklung von Arzneimitteln gewährleistet werden, daß diese dieZellmembranen durchdringen können, falls sie ihre Wirkung in der Zelleselbst entfalten.In dieser Arbeit wurde eine voll hydratisierte DPPC-Membran in einerall-atom-Darstellung für 6 ns im mit Hilfe der SPME-Methode simuliert.Da die elektrostatischen Wechselwirkungen einen bedeutenden Einflußauf die Struktur und Dynamik des simulierten Systems ausüben wird,wurden die Partialladungen des DPPC-Moleküls quantenmechanischermittelt.Auf Grund der Anisotropie des Systems mußten viele strukturelle Größendurch mehrdimensionale Funktionen beschrieben werden, welche eine derwesentlichen in dieser Arbeit vorgestellten Neuerungen im Vergleich zuälteren Simulationen darstellen.Die ermittelten strukturellen Größen zeigen dabei eine in den meistenFällen zufriedenstellende Übereinstimmung mit experimentellen Daten,soweit diese vorhanden sind. So werden die CD-Ordnungsparameter unddie Anteile verschiedener Konformationen in der Alkylkette recht gutwiedergegeben. Dagegen zeigen sich für die Glyceringruppenregiondeutliche Abweichungen von experimentellen Daten. Dies läßt sich ausder langsamen Dynamik in der Glyceringruppenregion ableiten, welche zueiner vollständigen Equilibrierung deutlich längere Simulationszeitenerfordern würde. Die Struktur der Kopfgruppenregion, mit dem zurBilayernormalen deutlich gekippten PN-Vektor, entspricht wieder demexperimentell erhaltenen Bild. Die DPPC-Moleküle scheinen sich aufeinem annähernd hexagonalen Gitter anzuordnen. Eine genauereUntersuchung, welche die Artefakte der periodischen Randbedingungenweitgehend ausschließen sollte, ist jedoch nur mit einem deutlichgrößeren System zu erhalten. Die strukturellen Eigenschaften derWassermoleküle werden im wesentlichen von dem DPPC-Bilayeraufgeprägt. Dies ist gut aus derOrientierungswahrscheinlichkeitsdichte des Dipolmoments des Wassers zuentnehmen. Bis zur Alkylkettenregion liegt das Wasser überwiegend ineinem Netzwerk mit anderen Wassermolekülen gebunden vor, auch wenn derVerknüpfungsgrad dieses Netzwerks mit der Eindringtiefe des Wassers indie Membran deutlich abnimmt. Auch die dynamischen Eigenschaften derWasserphase werden durch die elektrostatischen Wechselwirkungen mitden DPPC-Molekülen entscheidend beeinflußt. So verlangsamt sich sowohldie Reorientierungsdynamik als auch die Diffusionsdynamik derWassermoleküle mit steigender Eindringtiefe in den Bilayerdeutlich. Die Dynamik des Wassers in der Alkylkettenregion konntejedoch auf Grund der geringen Wasserdichte in diesem Bereich nichtbzw. nur ansatzweise ermittelt werden. Die… Advisors/Committee Members: Geiger, A. (advisor), Winter, Roland (referee).

Subjects/Keywords: MD-Simulation; Membran; DPPC Phospholipid; 540

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schmelter, R. (2002). Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran. (Doctoral Dissertation). Technische Universität Dortmund. Retrieved from http://dx.doi.org/10.17877/DE290R-12161

Chicago Manual of Style (16^th Edition):

Schmelter, Ralf. “Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran.” 2002. Doctoral Dissertation, Technische Universität Dortmund. Accessed April 12, 2021. http://dx.doi.org/10.17877/DE290R-12161.

MLA Handbook (7^th Edition):

Schmelter, Ralf. “Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran.” 2002. Web. 12 Apr 2021.

Vancouver:

Schmelter R. Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran. [Internet] [Doctoral dissertation]. Technische Universität Dortmund; 2002. [cited 2021 Apr 12]. Available from: http://dx.doi.org/10.17877/DE290R-12161.

Council of Science Editors:

Schmelter R. Molekulardynamische Simulation einer voll hydratisierten Dipalmitoyl-glycero-phosphatidylcholin-Membran. [Doctoral Dissertation]. Technische Universität Dortmund; 2002. Available from: http://dx.doi.org/10.17877/DE290R-12161

University of Adelaide

17. Ayub, Md. Experimental and numerical investigation of a carbon nanotube acoustic absorber.

Degree: 2016, University of Adelaide

URL: http://hdl.handle.net/2440/112038

► The interest in applications of nanomaterials for acoustic absorption purposes is growing rapidly with advances in nanotechnology. A need also exists for a simulation framework… (more)

▼ The interest in applications of nanomaterials for acoustic absorption purposes is growing rapidly with advances in nanotechnology. A need also exists for a simulation framework that is applicable for modelling acoustic absorption in nanomaterials in order to develop an understanding of nanoscopic acoustic absorption mechanisms. The current study investigates the acoustic absorption characteristics of a carbon nanotube (CNT) acoustic absorber to develop an understanding of the absorption behaviour and mechanisms of the CNTs. This task involves undertaking an exploratory study of the absorption characteristics of a CNT forest and modelling the absorption effects of the CNT at the nanoscale. The absorption characteristics of the CNTs were explored by studying the normal incidence absorption coefficient of 3mmand 6mm-long vertically aligned CNT arrays measured experimentally using the two-microphone impedance tube method, while the modelling of the absorption effects was performed using a non-continuum particle-based method. The experimental investigation showed promising results for the acoustic absorption capability of CNT acoustic absorbers and suggests that the absorption performance could be enhanced with longer CNTs and a lower spatial density of the nanotube arrays. The study of absorption using a theoretical model based on classical absorption mechanisms indicated that the absorption behaviour of nanomaterials is likely to deviate from continuum behaviour emphasising the necessity of acoustic modelling at the nanoscale using non-continuum methods. An examination of the physical phenomena that are likely to be relevant for simulating acoustic wave propagation in the presence of CNTs revealed that the modelling of such a system would be a multi-physics problem involving heat transfer and dynamic interaction of particle vibrations. A study of various particle approaches of non-continuum methods indicated that molecular dynamics (MD) is the method best suited to simulate and study the acoustic absorption of CNTs at the nanoscale. A survey of previous molecular simulations demonstrated that the MD simulations carried out thus far have not simultaneously accounted for all relevant aspects of the multi-physics problem required for modelling the acoustic absorption effects of CNTs. Hence, three independent validation studies were performed using MD simulations for modelling a subset of the relevant phenomena, namely fluid/structure interactions, bi-directional heat transfer, and acoustic wave propagation. Each of these MD simulations were performed for a model incorporating Lennard-Jones (LJ) potentials for the non-bonded interactions of gas and CNT atoms and the REBO potential for the CNT, and the results validated against the reference case studies. A molecular system was then designed to study acoustic wave propagation in a simple monatomic gas in a domain containing a 50nm-long CNT opposite to the sound source and parallel to the direction of the acoustic wave propagation. The simulation domain was modelled using… Advisors/Committee Members: Zander, Anthony Charles (advisor), Cazzolato, Benjamin Seth (advisor), Howard, Carl Quentin (advisor), Huang, David M. (advisor), School of Mechanical Engineering (school).

Subjects/Keywords: carbon nanotube; molecular dynamics (MD) simulation; acoustic absorber; exergy concepts; high frequency sound

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ayub, M. (2016). Experimental and numerical investigation of a carbon nanotube acoustic absorber. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/112038

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ayub, Md. “Experimental and numerical investigation of a carbon nanotube acoustic absorber.” 2016. Thesis, University of Adelaide. Accessed April 12, 2021. http://hdl.handle.net/2440/112038.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ayub, Md. “Experimental and numerical investigation of a carbon nanotube acoustic absorber.” 2016. Web. 12 Apr 2021.

Vancouver:

Ayub M. Experimental and numerical investigation of a carbon nanotube acoustic absorber. [Internet] [Thesis]. University of Adelaide; 2016. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/2440/112038.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ayub M. Experimental and numerical investigation of a carbon nanotube acoustic absorber. [Thesis]. University of Adelaide; 2016. Available from: http://hdl.handle.net/2440/112038

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

18. Ndumbe Ngale, Kenneth. Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions.

Degree: PhD, Chemistry, 2013, University of North Dakota

URL: https://commons.und.edu/theses/1460

► The most familiar phase transitions observed in nature are associated with a change in the state of matter (solid, liquid, and gas). In some… (more)

▼ The most familiar phase transitions observed in nature are associated with a change in the state of matter (solid, liquid, and gas). In some rare cases this may involve the plasma phase. Such transitions are often referred to as first order phase transitions and often occur commonly such as during the melting of snow or freezing of lakes and rivers during winter. This project focuses on the most ubiquitous phase changes such as, liquid-solid and vapor-liquid as well as the less prevalent vapor-solid transitions. These types of phase transitions are also known as classical phase transitions. They usually involve symmetry breaking and can be identified by a singularity in the free energy or one of its derivatives. More modern classification of phase transitions relies on the order parameters as exemplified by the Landau's theory. An order parameter is a quantity that takes a value of zero in the disordered phase and assumes finite values in the ordered phase. In the case of liquid-vapor transition, the order parameter is the density. The study of phase transitions is often complicated by the amount of time required by these phase changes and the presence of a high free energy barrier. Consequently, changes occurring close to coexistence are hard or even impossible to follow via conventional experimental techniques. Molecular simulation is therefore the method of choice to study these processes. Molecular simulations are numerical experiments carried out on model systems and have a number of advantages over traditional experiments. Simulations do not have any limitation as to the type of molecules or conditions under which they can be applied. Current simulation methods used to accomplish this task, such as the grand canonical and Gibbs ensemble Monte Carlo methods, employ the concept of particles insertion and deletion moves or requires the knowledge of at least one point at coexistence. These types of moves are extremely inefficient when dense fluids are involved and limit the accuracy of these methods. To circumvent these difficulties, non-Boltzmann sampling methods such as the umbrella sampling and Wang-Landau sampling techniques, have been employed to study these phase transitions. Vapor-solid and liquid-solid phase transitions were studied using a combination of hybrid Monte Carlo (HMC) and the umbrella sampling on a system of C₆₀ molecules. The crystallization process occurs in two steps, nucleation and growth. The nucleation step is an activated process that involves a high free energy barrier. The free energy barrier is overcome through a series of HMC steps. The growth step on the other hand is studied by means of unconstrained molecular dynamics (MD). This study illustrates that the body centered cubic structure plays no role in the crystallization of C₆₀. This is because only the face centered cubic and the hexagonal closed parked crystal structures were observed in both the nucleation and growth steps. In addition, the growth process… Advisors/Committee Members: Jerome Delhommelle.

Subjects/Keywords: Critical properties; Crystallization; Molecular Dynamics (MD); Monte Carlo (MC); Phase Change; Simulation

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ndumbe Ngale, K. (2013). Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions. (Doctoral Dissertation). University of North Dakota. Retrieved from https://commons.und.edu/theses/1460

Chicago Manual of Style (16^th Edition):

Ndumbe Ngale, Kenneth. “Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions.” 2013. Doctoral Dissertation, University of North Dakota. Accessed April 12, 2021. https://commons.und.edu/theses/1460.

MLA Handbook (7^th Edition):

Ndumbe Ngale, Kenneth. “Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions.” 2013. Web. 12 Apr 2021.

Vancouver:

Ndumbe Ngale K. Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions. [Internet] [Doctoral dissertation]. University of North Dakota; 2013. [cited 2021 Apr 12]. Available from: https://commons.und.edu/theses/1460.

Council of Science Editors:

Ndumbe Ngale K. Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions. [Doctoral Dissertation]. University of North Dakota; 2013. Available from: https://commons.und.edu/theses/1460

University of Edinburgh

19. Patrick, Lisa. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.

Degree: PhD, 2020, University of Edinburgh

URL: http://hdl.handle.net/1842/37111

► Allosteric signalling was first discovered over 50 years ago, yet the underlying molecular determinants are not yet completely understood. The ability to predict the activity… (more)

▼ Allosteric signalling was first discovered over 50 years ago, yet the underlying molecular determinants are not yet completely understood. The ability to predict the activity of allosteric small molecules could have a huge therapeutic impact, as targeting allosteric sites in proteins potentially presents significant benefits over active site inhibitors, in both selectivity and efficacy. While some systems undergo fairly well understood structural changes, there is no overall model that satisfactorily describes how allostery works. Molecular dynamics (MD) simulations provide a tool to study protein dynamics at the atomistic level, however traditionally employed analysis methods have proven inadequate to deliver a mechanistic description of allostery, which can be applied broadly to a range of allosteric systems. This thesis presents the development of a Python workflow for the analysis of Molecular Dynamics (MD) simulations of proteins subjected to allosteric regulation. The end goal is to provide a new tool for structure-based drug design (SBDD) for these systems. This tool computes various descriptors, such as distances, torsions, collective motions and interaction energies, and then utilises two concepts from information theory to compare these descriptors: Kullback-Leibler (KL) divergence and Mutual Information (MI). MI is used to determine correlation between simulation descriptors that can aid explanation of conformation/activity relationships; while KL divergence is used to highlight differences of one descriptor between simulations of related molecular systems. Proof of concept for this approach utilises the protein phosphoinositide dependent kinase-1 (PDK1) as a test case. This protein plays a crucial role in cell signalling, by activation of other kinases within the same family (AGC kinases). Inhibition of PDK1 has been of much interest, as over-expression and dysfunction is related to several diseases, most notably cancer. Active site compounds suffer from selectivity issues, as the active site is well conserved across all AGC kinases, however PDK1 has a well defined allosteric site, with known peptide and small molecule activators and inhibitors. Therefore, understanding this mechanism could facilitate design of more selective allosteric drugs. Long MD trajectories were run for PDK1 in complex with three different drug like molecules for which crystallographic data was available: two activators, and one inhibitor. In order to mimic experimental assay conditions, simulation systems were composed of PDK1, the covalently bound allosteric small molecule, ATP, two Mg2+ ions, a model of a substrate peptide, and a box of explicitly modelled water molecules. Simulations were performed with the software Sire/OpenMM Molecular Dynamics (SOMD). From the resulting trajectories, the KL analysis workflow was able to identify conformational differences between the activated and inhibited systems, and identify the dominant motions leading to these structural changes. Subsequently, an energetic comparison was performed…

Subjects/Keywords: protein simulations; allostery; Molecular Dynamics simulations; MD simulation; Mutual Information; Kullback-Leibler divergence

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Patrick, L. (2020). Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/37111

Chicago Manual of Style (16^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Doctoral Dissertation, University of Edinburgh. Accessed April 12, 2021. http://hdl.handle.net/1842/37111.

MLA Handbook (7^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Web. 12 Apr 2021.

Vancouver:

Patrick L. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. [Internet] [Doctoral dissertation]. University of Edinburgh; 2020. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1842/37111.

Council of Science Editors:

Patrick L. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. [Doctoral Dissertation]. University of Edinburgh; 2020. Available from: http://hdl.handle.net/1842/37111

University of Edinburgh

20. Patrick, Lisa. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.

Degree: PhD, 2020, University of Edinburgh

URL: https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132

► Allosteric signalling was first discovered over 50 years ago, yet the underlying molecular determinants are not yet completely understood. The ability to predict the activity… (more)

▼ Allosteric signalling was first discovered over 50 years ago, yet the underlying molecular determinants are not yet completely understood. The ability to predict the activity of allosteric small molecules could have a huge therapeutic impact, as targeting allosteric sites in proteins potentially presents significant benefits over active site inhibitors, in both selectivity and efficacy. While some systems undergo fairly well understood structural changes, there is no overall model that satisfactorily describes how allostery works. Molecular dynamics (MD) simulations provide a tool to study protein dynamics at the atomistic level, however traditionally employed analysis methods have proven inadequate to deliver a mechanistic description of allostery, which can be applied broadly to a range of allosteric systems. This thesis presents the development of a Python workflow for the analysis of Molecular Dynamics (MD) simulations of proteins subjected to allosteric regulation. The end goal is to provide a new tool for structure-based drug design (SBDD) for these systems. This tool computes various descriptors, such as distances, torsions, collective motions and interaction energies, and then utilises two concepts from information theory to compare these descriptors: Kullback-Leibler (KL) divergence and Mutual Information (MI). MI is used to determine correlation between simulation descriptors that can aid explanation of conformation/activity relationships; while KL divergence is used to highlight differences of one descriptor between simulations of related molecular systems. Proof of concept for this approach utilises the protein phosphoinositide dependent kinase-1 (PDK1) as a test case. This protein plays a crucial role in cell signalling, by activation of other kinases within the same family (AGC kinases). Inhibition of PDK1 has been of much interest, as over-expression and dysfunction is related to several diseases, most notably cancer. Active site compounds suffer from selectivity issues, as the active site is well conserved across all AGC kinases, however PDK1 has a well defined allosteric site, with known peptide and small molecule activators and inhibitors. Therefore, understanding this mechanism could facilitate design of more selective allosteric drugs. Long MD trajectories were run for PDK1 in complex with three different drug like molecules for which crystallographic data was available: two activators, and one inhibitor. In order to mimic experimental assay conditions, simulation systems were composed of PDK1, the covalently bound allosteric small molecule, ATP, two Mg2+ ions, a model of a substrate peptide, and a box of explicitly modelled water molecules. Simulations were performed with the software Sire/OpenMM Molecular Dynamics (SOMD). From the resulting trajectories, the KL analysis workflow was able to identify conformational differences between the activated and inhibited systems, and identify the dominant motions leading to these structural changes. Subsequently, an energetic comparison was performed…

Subjects/Keywords: protein simulations; allostery; Molecular Dynamics simulations; MD simulation; Mutual Information; Kullback-Leibler divergence

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Patrick, L. (2020). Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. (Doctoral Dissertation). University of Edinburgh. Retrieved from https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132

Chicago Manual of Style (16^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Doctoral Dissertation, University of Edinburgh. Accessed April 12, 2021. https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132.

MLA Handbook (7^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Web. 12 Apr 2021.

Vancouver:

Patrick L. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. [Internet] [Doctoral dissertation]. University of Edinburgh; 2020. [cited 2021 Apr 12]. Available from: https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132.

Council of Science Editors:

Patrick L. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. [Doctoral Dissertation]. University of Edinburgh; 2020. Available from: https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132

University of Akron

21. Tian, Yuan, TIAN. How to Measure Work of Adhesion and Surface Tension of Soft Materials.

Degree: MS, Polymer Science, 2018, University of Akron

URL: http://rave.ohiolink.edu/etdc/view?acc_num=akron1523295919890025

► Knowledge of the work of adhesion and surface tension plays an important role in the design of new materials for applications such as coatings, adhesives,… (more)

Subjects/Keywords: Physics; Polymers; Materials Science; work of adhesion; surface tension; MD simulation; networks; soft materials

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tian, Yuan, T. (2018). How to Measure Work of Adhesion and Surface Tension of Soft Materials. (Masters Thesis). University of Akron. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=akron1523295919890025

Chicago Manual of Style (16^th Edition):

Tian, Yuan, TIAN. “How to Measure Work of Adhesion and Surface Tension of Soft Materials.” 2018. Masters Thesis, University of Akron. Accessed April 12, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=akron1523295919890025.

MLA Handbook (7^th Edition):

Tian, Yuan, TIAN. “How to Measure Work of Adhesion and Surface Tension of Soft Materials.” 2018. Web. 12 Apr 2021.

Vancouver:

Tian, Yuan T. How to Measure Work of Adhesion and Surface Tension of Soft Materials. [Internet] [Masters thesis]. University of Akron; 2018. [cited 2021 Apr 12]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=akron1523295919890025.

Council of Science Editors:

Tian, Yuan T. How to Measure Work of Adhesion and Surface Tension of Soft Materials. [Masters Thesis]. University of Akron; 2018. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=akron1523295919890025

Swedish University of Agricultural Sciences

22. Eklund, Lars. Hydration of oxo anions.

Degree: 2014, Swedish University of Agricultural Sciences

URL: http://pub.epsilon.slu.se/11192/

► The structure and dynamics of several hydrated oxo anions were studied using multiple methodologies. Aqueous solutions of sulfate, sulfite, thiosulfate, peroxysulfate, selenite, selenate, hypochlorite, chlorite,… (more)

Subjects/Keywords: hydration; solutions; chemicophysical properties; simulation; models; hydration; oxoanion; coordination; QMCF/MD; LAXS; EXSAFS; DDIR; simulation; XANES

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Eklund, L. (2014). Hydration of oxo anions. (Doctoral Dissertation). Swedish University of Agricultural Sciences. Retrieved from http://pub.epsilon.slu.se/11192/

Chicago Manual of Style (16^th Edition):

Eklund, Lars. “Hydration of oxo anions.” 2014. Doctoral Dissertation, Swedish University of Agricultural Sciences. Accessed April 12, 2021. http://pub.epsilon.slu.se/11192/.

MLA Handbook (7^th Edition):

Eklund, Lars. “Hydration of oxo anions.” 2014. Web. 12 Apr 2021.

Vancouver:

Eklund L. Hydration of oxo anions. [Internet] [Doctoral dissertation]. Swedish University of Agricultural Sciences; 2014. [cited 2021 Apr 12]. Available from: http://pub.epsilon.slu.se/11192/.

Council of Science Editors:

Eklund L. Hydration of oxo anions. [Doctoral Dissertation]. Swedish University of Agricultural Sciences; 2014. Available from: http://pub.epsilon.slu.se/11192/

University of Illinois – Urbana-Champaign

23. Yu, Hang. Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease.

Degree: PhD, Biophysics & Computional Biology, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/89115

► Proteins are complex machineries dedicated to drive many functions in eukaryotic cells. In this article, two cases of protein dynamics and their implications to cellular… (more)

▼ Proteins are complex machineries dedicated to drive many functions in eukaryotic cells. In this article, two cases of protein dynamics and their implications to cellular functions are discussed with computational approaches: membrane sculpting by F-BAR domains and transient β-hairpin structure in α-synuclein. Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called “scaffolding” mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domain’s 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy. The molecular dynamics study others, thereby, both a large-scale picture of membrane sculpting by F-BAR domain lattices as well as atomic-level dynamic information about the involvement of the individual F-BAR domain and its interactions with partner F-BAR domains and membrane in the sculpting process. Parkinson’s disease is a common neurodegenerative disorder that originates from the intrinsically disordered peptide α-synuclein aggregating into fibrils. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 150 μs in aggregated time) using a hybrid-resolution model, PACE, to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts and 3J(HNHCα )-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-Amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, ﬂuctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key… Advisors/Committee Members: Schulten, Klaus (advisor), Schulten, Klaus (Committee Chair), Tajkhorshid, Emad (committee member), Grosman, Claudio (committee member), Luthey-Schulten, Zan (committee member).

Subjects/Keywords: Molecular dynamics simulation; molecular dynamics (MD) simulation; Protein; Membrane; Curvature; F-BAR domain; Parkinson’s disease; α-synuclein; β-hairpin

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yu, H. (2015). Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/89115

Chicago Manual of Style (16^th Edition):

Yu, Hang. “Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 12, 2021. http://hdl.handle.net/2142/89115.

MLA Handbook (7^th Edition):

Yu, Hang. “Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease.” 2015. Web. 12 Apr 2021.

Vancouver:

Yu H. Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/2142/89115.

Council of Science Editors:

Yu H. Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/89115

Université Montpellier II

24. Gołębiowska, Monika R. Mechanism of self-assembly and adsorption of molecules on surfaces : multiscale computer modeling : Mécanisme d'auto-assemblage et l'adsorption de molécules sur des surfaces : modélisation informatique multi-échelles.

Degree: Docteur es, Milieux denses et matériaux, 2011, Université Montpellier II

URL: http://www.theses.fr/2011MON20012

►

Le mémoire est consacré à l'étude numérique des phénomènes survenant à l'interface solide-fluide. Trois processus ont été étudiés: auto-organisation de films moléculaires sur un substrat… (more)

▼

Le mémoire est consacré à l'étude numérique des phénomènes survenant à l'interface solide-fluide. Trois processus ont été étudiés: auto-organisation de films moléculaires sur un substrat solide, adsorption du gaz moléculaires dans un matériau nanoporeux et la cristallisation à l'interface organique/inorganique. L'étude de l'auto-organisation et des transitions de phase dans des multicouches de l'azote moléculaires adsorbées sur graphite est présentée dans le chapitre III. L'analyse est focalisée sur l'hétérogénéité spatiale du système et son influence sur le mécanisme et température de transitions ordre/désordre et la fusion des couches. Elle complète ainsi l'étude numérique du diagramme de phase de l'azote moléculaire, bien connu pour le matériau massif (3D) et les monocouches (2D) adsorbées sur un substrat. Le chapitre IV présente une étude de cinétique du mélange des gaz (méthane et méthyle-mercaptan) confiné dans les nanopores de carbone (pores en forme de fentes, de dimensions latérales finies et largeur nanométrique). L'étude porte sur la capacité de stockage de pores, la dynamique des composantes du mélange des gaz sous confinement et l'évaluation de la quantité de l'odorant nécessaire pour une détection facile en cas de fuite. Chapitre V résume les résultats de l'étude préliminaire ayant pour but la mise en place des simulations de biomineralization à l'interface organique/inorganique. Les structures secondaires de deux biomolécules, human leucine-rich peptide hLRAP et full length amelogenin, rM179 ont été prédéterminées. Les plus probables configurations ont été optimisées dans un environnement aqueux.

The present work is devoted to computer simulations of phenomena occurring at solid-fluid interfaces. Three processes have been studied in details: auto organization of molecular films at a solid substrate, adsorption of molecular gas in confined geometry and crystal formation at organic-inorganic interface. Two classical simulation methods have been used: stochastic Monte Carlo and deterministic Molecular Dynamics.The study of self-organisation and phase transitions in molecular nitrogen multilayers adsorbed on the basal plane of graphite is presented in chapter III. It focusses on the systems' spatial heterogeneity and its influence on temperatures of order-disorder and melting transitions. This study completes the numerical analysis of molecular nitrogen phase diagram, well described and understood for 3d (bulk) and 2D (monolayer film) systems.The analysis of kinetics of fluid confined in nanopores is presented in chapter IV. The working case consists of methane-methyl mercaptan mixtures confined in slit-shaped carbon nanopores. Simulations focused on both: storage capacity of carbon pores of finite size and nanometric width, and dynamics of gas mixture components under confinement. An evaluation of odorant content necessary for easy gas leak detection is presented.Chapter V gathers the results of calculations performed to set up the simulations of biomineralization at the organic-inorganic interface.…

Advisors/Committee Members: Firlej, Lucyna (thesis director).

Subjects/Keywords: Simulations numeriques MC; Md; Adsorption; Transitions de phase; Stockage des gaz; Simulation de biomolecules; Computer simulations MC; Md; Adsorption; Phase transitions; Gas storage; BioSimulation de biommolecules simulations

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gołębiowska, M. R. (2011). Mechanism of self-assembly and adsorption of molecules on surfaces : multiscale computer modeling : Mécanisme d'auto-assemblage et l'adsorption de molécules sur des surfaces : modélisation informatique multi-échelles. (Doctoral Dissertation). Université Montpellier II. Retrieved from http://www.theses.fr/2011MON20012

Chicago Manual of Style (16^th Edition):

Gołębiowska, Monika R. “Mechanism of self-assembly and adsorption of molecules on surfaces : multiscale computer modeling : Mécanisme d'auto-assemblage et l'adsorption de molécules sur des surfaces : modélisation informatique multi-échelles.” 2011. Doctoral Dissertation, Université Montpellier II. Accessed April 12, 2021. http://www.theses.fr/2011MON20012.

MLA Handbook (7^th Edition):

Gołębiowska, Monika R. “Mechanism of self-assembly and adsorption of molecules on surfaces : multiscale computer modeling : Mécanisme d'auto-assemblage et l'adsorption de molécules sur des surfaces : modélisation informatique multi-échelles.” 2011. Web. 12 Apr 2021.

Vancouver:

Gołębiowska MR. Mechanism of self-assembly and adsorption of molecules on surfaces : multiscale computer modeling : Mécanisme d'auto-assemblage et l'adsorption de molécules sur des surfaces : modélisation informatique multi-échelles. [Internet] [Doctoral dissertation]. Université Montpellier II; 2011. [cited 2021 Apr 12]. Available from: http://www.theses.fr/2011MON20012.

Council of Science Editors:

Gołębiowska MR. Mechanism of self-assembly and adsorption of molecules on surfaces : multiscale computer modeling : Mécanisme d'auto-assemblage et l'adsorption de molécules sur des surfaces : modélisation informatique multi-échelles. [Doctoral Dissertation]. Université Montpellier II; 2011. Available from: http://www.theses.fr/2011MON20012

25. 中村, 大城. データマイニングによる塩水濃度と水溶液の動的構造の関連性に関する研究.

Degree: Japan Advanced Institute of Science and Technology / 北陸先端科学技術大学院大学

URL: http://hdl.handle.net/10119/10470

Supervisor:DAM HIEU CHI 准教授

知識科学研究科

修士

Subjects/Keywords: data mining; MD simulation; 塩水; water behavior

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

中村, �. (n.d.). データマイニングによる塩水濃度と水溶液の動的構造の関連性に関する研究. (Thesis). Japan Advanced Institute of Science and Technology / 北陸先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10119/10470

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

中村, 大城. “データマイニングによる塩水濃度と水溶液の動的構造の関連性に関する研究.” Thesis, Japan Advanced Institute of Science and Technology / 北陸先端科学技術大学院大学. Accessed April 12, 2021. http://hdl.handle.net/10119/10470.

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

中村, 大城. “データマイニングによる塩水濃度と水溶液の動的構造の関連性に関する研究.” Web. 12 Apr 2021.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Vancouver:

中村 �. データマイニングによる塩水濃度と水溶液の動的構造の関連性に関する研究. [Internet] [Thesis]. Japan Advanced Institute of Science and Technology / 北陸先端科学技術大学院大学; [cited 2021 Apr 12]. Available from: http://hdl.handle.net/10119/10470.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Council of Science Editors:

中村 �. データマイニングによる塩水濃度と水溶液の動的構造の関連性に関する研究. [Thesis]. Japan Advanced Institute of Science and Technology / 北陸先端科学技術大学院大学; Available from: http://hdl.handle.net/10119/10470

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Baylor University

26. Ashtekar, Nikhil A. Non-deterministic modeling of the bulk thermal and electrical conductivity for dense thin film carbon nanotube networks.

Degree: M.S.M.E., Engineering., 2011, Baylor University

URL: http://hdl.handle.net/2104/8113

► Thin films composed of single-walled carbon nanotubes, enjoy very high thermal and electrical conductivities, well beyond that of polymer matrix composites, and are very light… (more)

Subjects/Keywords: Carbon nanotubes.; CNT thin films.; Buckypapers.; Thermal conductivity.; Electrical conductivity.; Mathematical modeling and MD simulation.; Sensitivity analysis.

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ashtekar, N. A. (2011). Non-deterministic modeling of the bulk thermal and electrical conductivity for dense thin film carbon nanotube networks. (Masters Thesis). Baylor University. Retrieved from http://hdl.handle.net/2104/8113

Chicago Manual of Style (16^th Edition):

Ashtekar, Nikhil A. “Non-deterministic modeling of the bulk thermal and electrical conductivity for dense thin film carbon nanotube networks.” 2011. Masters Thesis, Baylor University. Accessed April 12, 2021. http://hdl.handle.net/2104/8113.

MLA Handbook (7^th Edition):

Ashtekar, Nikhil A. “Non-deterministic modeling of the bulk thermal and electrical conductivity for dense thin film carbon nanotube networks.” 2011. Web. 12 Apr 2021.

Vancouver:

Ashtekar NA. Non-deterministic modeling of the bulk thermal and electrical conductivity for dense thin film carbon nanotube networks. [Internet] [Masters thesis]. Baylor University; 2011. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/2104/8113.

Council of Science Editors:

Ashtekar NA. Non-deterministic modeling of the bulk thermal and electrical conductivity for dense thin film carbon nanotube networks. [Masters Thesis]. Baylor University; 2011. Available from: http://hdl.handle.net/2104/8113

Uppsala University

27. André, Tomas. Benchmarking Physical Properties of Water Models.

Degree: Molecular and Condensed Matter Physics, 2019, Uppsala University

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-388336

►

Water is a fundamental part of life as we know it, and by that also a fundamental for biology, chemistry, and parts of… (more)

Subjects/Keywords: Water Models; Molecular Dynamics; Properties of water; MD; Simulation; GROMACS; Atom and Molecular Physics and Optics; Atom- och molekylfysik och optik

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

André, T. (2019). Benchmarking Physical Properties of Water Models. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-388336

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

André, Tomas. “Benchmarking Physical Properties of Water Models.” 2019. Thesis, Uppsala University. Accessed April 12, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-388336.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

André, Tomas. “Benchmarking Physical Properties of Water Models.” 2019. Web. 12 Apr 2021.

Vancouver:

André T. Benchmarking Physical Properties of Water Models. [Internet] [Thesis]. Uppsala University; 2019. [cited 2021 Apr 12]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-388336.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

André T. Benchmarking Physical Properties of Water Models. [Thesis]. Uppsala University; 2019. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-388336

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Oklahoma State University

28. Abdul Samadh, Abdul Nizam. Molecular Dynamics (MD) Simulations of Chemical Vapor Deposition (CVD) of Carbon Dimer on a Diamond (100) Surface and Application of Neural Networks (NN) for Event Probability Predictions.

Degree: Mechanical & Aerospace Engineering, 2005, Oklahoma State University

URL: http://hdl.handle.net/11244/10052

► Carbon dimers are found to be an important growth species in the growth of nanocrystalline diamond (NCD) through CVD process. Events, such as chemisorption, reflection,… (more)

▼ Carbon dimers are found to be an important growth species in the growth of nanocrystalline diamond (NCD) through CVD process. Events, such as chemisorption, reflection, and desorption occur during the deposition of carbon dimers on to the substrate on which the diamond films are to be grown. The probabilities of each of these events have a significant effect on diamond growth. Molecular Dynamics (MD) simulations are widely used to predict the probabilities of such events. Though, MD simulations give agreeable results with experimental values, the calculation of the effect of different input parameters on various events involve time consuming numerical methods and hence the process is cumbersome. In this study, initially MD simulations of carbon dimer deposition on diamond (100) surface were performed using a many body empirical potential and the probabilities of the aforesaid events were calculated by varying the input conditions. This information was used to implement Neural Networks (NN) to predict the probabilities of the events. The neural network was also used to predict the underlying relationship between various input parameters and event probabilities. Neural Network could be effectively used to predict the relationship between the input parameters and event probabilities in minutes as compared to days taken by MD simulations. The chemisorption probability is found to decrease with increase in the incidence angle (θ), impact parameter (b), and rotational energy (ERot) of the carbon dimer, but the scattering and desorption probabilities are found to increase these three parameters. The chemisorption probability is found to increase with an increase in the translational energy (ETrans) of the dimer, but the scattering and desorption probabilities are found to decrease with the translation energy (ETrans). The three event probabilities are found to be independent of the rotation angle (?) of the carbon dimer. Advisors/Committee Members: Komanduri, Ranga (advisor), Raff, Lionel Mischa (committee member), Hagan, M.T. (committee member), Lu, H. B. (committee member).

Subjects/Keywords: md simulation; neural network; cvd; carbon dimer

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Abdul Samadh, A. N. (2005). Molecular Dynamics (MD) Simulations of Chemical Vapor Deposition (CVD) of Carbon Dimer on a Diamond (100) Surface and Application of Neural Networks (NN) for Event Probability Predictions. (Thesis). Oklahoma State University. Retrieved from http://hdl.handle.net/11244/10052

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Abdul Samadh, Abdul Nizam. “Molecular Dynamics (MD) Simulations of Chemical Vapor Deposition (CVD) of Carbon Dimer on a Diamond (100) Surface and Application of Neural Networks (NN) for Event Probability Predictions.” 2005. Thesis, Oklahoma State University. Accessed April 12, 2021. http://hdl.handle.net/11244/10052.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Abdul Samadh, Abdul Nizam. “Molecular Dynamics (MD) Simulations of Chemical Vapor Deposition (CVD) of Carbon Dimer on a Diamond (100) Surface and Application of Neural Networks (NN) for Event Probability Predictions.” 2005. Web. 12 Apr 2021.

Vancouver:

Abdul Samadh AN. Molecular Dynamics (MD) Simulations of Chemical Vapor Deposition (CVD) of Carbon Dimer on a Diamond (100) Surface and Application of Neural Networks (NN) for Event Probability Predictions. [Internet] [Thesis]. Oklahoma State University; 2005. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/11244/10052.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Abdul Samadh AN. Molecular Dynamics (MD) Simulations of Chemical Vapor Deposition (CVD) of Carbon Dimer on a Diamond (100) Surface and Application of Neural Networks (NN) for Event Probability Predictions. [Thesis]. Oklahoma State University; 2005. Available from: http://hdl.handle.net/11244/10052

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Southern California

29. Wei, Tao. Experimental study and atomic simulation of protein adsorption.

Degree: PhD, Chemical Engineering, 2008, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/121195/rec/2633

► The studies of protein adsorption at solid-liquid interface are important in various applications. Multilayer and irreversible adsorption behaviors are commonly observed. In this work, protein… (more)

▼ The studies of protein adsorption at solid-liquid interface are important in various applications. Multilayer and irreversible adsorption behaviors are commonly observed. In this work, protein adsorption behavior at the solid-liquid interface was investigated by a combination of experimental Fourier transform infrared/attenuated total reflectance (FTIR/ATR) studies and computer simulations: Molecular Dynamics (MD) simulation and hybrid Genetic-Algorithm (GA) schemes.; BSA, lysozyme, IgG and fibrinogen adsorption was studied with FTIR/ATR in tris(hydroxymethyl)-aminomethane hydrochloride (Tris-HCl) and phosphate buffered saline (PBS) buffers on a Ge surface. Buffer choice was shown to drastically affect adsorption kinetics. In comparison with Tris-HCl, PBS buffer depresses the adsorption of BSA, IgG and fibrinogen in the prolonged quasi-linear kinetic region while lysozyme adsorption is relatively insensitive to buffer choice. Buffer concentration can also significantly affect protein adsorption. The secondary structures in the adsorbed phase are generally quite different from the bulk structure; however, buffer choice has negligible effect on structural evolution. Significant secondary structure changes occur during adsorption. The secondary structures in the adsorbed phase are inhomogeneous. The role of phosphate ions in PBS buffer and their effect on protein adsorption are rather complex. Phosphate ions adsorb competitively against protein molecules and their deprotonation equilibrium can be altered at the solid-liquid interface due to the adsorbed protein.; The effect of surface on adsorption is examined by adsorbing IgG on various polymer-coated surfaces. IgG adsorption is higher on more hydrophobic surface. IgG molecules adsorbed in layers near hydrophilic solid surfaces suffer less secondary structure changes.; The behavior of lysozyme during adsorption on a hydrogen-terminated Si surface (Si-H) is studied using MD simulations. Although atomistic simulations are highly time-consuming for direct observations of complete secondary structure changes, indications of molecular deformations are observed over nanosecond simulation time scale. Lysozyme molecule undergoes deformation onto the Si-H surface, as is evidenced by the reduction in the volume, the increase in solvent accessible surface area, the change of the overall shape, and certain amount of alteration in secondary structures. The main α-helix domains experience some loss while the beta-sheet domains remain almost intact. The hydrophobic character of the surface is believed to contribute to the loss of the organized structures of the amino residues in close proximity to the surface.; An efficient hybrid GA/spatial-grid method was developed to search for low adsorption-energy orientations and locations of a protein molecule on a solid surface. The surface and the protein molecule are treated as rigid bodies, whereas the bulk fluid is represented by spatial grids. The hybrid search procedure consists of two interlinked loops. In 1st loop (A), a GA is… Advisors/Committee Members: Shing, Katherine (Committee Chair), Nakano, Aiichiro (Committee Member), Goo, Edward K. (Committee Member).

Subjects/Keywords: protein adsorption; FTIR/ATR; MD simulation; hybrid genetic algorithm

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wei, T. (2008). Experimental study and atomic simulation of protein adsorption. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/121195/rec/2633

Chicago Manual of Style (16^th Edition):

Wei, Tao. “Experimental study and atomic simulation of protein adsorption.” 2008. Doctoral Dissertation, University of Southern California. Accessed April 12, 2021. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/121195/rec/2633.

MLA Handbook (7^th Edition):

Wei, Tao. “Experimental study and atomic simulation of protein adsorption.” 2008. Web. 12 Apr 2021.

Vancouver:

Wei T. Experimental study and atomic simulation of protein adsorption. [Internet] [Doctoral dissertation]. University of Southern California; 2008. [cited 2021 Apr 12]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/121195/rec/2633.

Council of Science Editors:

Wei T. Experimental study and atomic simulation of protein adsorption. [Doctoral Dissertation]. University of Southern California; 2008. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/121195/rec/2633

University of Tennessee – Knoxville

30. Huang, Zuya. Modeling and Experimental Investigation on the Influence of Radiation Defects on Helium Behavior in BCC Iron.

Degree: MS, Nuclear Engineering, 2016, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_gradthes/3776

► Fe-based alloys are important structural materials for both fission and fusion energy. For fusion applications, the challenges of radiation-induced changes in microstructure, properties and… (more)

▼ Fe-based alloys are important structural materials for both fission and fusion energy. For fusion applications, the challenges of radiation-induced changes in microstructure, properties and performance is further challenged by the concomitant production of helium from (n, alpha) nuclear reactions and fusion reactions. Due to the lack of a volumetric, high flux 14-MeV neutron source, studying these phenomena require the use of computational materials modeling and novel experimental methods. In this thesis, molecular dynamics (MD) simulations was used to investigate the synergistic interactions of helium with prismatic dislocation loops characteristic of those observed in neutron irradiated iron to determine how the presence of these loops modify the helium clustering and gas bubble nucleation process. In particular, multiple MD simulations have been conducted to investigate the role of a/2or aprismatic interstitial type dislocation loops on the helium clustering dynamics upon inserting interstitial helium into the body-centered cubic iron lattice at temperatures from 773 °K to 1173 °K. The simulations indicate a strong elastic interaction, which significantly influences the early stages of helium clustering that can aid bubble nucleation. In addition, helium interactions with defect clusters in iron are probed experimentally, which has specifically focused on performing low energy helium ion implantation on neutron irradiated iron specimens followed by thermal desorption spectroscopy (TDS). The results show a limited increase in the dislocation line density, along with a relatively low volume fraction of cavities is observed after neutron irradiation of both single crystal and poly-crystalline iron samples. The TDS results indicate that the major helium desorption peaks shift to higher temperature due to the existence of the radiation induced defects, which are believed to act as strong trapping sites for helium. Overall, the research performed in this thesis has confirmed that synergistic interactions occur between helium and point defect clusters, as well as the potential to combine computational modeling with experimental measurements using thermal desorption spectroscopy. The presented simulation and experimental results along with the proposed future work are expected to enhance the current understanding of the fundamentals of helium-defect interactions in neutron-irradiated iron. Advisors/Committee Members: Brian D. Wirth, Steven J. Zinkle, Maik K. Lang.

Subjects/Keywords: Helium; Iron; MD Simulation; Thermal Desorption Spectrometry (TDS); Thermal Desorption Spectrum (TDS) Measurement; Mechanics of Materials; Nuclear Engineering; Structural Materials

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Huang, Z. (2016). Modeling and Experimental Investigation on the Influence of Radiation Defects on Helium Behavior in BCC Iron. (Thesis). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_gradthes/3776

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Huang, Zuya. “Modeling and Experimental Investigation on the Influence of Radiation Defects on Helium Behavior in BCC Iron.” 2016. Thesis, University of Tennessee – Knoxville. Accessed April 12, 2021. https://trace.tennessee.edu/utk_gradthes/3776.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Huang, Zuya. “Modeling and Experimental Investigation on the Influence of Radiation Defects on Helium Behavior in BCC Iron.” 2016. Web. 12 Apr 2021.

Vancouver:

Huang Z. Modeling and Experimental Investigation on the Influence of Radiation Defects on Helium Behavior in BCC Iron. [Internet] [Thesis]. University of Tennessee – Knoxville; 2016. [cited 2021 Apr 12]. Available from: https://trace.tennessee.edu/utk_gradthes/3776.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Huang Z. Modeling and Experimental Investigation on the Influence of Radiation Defects on Helium Behavior in BCC Iron. [Thesis]. University of Tennessee – Knoxville; 2016. Available from: https://trace.tennessee.edu/utk_gradthes/3776

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

		in
And / Or
		in
And / Or
		in
And / Or
		in

Open Access Theses and Dissertations