subject:(Molecular Modeling)

Universiteit Utrecht

1. Enckevort, C.M.W. van. Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease.

Degree: 2014, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/298078

► Models are important tools used in the production, dissemination and acceptance of scientific knowledge (Dori & Barak, 2001, p. 62). The skills to learn with,… (more)

Subjects/Keywords: Molecular modeling

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APA (6^th Edition):

Enckevort, C. M. W. v. (2014). Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/298078

Chicago Manual of Style (16^th Edition):

Enckevort, C M W van. “Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease.” 2014. Masters Thesis, Universiteit Utrecht. Accessed March 04, 2021. http://dspace.library.uu.nl:8080/handle/1874/298078.

MLA Handbook (7^th Edition):

Enckevort, C M W van. “Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease.” 2014. Web. 04 Mar 2021.

Vancouver:

Enckevort CMWv. Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease. [Internet] [Masters thesis]. Universiteit Utrecht; 2014. [cited 2021 Mar 04]. Available from: http://dspace.library.uu.nl:8080/handle/1874/298078.

Council of Science Editors:

Enckevort CMWv. Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease. [Masters Thesis]. Universiteit Utrecht; 2014. Available from: http://dspace.library.uu.nl:8080/handle/1874/298078

Vanderbilt University

2. Bu, Jingjing. Molecular Scale Interactions Between Hydrated Cement Phases and Radionuclides Using Molecular Dynamics Modeling.

Degree: PhD, Environmental Engineering, 2018, Vanderbilt University

URL: http://hdl.handle.net/1803/15404

► Cesium (137Cs) and technetium (99Tc) are two radionuclides of significant concern in spent nuclear fuel because of their long half-life, high decay energy, and high… (more)

▼ Cesium (137Cs) and technetium (99Tc) are two radionuclides of significant concern in spent nuclear fuel because of their long half-life, high decay energy, and high solubility. Cementitious materials are considered as potential candidates for nuclear waste immobilization. The study of the interaction of radionuclides with the cement matrix is thus essential to determine the capability of cementitious materials to immobilize radioactive isotopes such as 137Cs and 99Tc. Calcium-silicate-hydrate (C-S-H) and calcium-aluminate-sulfate hydrate (ettringite) are two main products of cement hydration in Portland Cement (PC). The interactions of CsCl solution with different crystalline C-S-H structures (9Å tobermorite, 14Å tobermorite and jennite) and the interactions of KTcO4 solution with crystalline C-S-H structures (14Å tobermorite and jennite) and ettringite were studied using Molecular Dynamics (MD) simulations. MD simulation results indicated that Cs+ ions were mainly adsorbed as inner-sphere complexes at the tetrahedral SiO4 surface ((0 0 1) plane) of 9Å tobermorite, 14Å tobermorite, and jennite. The tobermorites showed higher adsorption capacity of Cs+ ions than jennite. Jennite had weak affinity to Cs+ ions. MD simulation results indicated that TcO4- ions can be adsorbed on the surfaces of 14Å tobermorite and ettringite. On the octahedral CaO6 surface ((0 0 -1) plane) of 14Å tobermorite, inner-sphere Tc complexes coexisted with outer-sphere Tc complexes. Co-ion adsorption affected the adsorption of outer-sphere Tc complexes and pushed outer-sphere complexes further away from the surface. On the octahedral CaO6 surface ((0 0 -1) plane) of ettringite, TcO4- ions were mainly adsorbed as outer-sphere complexes. Two types (i.e. type 1: tetragonal geometry and type 2: tetrahedral geometry) of outer-sphere Tc complexes were predicted on both surfaces of 14Å tobermorite and ettringite. Jennite had no affinity to TcO4- ions. In conclusion, 9Å tobermorite and 14Å tobermorite were better candidates for the immobilization of Cs+ ions than jennite. Ettringite and 14Å tobermorite also showed better affinity to TcO4- ions than jennite. Ca2+ ions on the surface played an important role and formed complexes with TcO4- ions. Advisors/Committee Members: Kevin G. Brown (committee member), David S. Kosson (committee member), James H. Clarke (committee member), Hans A. van der Sloot (committee member), Florence Sanchez (Committee Chair).

Subjects/Keywords: Molecular dynaimics modeling; cement; radionuclides

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APA (6^th Edition):

Bu, J. (2018). Molecular Scale Interactions Between Hydrated Cement Phases and Radionuclides Using Molecular Dynamics Modeling. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/15404

Chicago Manual of Style (16^th Edition):

Bu, Jingjing. “Molecular Scale Interactions Between Hydrated Cement Phases and Radionuclides Using Molecular Dynamics Modeling.” 2018. Doctoral Dissertation, Vanderbilt University. Accessed March 04, 2021. http://hdl.handle.net/1803/15404.

MLA Handbook (7^th Edition):

Bu, Jingjing. “Molecular Scale Interactions Between Hydrated Cement Phases and Radionuclides Using Molecular Dynamics Modeling.” 2018. Web. 04 Mar 2021.

Vancouver:

Bu J. Molecular Scale Interactions Between Hydrated Cement Phases and Radionuclides Using Molecular Dynamics Modeling. [Internet] [Doctoral dissertation]. Vanderbilt University; 2018. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1803/15404.

Council of Science Editors:

Bu J. Molecular Scale Interactions Between Hydrated Cement Phases and Radionuclides Using Molecular Dynamics Modeling. [Doctoral Dissertation]. Vanderbilt University; 2018. Available from: http://hdl.handle.net/1803/15404

University of South Florida

3. Fogarty, Joseph C. High Dimensional Non-Linear Optimization of Molecular Models.

Degree: 2014, University of South Florida

URL: https://scholarcommons.usf.edu/etd/5618

► Molecular models allow computer simulations to predict the microscopic properties of macroscopic systems. Molecular modeling can also provide a fully understood test system for the… (more)

Subjects/Keywords: Molecular Modeling; Optimization; Simulation; Physics

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APA (6^th Edition):

Fogarty, J. C. (2014). High Dimensional Non-Linear Optimization of Molecular Models. (Thesis). University of South Florida. Retrieved from https://scholarcommons.usf.edu/etd/5618

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):

Fogarty, Joseph C. “High Dimensional Non-Linear Optimization of Molecular Models.” 2014. Thesis, University of South Florida. Accessed March 04, 2021. https://scholarcommons.usf.edu/etd/5618.

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

MLA Handbook (7^th Edition):

Fogarty, Joseph C. “High Dimensional Non-Linear Optimization of Molecular Models.” 2014. Web. 04 Mar 2021.

Vancouver:

Fogarty JC. High Dimensional Non-Linear Optimization of Molecular Models. [Internet] [Thesis]. University of South Florida; 2014. [cited 2021 Mar 04]. Available from: https://scholarcommons.usf.edu/etd/5618.

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

Council of Science Editors:

Fogarty JC. High Dimensional Non-Linear Optimization of Molecular Models. [Thesis]. University of South Florida; 2014. Available from: https://scholarcommons.usf.edu/etd/5618

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

The Ohio State University

4. Polen, Shane M, Polen. Application of Molecular Modeling Techniques Towards the Development of Molecular Baskets and HER Catalysts.

Degree: PhD, Chemistry, 2017, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1500564483601742

► Acetylcholinesterase (AChE) is a serine hydrolase responsible for the hydrolysis of the neurotransmitter acetylcholine and is found throughout the body in synaptic clefts and in… (more)

▼ Acetylcholinesterase (AChE) is a serine hydrolase responsible for the hydrolysis of the neurotransmitter acetylcholine and is found throughout the body in synaptic clefts and in neuromuscular junctions. Acetylcholine (ACh) is released into the synaptic cleft following a neuronal impulse; ACh then binds to cholinergic receptors on postsynaptic cell membranes and triggers a response, such as a muscle contraction. In other words, ACh is the chemical that motor neurons of the nervous system release in order to activate muscles. Afterwards, ACh is released into the synaptic cleft where it is rapidly hydrolyzed by AChE. Organophosphorus (OP) compounds are substrate analogs to ACh and thus enter the active site and are attacked by Ser203 in a similar manner. This results in an inhibited phosphylated enzyme, and AChE is no longer able to bind and hydrolyze ACh. After inhibition, a process known as aging occurs through O-dealkylation of the OP-AChE adduct, which results in an anionic phosphylated serine residue that is resistant to nucleophilic attack. At this point, the enzyme is referred to as “aged” because it is resistant to reactivation. The result of inhibition and aging is the accumulation of ACh in neuromuscular junctions, which causes a cholinergic crisis, the overstimulation of nicotinic (nAChR) and muscarinic (mAChR) receptors. There are mulptiple strategies to combat OP poisioning; the first part of this dissertation explores the design of a series of bioscavengers that can be used to sequester the OP before inhibition of AChE occurs. The his dissertation focuses on the application of a wide variety of molecular modeling to better understand the non-covalent interactions between molecular baskets and their target guest molecules and to verify observed experimental properties of these systems. The second main focus of this thesis is the application of molecular modeling techniques to the development of molybdenum sulfide based hydrogen evolution reaction (HER) catalysts. In 2011 total worldwide hydrogen production exceeded 31 million metric tons; most of this hydrogen was used to manufacture ammonia via the Haber-Bosch process or in the petrochemical industry. Hydrogen is an ideal alternative fuel source due to its high energy density and carbon free emissions. The electrolysis of water to form H2 and O2 (water splitting) is an attractive alternative for fossil fuel reformation as the starting material (water) is recovered when hydrogen fuel is consumed and the input energy required to electrolyze the water can be provided by renewable sources. Water splitting can be divided into two half reactions: the oxygen evolution reaction (OER) and the hydrogen evolution reaction (HER). Both of these reactions require a catalyst to reduce the overpotential of the reaction, thereby increasing the energy efficiency. The best HER electrocatalyst to date is platinum, which has a near-zero overpotential. Given the cost and scarcity of platinum, the development of robust and sustainable alternative catalysts is critical to the… Advisors/Committee Members: Hadad, Christopher (Advisor).

Subjects/Keywords: Chemistry; Chemistry, Molecular Modeling Techniques

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APA (6^th Edition):

Polen, Shane M, P. (2017). Application of Molecular Modeling Techniques Towards the Development of Molecular Baskets and HER Catalysts. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1500564483601742

Chicago Manual of Style (16^th Edition):

Polen, Shane M, Polen. “Application of Molecular Modeling Techniques Towards the Development of Molecular Baskets and HER Catalysts.” 2017. Doctoral Dissertation, The Ohio State University. Accessed March 04, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1500564483601742.

MLA Handbook (7^th Edition):

Polen, Shane M, Polen. “Application of Molecular Modeling Techniques Towards the Development of Molecular Baskets and HER Catalysts.” 2017. Web. 04 Mar 2021.

Vancouver:

Polen, Shane M P. Application of Molecular Modeling Techniques Towards the Development of Molecular Baskets and HER Catalysts. [Internet] [Doctoral dissertation]. The Ohio State University; 2017. [cited 2021 Mar 04]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1500564483601742.

Council of Science Editors:

Polen, Shane M P. Application of Molecular Modeling Techniques Towards the Development of Molecular Baskets and HER Catalysts. [Doctoral Dissertation]. The Ohio State University; 2017. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1500564483601742

University of Utah

5. DeMille, Robert Curtis. Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail.

Degree: PhD, Chemistry, 2012, University of Utah

URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656

► A theoretical study of a chemical system is focused on representing the systemproperly with a model and using it to accurately represent and predict physical… (more)

Subjects/Keywords: Computational efficiency; DNA; Modeling; Molecular Dynamics

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APA (6^th Edition):

DeMille, R. C. (2012). Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656

Chicago Manual of Style (16^th Edition):

DeMille, Robert Curtis. “Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail.” 2012. Doctoral Dissertation, University of Utah. Accessed March 04, 2021. http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656.

MLA Handbook (7^th Edition):

DeMille, Robert Curtis. “Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail.” 2012. Web. 04 Mar 2021.

Vancouver:

DeMille RC. Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail. [Internet] [Doctoral dissertation]. University of Utah; 2012. [cited 2021 Mar 04]. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656.

Council of Science Editors:

DeMille RC. Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail. [Doctoral Dissertation]. University of Utah; 2012. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656

Universidade do Rio Grande do Sul

6. Vendruscolo, Maria Helena. Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular.

Degree: 2017, Universidade do Rio Grande do Sul

URL: http://hdl.handle.net/10183/166272

►

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo… (more)

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Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase.

Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima…

Advisors/Committee Members: Von Poser, Gilsane Lino.

Subjects/Keywords: Iridoids; Iridoides; Leishmania; Pharmacophore; Molecular modeling

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APA (6^th Edition):

Vendruscolo, M. H. (2017). Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular. (Thesis). Universidade do Rio Grande do Sul. Retrieved from http://hdl.handle.net/10183/166272

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):

Vendruscolo, Maria Helena. “Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular.” 2017. Thesis, Universidade do Rio Grande do Sul. Accessed March 04, 2021. http://hdl.handle.net/10183/166272.

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

MLA Handbook (7^th Edition):

Vendruscolo, Maria Helena. “Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular.” 2017. Web. 04 Mar 2021.

Vancouver:

Vendruscolo MH. Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular. [Internet] [Thesis]. Universidade do Rio Grande do Sul; 2017. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10183/166272.

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

Council of Science Editors:

Vendruscolo MH. Obtenção de iridoides de espécies nativas da flora do Rio Grande do Sul, modificações estruturais, determinação da atividade anti-Leishmania amazonensis in vitro e modelagem molecular. [Thesis]. Universidade do Rio Grande do Sul; 2017. Available from: http://hdl.handle.net/10183/166272

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

Georgia Tech

7. Park, Jongwoo. Atomistic characterization of metal-organic frameworks for sub-ambient pressure swing adsorption of post-combustion CO2 capture and separation.

Degree: PhD, Chemical and Biomolecular Engineering, 2019, Georgia Tech

URL: http://hdl.handle.net/1853/62308

► Developing cost-effective and less energy-intensive carbon capture processes for dilute CO2 sources is of high interest. Adsorption-based CO2 capture such as pressure swing adsorption (PSA)… (more)

▼ Developing cost-effective and less energy-intensive carbon capture processes for dilute CO2 sources is of high interest. Adsorption-based CO2 capture such as pressure swing adsorption (PSA) is one promising approach to this challenge. PSA and other cyclic adsorption processes are materials-enabled separations that use porous adsorbents, including metal-organic frameworks (MOFs). This thesis examines post-combustion carbon capture in sub-ambient PSA, a potential route to an effective adsorption process, using MOF materials via molecular modeling. We first estimated the reproducibility of CO2 adsorption isotherm measurements in MOFs via literature meta-analysis. This chapter provides a comprehensive summary of the state of knowledge regarding CO2 adsorption in MOFs and its implications for molecular modeling of adsorption in MOFs. We then examined the upper bounds on CO2 swing capacity in sub-ambient PSA by Grand Canonical Monte Carlo (GCMC) simulation of an extensive collection of MOFs. A wide variety of MOFs was found to have swing capacity exceeding 10 mol/kg at sub-ambient temperatures provided that MOFs are appropriately selected based on their physical properties. We also assessed the capability of simple proxies for adsorbent performance and approximate models of cyclic adsorption to predict the outcomes of detailed process models of adsorption-based CO2 capture processes. To this end, we discuss the correlations between predictions from the simpler models and detailed process models. As a separate contribution, molecular modeling of chemical warfare agents (CWAs) adsorption in MOFs was analyzed. Molecular models of adsorption of CO2, CWAs or other molecules typically employ a rigid framework approximation for computational convenience. All real frameworks including MOFs, however, have intrinsic flexibility due to thermal vibrations. We examine the implications of this simple observation for quantitative predictions of the properties of adsorbed CWAs. Advisors/Committee Members: Sholl, David S. (advisor), Lively, Ryan P. (committee member), Walton, Krista S. (committee member), Realff, Matthew J. (committee member), Gumbart, James C. (committee member).

Subjects/Keywords: CO2 adsorption; Metal-organic frameworks; Molecular modeling

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

APA (6^th Edition):

Park, J. (2019). Atomistic characterization of metal-organic frameworks for sub-ambient pressure swing adsorption of post-combustion CO2 capture and separation. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/62308

Chicago Manual of Style (16^th Edition):

Park, Jongwoo. “Atomistic characterization of metal-organic frameworks for sub-ambient pressure swing adsorption of post-combustion CO2 capture and separation.” 2019. Doctoral Dissertation, Georgia Tech. Accessed March 04, 2021. http://hdl.handle.net/1853/62308.

MLA Handbook (7^th Edition):

Park, Jongwoo. “Atomistic characterization of metal-organic frameworks for sub-ambient pressure swing adsorption of post-combustion CO2 capture and separation.” 2019. Web. 04 Mar 2021.

Vancouver:

Park J. Atomistic characterization of metal-organic frameworks for sub-ambient pressure swing adsorption of post-combustion CO2 capture and separation. [Internet] [Doctoral dissertation]. Georgia Tech; 2019. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1853/62308.

Council of Science Editors:

Park J. Atomistic characterization of metal-organic frameworks for sub-ambient pressure swing adsorption of post-combustion CO2 capture and separation. [Doctoral Dissertation]. Georgia Tech; 2019. Available from: http://hdl.handle.net/1853/62308

Vanderbilt University

8. Haley, Jessica Deloris. Predicting the Thermodynamic Properties of Complex Molecular Systems for Environmental Applications.

Degree: PhD, Chemical Engineering, 2015, Vanderbilt University

URL: http://hdl.handle.net/1803/13135

► The call for the advancement in our ability to design cleaner technologies, as well as mitigate our ecological footprint, requires the investigation of new energy… (more)

▼ The call for the advancement in our ability to design cleaner technologies, as well as mitigate our ecological footprint, requires the investigation of new energy related systems. Fundamental knowledge of the thermodynamics and phase behavior of such systems is essential for their development and industrial application. Accurate thermophysical properties are required, as limited or inaccurate data may affect the design of processes resulting in a financial or product yield loss; thus, the ability to reliably predict the properties and phase behavior of energy relevant fluids is essential to the development of new and continual improvement of existing chemical and energy processes. Traditional theoretical approaches based on semi-empirical or empirical equations of state that do not reflect molecular-level structure and interactions, are typically heavily reliant on correlations from experimental data, which may limit their general applicability. Molecular-based equations of state that take into account molecular structure are an attractive alternative because they yield a more accurate and predictive approach by accounting for the intrinsic effects of the microscopic interactions between molecules that ultimately determine the thermodynamic properties of the fluid. This results in parameters that are typically transferrable to entire classes of molecules. The statistical associating fluid theory for potentials of variable range (SAFT-VR) is one such molecular-based approach that describes chain molecules formed from hard-core monomers that interact via square well potentials of variable attractive range. In this work, systems with significant environmental applications, including carbon dioxide, organic sulfur and fluorine molecules, fatty acid methyl esters, and nanoparticle systems, are studied with the SAFT-VR approach. These systems were specifically chosen, as their unique features (e.g., large molecules, association interactions, electrostatics) have historically made their thermodynamic modeling difficult. Advisors/Committee Members: Peter Cummings (committee member), Doug LeVan (committee member), Mark Abkowitz (committee member), Clare McCabe (Committee Chair).

Subjects/Keywords: SAFT; Equation of State; Molecular Modeling

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APA (6^th Edition):

Haley, J. D. (2015). Predicting the Thermodynamic Properties of Complex Molecular Systems for Environmental Applications. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/13135

Chicago Manual of Style (16^th Edition):

Haley, Jessica Deloris. “Predicting the Thermodynamic Properties of Complex Molecular Systems for Environmental Applications.” 2015. Doctoral Dissertation, Vanderbilt University. Accessed March 04, 2021. http://hdl.handle.net/1803/13135.

MLA Handbook (7^th Edition):

Haley, Jessica Deloris. “Predicting the Thermodynamic Properties of Complex Molecular Systems for Environmental Applications.” 2015. Web. 04 Mar 2021.

Vancouver:

Haley JD. Predicting the Thermodynamic Properties of Complex Molecular Systems for Environmental Applications. [Internet] [Doctoral dissertation]. Vanderbilt University; 2015. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1803/13135.

Council of Science Editors:

Haley JD. Predicting the Thermodynamic Properties of Complex Molecular Systems for Environmental Applications. [Doctoral Dissertation]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/13135

Mahatma Gandhi University

9. Satheesh, Nisha. Molecular modelling of dendrimers;.

Degree: Chemistry, 2014, Mahatma Gandhi University

URL: http://shodhganga.inflibnet.ac.in/handle/10603/25742

newline

Bibliography in each chapters, Appendices p. 155-216

Advisors/Committee Members: Padmanabhan, A S.

Subjects/Keywords: Dendrimers; Molecular modeling

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APA (6^th Edition):

Satheesh, N. (2014). Molecular modelling of dendrimers;. (Thesis). Mahatma Gandhi University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/25742

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):

Satheesh, Nisha. “Molecular modelling of dendrimers;.” 2014. Thesis, Mahatma Gandhi University. Accessed March 04, 2021. http://shodhganga.inflibnet.ac.in/handle/10603/25742.

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

MLA Handbook (7^th Edition):

Satheesh, Nisha. “Molecular modelling of dendrimers;.” 2014. Web. 04 Mar 2021.

Vancouver:

Satheesh N. Molecular modelling of dendrimers;. [Internet] [Thesis]. Mahatma Gandhi University; 2014. [cited 2021 Mar 04]. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/25742.

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

Council of Science Editors:

Satheesh N. Molecular modelling of dendrimers;. [Thesis]. Mahatma Gandhi University; 2014. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/25742

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

10. ZHANG, SHIMIAO. EFFECTS OF PROCESS CONDITIONS ON POLYMER NETWORK FORMATION: APPLICATION IN PARTICLE COATING AND MODELING USING MOLECULAR DYNAMICS.

Degree: MASc, 2016, McMaster University

URL: http://hdl.handle.net/11375/20507

►

Cross-linked polymers are of great importance to industrial practice and theoretical studies. The unique network structures of these materials have endowed them with many superior… (more)

▼

Cross-linked polymers are of great importance to industrial practice and theoretical studies. The unique network structures of these materials have endowed them with many superior properties. In this thesis, we study cross-linked polymers from both of experimental and theoretical sides, with an emphasis on the formation process and properties of the prepared networks. Two specific problems are investigated: development of polymer coatings over solid particles with in situ curing, and molecular dynamics (MD) study of network formation kinetics and structure-property relationship. In the study of polymer coating, a hot-melt coating process for solid particles is developed. Phenolic resin is used to coat the substrates and subsequently cured in situ. Among various processing parameters, temperature is found to play an especially important role in the coating performance. Higher temperature leads to stronger coating layers with better barrier properties, whereas lower temperature is preferable for better surface morphology. These two trends can be partially reconciled with ramping temperature profiles; however, the improvement is eventually limited by the rate of heat transfer. In MD study, the effects of precursor topology on the formation, structure and mechanical properties of polymer networks are studied. Cross-linked polymer networks are synthesized from three sets of precursors with varying chain length. Little difference is observed between these networks in typical properties including radial distribution function, overall statistics of network connectivity, and glass transition behaviors. The elastic modulus of the network is found to correlate strongly with the number of elastic strands in the network, except at the highly-cross-linked limit where substantial discrepancy is observed between networks from different precursors. Although these final networks contain a similar level of structural defects, the choice of precursor has a significant effect on the spatial distribution of the defects, which explains the precursor dependence of their mechanical property observed in the tensile test.

Thesis

Master of Applied Science (MASc)

Advisors/Committee Members: Xi, Li, Chemical Engineering.

Subjects/Keywords: Polymer Network; Surface Coating; Molecular Modeling

13 more images…

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APA (6^th Edition):

ZHANG, S. (2016). EFFECTS OF PROCESS CONDITIONS ON POLYMER NETWORK FORMATION: APPLICATION IN PARTICLE COATING AND MODELING USING MOLECULAR DYNAMICS. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/20507

Chicago Manual of Style (16^th Edition):

ZHANG, SHIMIAO. “EFFECTS OF PROCESS CONDITIONS ON POLYMER NETWORK FORMATION: APPLICATION IN PARTICLE COATING AND MODELING USING MOLECULAR DYNAMICS.” 2016. Masters Thesis, McMaster University. Accessed March 04, 2021. http://hdl.handle.net/11375/20507.

MLA Handbook (7^th Edition):

ZHANG, SHIMIAO. “EFFECTS OF PROCESS CONDITIONS ON POLYMER NETWORK FORMATION: APPLICATION IN PARTICLE COATING AND MODELING USING MOLECULAR DYNAMICS.” 2016. Web. 04 Mar 2021.

Vancouver:

ZHANG S. EFFECTS OF PROCESS CONDITIONS ON POLYMER NETWORK FORMATION: APPLICATION IN PARTICLE COATING AND MODELING USING MOLECULAR DYNAMICS. [Internet] [Masters thesis]. McMaster University; 2016. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/11375/20507.

Council of Science Editors:

ZHANG S. EFFECTS OF PROCESS CONDITIONS ON POLYMER NETWORK FORMATION: APPLICATION IN PARTICLE COATING AND MODELING USING MOLECULAR DYNAMICS. [Masters Thesis]. McMaster University; 2016. Available from: http://hdl.handle.net/11375/20507

North Carolina State University

11. Jeong, Euigyung. Synthesis, Mutagenicity, and Metabolism of Substituted 4,4'-Aminoakoxyazobenzene dyes.

Degree: PhD, Fiber and Polymer Science, 2009, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/5714

► This study is an extension of previous work in our laboratories pertaining to the effects of substituents on the mutagenicity of aminoazobenzene-based dyes. The previous… (more)

▼ This study is an extension of previous work in our laboratories pertaining to the effects of substituents on the mutagenicity of aminoazobenzene-based dyes. The previous work included a study aimed at exploiting the ability of bulky alkoxy groups to reduce the mutagenic potential of aminoazobenzene dyes, which unexpectedly revealed that 4-((3-(2-hydroxyethoxy-4-amino)phenylazo) N,N-bis(2-hydroxyethyl)aniline (dye 80) was among the more mutagenic dyes in that study, despite having non-mutagenic amines as reductive-cleavage products. The present study was undertaken to unveil the basis for the mutagenic activity of dye 80. To accomplish this goal, a group of substituted 4,4Ã¢â‚¬â„¢ Ã¢â‚¬â€œdiaminoazobenzene dyes (80, 89-92) was synthesized and their structures were characterized using 1H NMR, TOF-LC-ESI mass spectrometry, and combustion analysis. The purity of each dye was shown by HPLC to be 98-100 %. These new compounds were designed as tests of our hypothesis which stated that the mutagenicity of dye 80 arises from the metabolic cleavage of N-hydroxyethyl groups to give 4-((3-(2-hydroxyethoxy)-4-amino)phenylazo) N-(2-hydroxyethyl)-aniline (dyes 89) and 4-((3-(2-hydroxyethoxy-4-amino)phenylazo)aniline (dye 90) as direct-acting mutagens. 4-((3-(2-hydroxyethoxy-4-amino)phenylazo) N,N-bis-(3-hydroxypropyl)aniline (dye 91) arises from lengthening the N-alkyl groups of dye 80 from 2 to 3 carbons, while 4-((3-(2-hydroxyethoxy-4-amino)phenylazo)-N,N-bis(2-acetoxyethyl)aniline (dye 92) is a capped form of dye 80. Mutagenicity was determined using the standard Ames test in Salmonella strains TA98, TA100, and TA1538 with and without S9 enzyme activation. The results showed that all of the dyes tested were mutagenic at various levels with and without S9 enzyme activation in TA1538. Dye 90 was also mutagenic in TA98 and TA100 with and without S9 enzyme activation, whereas dye 91 was mutagenic only in TA98 with S9 enzyme activation. These results indicated that dye 90 was a direct-acting mutagen. The results also suggested that removing one N-hydroxyethyl group and capping both Ã¢â‚¬â€œOH groups in the parent dye 80 did not affect mutagenicity, whereas removing both N-hydroxyethyl groups produced a strong direct-acting mutagen (dye 90) in all three bacterial strains. Increasing the length of the N-alkyl chain from two to three carbon atoms (dye 91) removed mutagenicity in TA98 without S9 activation. The results from TLC and HPLC analysis of product mixtures from rat liver and hamster liver enzyme S9 treatments of dye 80 and 89 confirmed that the metabolism of dye 80 involved de-hydroxyethylation of the substituted amino group. The analysis of product mixtures from rat liver S9 treatments of dye 92 indicated that the metabolism of dye 92 involved de-acetylation of the O-acetyl groups. Computational studies conducted in this research indicated that the shapes of HOMO and HOMO-1 and their energy differences did not provide a direct correlation between electronic properties and mutagenicity. Similarly, there was no… Advisors/Committee Members: Dr. Larry D. Claxton, Committee Member (advisor), Dr. Jonathan S. Lindsey, Committee Member (advisor), Dr. David Hinks, Committee Co-Chair (advisor), Dr. Harold S. Freeman, Committee Chair (advisor).

Subjects/Keywords: Monoazo dyes; Metabolism; Molecular Modeling; Mutagenicity; Synthesis

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APA (6^th Edition):

Jeong, E. (2009). Synthesis, Mutagenicity, and Metabolism of Substituted 4,4'-Aminoakoxyazobenzene dyes. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/5714

Chicago Manual of Style (16^th Edition):

Jeong, Euigyung. “Synthesis, Mutagenicity, and Metabolism of Substituted 4,4'-Aminoakoxyazobenzene dyes.” 2009. Doctoral Dissertation, North Carolina State University. Accessed March 04, 2021. http://www.lib.ncsu.edu/resolver/1840.16/5714.

MLA Handbook (7^th Edition):

Jeong, Euigyung. “Synthesis, Mutagenicity, and Metabolism of Substituted 4,4'-Aminoakoxyazobenzene dyes.” 2009. Web. 04 Mar 2021.

Vancouver:

Jeong E. Synthesis, Mutagenicity, and Metabolism of Substituted 4,4'-Aminoakoxyazobenzene dyes. [Internet] [Doctoral dissertation]. North Carolina State University; 2009. [cited 2021 Mar 04]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/5714.

Council of Science Editors:

Jeong E. Synthesis, Mutagenicity, and Metabolism of Substituted 4,4'-Aminoakoxyazobenzene dyes. [Doctoral Dissertation]. North Carolina State University; 2009. Available from: http://www.lib.ncsu.edu/resolver/1840.16/5714

12. Dambrauskaitė, Justė. Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas.

Degree: Master, Pharmacy, 2011, Lithuanian Academic Libraries Network (LABT)

URL: http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;

►

Vykdytas tyrimas, kurio tikslas - atlikti junginių - α-GalCer analogų – paiešką. Analogai turėtų pasižymėti α-GalCer agonistiniu poveikiu NKT ląstelėms, tačiau, skirtingai nei α-GalCer, neturėtų… (more)

▼

Vykdytas tyrimas, kurio tikslas - atlikti junginių - α-GalCer analogų – paiešką. Analogai turėtų pasižymėti α-GalCer agonistiniu poveikiu NKT ląstelėms, tačiau, skirtingai nei α-GalCer, neturėtų būti toksiški. Ieškomi junginiai – potencialios vaistinės medžiagos, skirtos opinio kolito ir kitų uždegiminių žarnyno ligų gydymui. Atlikus atitinkamos mokslinės literatūros analizę, išnagrinėjus α-GalCer bei baltymo CD1d struktūrą, jų jungimosi ypatumus ir reikalavimus junginio, kuris galėtų pakeisti α-GalCer, struktūrai, sumodeliuoti junginiai, kurie ištirti kompleksacijos būdu. Kompleksacijos proceso metu atrinkti šeši junginiai, kurie panašiausiai į α-GalCer jungiasi su baltymu CD1d bei turėtų pasižymėti pageidaujamomis savybėmis. Šių junginių struktūros pasiūlytos sintezei.

The aim of investigation performed is to propose possible analogues of α-GalCer. The analogues must have same beneficial properties as α-GalCer except the toxicity. The compounds we are looking for is a potential therapeutic agents to treat ulcerative colitis and other inflamatory bowel diseases. After studying scietific literature, the structure of α-GalCer and protein CD1d, their binding properties, and the requirements for the structure of possible analogue of α-GalCer, we accomplished molecular modeling of several compounds and performed docking. Docking revealed six compounds that are the most believable to have same binding properties with CD1d as α-GalCer does and same therapeutic properties. The structures of those compounds were proposed for a synthesis and other examination will be performed later.

Advisors/Committee Members: Briedis, Vitalis (Master’s thesis supervisor), Petrikaitė, Vilma (Master’s thesis reviewer), Tarasevičius, Eduardas (Master’s degree committee chair), Lukošius , Audronis (Master’s degree committee member), Janulis, Valdimaras (Master’s degree committee member), Ivanauskas, Liudas (Master’s degree committee member), Savickas, Arūnas (Master’s degree committee member), Briedis , Vitalis (Master’s degree committee member), Ramanauskienė , Kristina (Master’s degree committee member), Radžiūnas , Raimondas (Master’s degree committee member), Pečiūra , Rimantas (Master’s degree committee member), Gumbrevičius, Gintautas (Master’s degree committee member), Rodovičius , Hiliaras (Master’s degree committee member).

Subjects/Keywords: Molekulinis; Modeliavimas; Kompleksacija; Molecular; Modeling; Docking

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APA (6^th Edition):

Dambrauskaitė, Justė. (2011). Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas. (Masters Thesis). Lithuanian Academic Libraries Network (LABT). Retrieved from http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

Dambrauskaitė, Justė. “Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas.” 2011. Masters Thesis, Lithuanian Academic Libraries Network (LABT). Accessed March 04, 2021. http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

Dambrauskaitė, Justė. “Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas.” 2011. Web. 04 Mar 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

Dambrauskaitė, Justė. Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas. [Internet] [Masters thesis]. Lithuanian Academic Libraries Network (LABT); 2011. [cited 2021 Mar 04]. Available from: http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

Dambrauskaitė, Justė. Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas. [Masters Thesis]. Lithuanian Academic Libraries Network (LABT); 2011. Available from: http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

University of Houston

13. Dai, Wei. Multiscale Modeling of the Organization of Receptor Transmembrane Domains in Lipid Membranes.

Degree: MS, Chemical Engineering, 2014, University of Houston

URL: http://hdl.handle.net/10657/4672

► Membrane proteins have a critical role in signal transduction pathways. The current hypothesis is that different specific arrangements of transmembrane domains (TMD) facilitate the activation… (more)

Subjects/Keywords: Molecular simulations; Transmembrane Protein; Multiscale modeling; Receptors

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APA (6^th Edition):

Dai, W. (2014). Multiscale Modeling of the Organization of Receptor Transmembrane Domains in Lipid Membranes. (Masters Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/4672

Chicago Manual of Style (16^th Edition):

Dai, Wei. “Multiscale Modeling of the Organization of Receptor Transmembrane Domains in Lipid Membranes.” 2014. Masters Thesis, University of Houston. Accessed March 04, 2021. http://hdl.handle.net/10657/4672.

MLA Handbook (7^th Edition):

Dai, Wei. “Multiscale Modeling of the Organization of Receptor Transmembrane Domains in Lipid Membranes.” 2014. Web. 04 Mar 2021.

Vancouver:

Dai W. Multiscale Modeling of the Organization of Receptor Transmembrane Domains in Lipid Membranes. [Internet] [Masters thesis]. University of Houston; 2014. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10657/4672.

Council of Science Editors:

Dai W. Multiscale Modeling of the Organization of Receptor Transmembrane Domains in Lipid Membranes. [Masters Thesis]. University of Houston; 2014. Available from: http://hdl.handle.net/10657/4672

University of Manitoba

14. Upadhyaya, Jasbir Deol. Characterization of human bitter taste receptor T2R1.

Degree: Oral Biology, 2010, University of Manitoba

URL: http://hdl.handle.net/1993/4129

► Bitter taste signaling in humans is mediated by a group of 25 bitter receptors (T2Rs) that belong to the G-protein coupled receptor (GPCR) family. Previously,… (more)

Subjects/Keywords: T2R1; Peptides; Molecular modeling; C6 glial cells

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APA (6^th Edition):

Upadhyaya, J. D. (2010). Characterization of human bitter taste receptor T2R1. (Masters Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/4129

Chicago Manual of Style (16^th Edition):

Upadhyaya, Jasbir Deol. “Characterization of human bitter taste receptor T2R1.” 2010. Masters Thesis, University of Manitoba. Accessed March 04, 2021. http://hdl.handle.net/1993/4129.

MLA Handbook (7^th Edition):

Upadhyaya, Jasbir Deol. “Characterization of human bitter taste receptor T2R1.” 2010. Web. 04 Mar 2021.

Vancouver:

Upadhyaya JD. Characterization of human bitter taste receptor T2R1. [Internet] [Masters thesis]. University of Manitoba; 2010. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/1993/4129.

Council of Science Editors:

Upadhyaya JD. Characterization of human bitter taste receptor T2R1. [Masters Thesis]. University of Manitoba; 2010. Available from: http://hdl.handle.net/1993/4129

Delft University of Technology

15. De Flart, S. (author). Capturing Carbon Dioxide directly from the air: A theoretical modeling approach.

Degree: 2016, Delft University of Technology

URL: http://resolver.tudelft.nl/uuid:a3daa041-8a33-49ec-a0dc-26c88df0e83d

►

Direct Air Capture processes capture carbon dioxide directly from the air and aim to utilize the captured carbon dioxide; this would allow CO2 capture independent… (more)

▼

Direct Air Capture processes capture carbon dioxide directly from the air and aim to utilize the captured carbon dioxide; this would allow CO2 capture independent of source and location and can therefore address all CO2 emissions. Although already quite some processes and materials exist that are capable of this, it is still not yet widely applied in industry. The aim of this thesis is to first select a suitable material and then provide the tools to start designing such a process. The present work focuses on a solid (primary) amine-based sorbent and models the CO2 capture process on both a molecular scale, using quantum chemical calculations, as well as on a macroscopic scale, using a numerical representation of a fixed bed adsorption column. The quantum chemical calculations in the present work show that in order for this specific sorbent to capture CO2 the reaction needs a catalyst. It was found that functional amine groups are close enough to each other to catalyze CO2 capture. Besides that it was found that H2O can also catalyze the CO2 capture. The CO2 reacts with these molecules to either form a carbamic acid complex or a bicarbonate complex with the other (protonated) amine. The H2O catalyzed CO2 capture, where it reacts to form carbamic acid, was somewhat unexpected; no reports of this mechanism were encountered in literature during the study. The results of the quantum chemical calculations were successfully implemented in the numerical model and were able to describe the sorbent’s CO2 capacity as a function of temperature. The numerical model can be used as a design tool to estimate parameters such as speed of adsorption and can serve as an input for design calculations. Processes using solid sorbents seem to be highly scalable. They can be applied everywhere and can be designed as a modular system. Once a single DAC unit has been designed that captures 1 kg of CO2 a day it can used in a modular system of several units, eventually scaling up to tonnes of CO2 per day. The sorbent in this study regenerates the CO2 at a temperature of approximately 80 ⁰C which could be supplied in the form of waste heat. Using this technology, CO2 becomes available everywhere, makes further use of waste heat and is able to address CO2 emissions from every source (vehicles, industry, residential).

Mechanical, Maritime and Materials Engineering

Process and Energy

Advisors/Committee Members: Buijs, W. (mentor), Kramer, H.J.M. (mentor), Mulder, F.M. (mentor).

Subjects/Keywords: Direct Air Capture; molecular modeling; adsorption

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APA (6^th Edition):

De Flart, S. (. (2016). Capturing Carbon Dioxide directly from the air: A theoretical modeling approach. (Masters Thesis). Delft University of Technology. Retrieved from http://resolver.tudelft.nl/uuid:a3daa041-8a33-49ec-a0dc-26c88df0e83d

Chicago Manual of Style (16^th Edition):

De Flart, S (author). “Capturing Carbon Dioxide directly from the air: A theoretical modeling approach.” 2016. Masters Thesis, Delft University of Technology. Accessed March 04, 2021. http://resolver.tudelft.nl/uuid:a3daa041-8a33-49ec-a0dc-26c88df0e83d.

MLA Handbook (7^th Edition):

De Flart, S (author). “Capturing Carbon Dioxide directly from the air: A theoretical modeling approach.” 2016. Web. 04 Mar 2021.

Vancouver:

De Flart S(. Capturing Carbon Dioxide directly from the air: A theoretical modeling approach. [Internet] [Masters thesis]. Delft University of Technology; 2016. [cited 2021 Mar 04]. Available from: http://resolver.tudelft.nl/uuid:a3daa041-8a33-49ec-a0dc-26c88df0e83d.

Council of Science Editors:

De Flart S(. Capturing Carbon Dioxide directly from the air: A theoretical modeling approach. [Masters Thesis]. Delft University of Technology; 2016. Available from: http://resolver.tudelft.nl/uuid:a3daa041-8a33-49ec-a0dc-26c88df0e83d

Michigan Technological University

16. Hadden, Cameron. MOLECULAR MODELING OF EPON 862-DETDA / CARBON COMPOSITES.

Degree: PhD, Department of Mechanical Engineering-Engineering Mechanics, 2015, Michigan Technological University

URL: https://digitalcommons.mtu.edu/etds/946

► The thermoset epoxy resin EPON 862, coupled with the DETDA hardening agent, are utilized as the polymer matrix component in many graphite (carbon fiber)… (more)

▼ The thermoset epoxy resin EPON 862, coupled with the DETDA hardening agent, are utilized as the polymer matrix component in many graphite (carbon fiber) composites. Because it is difficult to experimentally characterize the interfacial region, computational molecular modeling is a necessary tool for understanding the influence of the interfacial molecular structure on bulk-level material properties. The purpose of this research is to investigate the many possible variables that may influence the interfacial structure and the effect they will have on the mechanical behavior of the bulk level composite. Molecular models are established for EPON 862-DETDA polymer in the presence of a graphite surface. Material characteristics such as polymer mass-density, residual stresses, and molecular potential energy are investigated near the polymer/fiber interface. Because the exact degree of crosslinking in these thermoset systems is not known, many different crosslink densities (degrees of curing) are investigated. It is determined that a region exists near the carbon fiber surface in which the polymer mass density is different than that of the bulk mass density. These surface effects extend ~10 Å into the polymer from the center of the outermost graphite layer. Early simulations predict polymer residual stress levels to be higher near the graphite surface. It is also seen that the molecular potential energy in polymer atoms decreases with increasing crosslink density. New models are then established in order to investigate the interface between EPON 862-DETDA polymer and graphene nanoplatelets (GNPs) of various atomic thicknesses. Mechanical properties are extracted from the models using Molecular Dynamics techniques. These properties are then implemented into micromechanics software that utilizes the generalized method of cells to create representations of macro-scale composites. Micromechanics models are created representing GNP doped epoxy with varying number of graphene layers and interfacial polymer crosslink densities. The initial micromechanics results for the GNP doped epoxy are then taken to represent the matrix component and are re-run through the micromechanics software with the addition of a carbon fiber to simulate a GNP doped epoxy/carbon fiber composite. Micromechanics results agree well with experimental data, and indicate GNPs of 1 to 2 atomic layers to be highly favorable. The effect of oxygen bonded to the surface of the GNPs is lastly investigated. Molecular Models are created for systems with varying graphene atomic thickness, along with different amounts of oxygen species attached to them. Models are created for graphene containing hydroxyl groups only, epoxide groups only, and a combination of epoxide and hydroxyl groups. Results show models of oxidized graphene to decrease in both tensile and shear modulus. Attaching only epoxide groups gives the best results for mechanical properties, though pristine graphene is still favored. Advisors/Committee Members: Gregory M. Odegard.

Subjects/Keywords: Carbon; Composites; Graphene; Modeling; Molecular; Mechanical Engineering

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

APA (6^th Edition):

Hadden, C. (2015). MOLECULAR MODELING OF EPON 862-DETDA / CARBON COMPOSITES. (Doctoral Dissertation). Michigan Technological University. Retrieved from https://digitalcommons.mtu.edu/etds/946

Chicago Manual of Style (16^th Edition):

Hadden, Cameron. “MOLECULAR MODELING OF EPON 862-DETDA / CARBON COMPOSITES.” 2015. Doctoral Dissertation, Michigan Technological University. Accessed March 04, 2021. https://digitalcommons.mtu.edu/etds/946.

MLA Handbook (7^th Edition):

Hadden, Cameron. “MOLECULAR MODELING OF EPON 862-DETDA / CARBON COMPOSITES.” 2015. Web. 04 Mar 2021.

Vancouver:

Hadden C. MOLECULAR MODELING OF EPON 862-DETDA / CARBON COMPOSITES. [Internet] [Doctoral dissertation]. Michigan Technological University; 2015. [cited 2021 Mar 04]. Available from: https://digitalcommons.mtu.edu/etds/946.

Council of Science Editors:

Hadden C. MOLECULAR MODELING OF EPON 862-DETDA / CARBON COMPOSITES. [Doctoral Dissertation]. Michigan Technological University; 2015. Available from: https://digitalcommons.mtu.edu/etds/946

University of Illinois – Urbana-Champaign

17. Kunal, Kumar. Computational modeling of intrinsic dissipation in nano-structure.

Degree: PhD, Theoretical & Applied Mechans, 2016, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/90707

► In this work, using computational modeling, we study the different mechanisms of intrinsic dissipation in nano-electro mechanical systems (NEMS). We, first, use molecular dynamics (MD)… (more)

▼ In this work, using computational modeling, we study the different mechanisms of intrinsic dissipation in nano-electro mechanical systems (NEMS). We, first, use molecular dynamics (MD) simulation and gain an understanding of the underlying loss mechanisms. Using insights from the MD simulation, a multi-scale method to model intrinsic damping is developed. The high frequency vibration in NEMS have important applications. A few examples include the sensing of atomic mass, detection of biological molecules and observation of quantum effects in macroscopic objects. For all these potential applications, dissipation plays a limiting role. While a number of experimental and theoretical studies have been performed, the individual role of different mechanisms remains unclear. In this work, we attempt to isolate and understand the surface and size effect on some of the intrinsic mechanisms. We, first, consider the case of the Akhiezer damping. The Akhiezer dynamics is expected to play an important role in nano-resonators with frequencies in the GHz range. Using a judiciously devised MD set-up, we isolate Akhiezer dynamics. We show that the surfaces aid in reducing the dissipation rate through increasing the rate of thermalization of the phonons. We, next, study damping under the flexure mode of operation. A comparative analysis with the stretching mode shows that the flexure mode is less dissipative. A reduced order model is considered to understand this novel behavior. We, also, investigate the role of tension on the Q factor, a measure of the inverse of dissipation rate. From these studies, we conclude that Akhiezer dynamics plays a dominant role in nano-resonators. We, then, develop a quasi-harmonic based multi-scale method to model Akhiezer damping. A stress component, that characterizes the non-equilibrium phonon population, is derived. We obtain constitutive relation that governs the time evolution of the non-equilibrium stress. Different methods to parametrize the constitutive relation are discussed. Using the proposed formulation, we compute the dissipation rate for different cases. The results are compared with those obtained using MD. Next, we use the Boltzmann transport equation and investigate the Q factor due to the thermo-elastic dissipation (TED). The Q factor obtained shows deviations from the classical theory of TED. Correction to the classical formula, for the case of longitudinal modes, is provided. We, then, study damping is low dimensional structure. We first consider the case of two dimensional graphene sheet and under in-plane stretching. We show that the coupling between the in-plane and the out-of-plane motions plays an important role in the loss of mechanical energy. Further, a hysteresis behavior in the out-of-plane dynamics is observed. Next, we investigate the stretching motion of graphene nano-ribbon. A normal mode Langevin dynamics is devised to understand the results from the MD simulation. Advisors/Committee Members: Aluru, Narayana R (advisor), Aluru, Narayana R (Committee Chair), Saif, M. Taher (committee member), Sinha, Sanjiv (committee member), Ertekin, Elif (committee member).

Subjects/Keywords: Dissipation; Computational Modeling; Molecular Dynamics; Multi-Scale

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APA (6^th Edition):

Kunal, K. (2016). Computational modeling of intrinsic dissipation in nano-structure. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/90707

Chicago Manual of Style (16^th Edition):

Kunal, Kumar. “Computational modeling of intrinsic dissipation in nano-structure.” 2016. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 04, 2021. http://hdl.handle.net/2142/90707.

MLA Handbook (7^th Edition):

Kunal, Kumar. “Computational modeling of intrinsic dissipation in nano-structure.” 2016. Web. 04 Mar 2021.

Vancouver:

Kunal K. Computational modeling of intrinsic dissipation in nano-structure. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2016. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2142/90707.

Council of Science Editors:

Kunal K. Computational modeling of intrinsic dissipation in nano-structure. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2016. Available from: http://hdl.handle.net/2142/90707

Duquesne University

18. Merchant, Bonnie A. Computational techniques to illuminate secrets of the monoamine transporters.

Degree: MS, Chemistry and Biochemistry, 2012, Duquesne University

URL: https://dsc.duq.edu/etd/924

► The solute carrier family regulates the flow of various substances such as drugs, amino acids, sugars and inorganic ions across the cell membrane. In particular,… (more)

Subjects/Keywords: Biophysics; Modeling; Molecular Dynamics; Neurotransmitter; Transporters

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APA (6^th Edition):

Merchant, B. A. (2012). Computational techniques to illuminate secrets of the monoamine transporters. (Masters Thesis). Duquesne University. Retrieved from https://dsc.duq.edu/etd/924

Chicago Manual of Style (16^th Edition):

Merchant, Bonnie A. “Computational techniques to illuminate secrets of the monoamine transporters.” 2012. Masters Thesis, Duquesne University. Accessed March 04, 2021. https://dsc.duq.edu/etd/924.

MLA Handbook (7^th Edition):

Merchant, Bonnie A. “Computational techniques to illuminate secrets of the monoamine transporters.” 2012. Web. 04 Mar 2021.

Vancouver:

Merchant BA. Computational techniques to illuminate secrets of the monoamine transporters. [Internet] [Masters thesis]. Duquesne University; 2012. [cited 2021 Mar 04]. Available from: https://dsc.duq.edu/etd/924.

Council of Science Editors:

Merchant BA. Computational techniques to illuminate secrets of the monoamine transporters. [Masters Thesis]. Duquesne University; 2012. Available from: https://dsc.duq.edu/etd/924

University of South Carolina

19. Jahan, Merina. Molecular Modeling of Tethered Polyelectrolytes for Novel Biomedical Applications.

Degree: PhD, Chemical Engineering, 2019, University of South Carolina

URL: https://scholarcommons.sc.edu/etd/5574

► Current research trends throughout the world focus on designing intelligent materi- als and systems for diverse applications in all courses of life. Biomaterials research… (more)

▼ Current research trends throughout the world focus on designing intelligent materi- als and systems for diverse applications in all courses of life. Biomaterials research encompasses a major part in this revolution due to the increased effort in fulfilling unmet medical needs to treat complex physiological and neurodegenerative disorders. Polymers play inevitable roles in these research endeavors for their ubiquitous pres- ence in biological systems. Therefore, it is crucial to understand how the polymeric molecules interact within diverse biological environments, to efficiently engineer them for various drug delivery and biosensing systems. The use of experimental design and selection of different polymers for diverse applications alone is an arduous task. Hence, theoretical studies on these biological systems become important starting points for projects that have previously been only studied with experimental techniques. Using theory can make the job easier for researchers in biomedical engineering by both coa- lescing large bodies of experimental data into conceptual frameworks and narrowing down a parameter search space. Along this line, our research focuses on theoretical molecular level modeling of complex polymeric molecules, both biological and synthetic, for drug delivery and biosensing applications. The objective is to design new polymeric systems based on their structural, thermodynamic and physicochemical properties to help enhance the experimental design. This research work uses a Self Consistent Field Theory (SCFT) based approach for different applications involving polymers, that are teth- ered and electrolytic in nature. The molecular theory studies the thermodynamic and structural behavior of the polymers as a function of their molecular composition and physicochemical environments. This theory is able to perform systematic thermody- namic calculations at low computational cost, while including a detailed molecular description of the molecules in the system. The competition of all relevant molecu- lar interactions, such as electrostatics, van der Waals, thermodynamic and chemical equilibrium is described in this model. The first study involves elucidating the behavior of ssDNA aptamers in different biological environments. Our study suggests that the structure of the aptamer chains varies significantly due to charge regulation effects, in response to changes in salt concentration, types and ionic strength of salt and density of the aptamer brush. The understanding gained from this study can help to facilitate aptamer selection process against specific target molecules. Our second study inquires the property changes of ssDNA aptamers in presence of divalent metal cations and quantifies the number of metal ions bound to the ap- tamer chains. The results imply that the ion cloud around the oligomers is uniformly distributed in different sequences and reinforces the dominance of non-specific elec- trostatic attraction between the nucleobases and the cations as the driving force… Advisors/Committee Members: Mark J. Uline.

Subjects/Keywords: Chemical Engineering; molecular; modeling; polyelectrolytes; biomedical; applications

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APA (6^th Edition):

Jahan, M. (2019). Molecular Modeling of Tethered Polyelectrolytes for Novel Biomedical Applications. (Doctoral Dissertation). University of South Carolina. Retrieved from https://scholarcommons.sc.edu/etd/5574

Chicago Manual of Style (16^th Edition):

Jahan, Merina. “Molecular Modeling of Tethered Polyelectrolytes for Novel Biomedical Applications.” 2019. Doctoral Dissertation, University of South Carolina. Accessed March 04, 2021. https://scholarcommons.sc.edu/etd/5574.

MLA Handbook (7^th Edition):

Jahan, Merina. “Molecular Modeling of Tethered Polyelectrolytes for Novel Biomedical Applications.” 2019. Web. 04 Mar 2021.

Vancouver:

Jahan M. Molecular Modeling of Tethered Polyelectrolytes for Novel Biomedical Applications. [Internet] [Doctoral dissertation]. University of South Carolina; 2019. [cited 2021 Mar 04]. Available from: https://scholarcommons.sc.edu/etd/5574.

Council of Science Editors:

Jahan M. Molecular Modeling of Tethered Polyelectrolytes for Novel Biomedical Applications. [Doctoral Dissertation]. University of South Carolina; 2019. Available from: https://scholarcommons.sc.edu/etd/5574

Virginia Tech

20. Aguilar Huacan, Boris Abner. Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling.

Degree: PhD, Computer Science and Applications, 2014, Virginia Tech

URL: http://hdl.handle.net/10919/64409

► Biomolecular Modeling is playing an important role in many practical applications such as biotechnology and structure-based drug design. One of the essential requirements of Biomolecular… (more)

▼ Biomolecular Modeling is playing an important role in many practical applications such as biotechnology and structure-based drug design. One of the essential requirements of Biomolecular modeling is an accurate description of the solvent (water). The challenge is to make this description computationally facile that is reasonably fast, simple, robust and easy to incorporate into existing software packages. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on average one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are represented by a continuum function, have become a popular alternative to explicit solvent methods as they are computationally more efficient. The Generalized Born (GB) implicit solvent has become quite popular due to its relative simplicity and computational efficiency. However, recent studies showed serious deficiencies of many GB variants when applied to Biomolecular Modeling such as an over- stabilization of alpha helical secondary structures and salt bridges. In this dissertation we present two new GB models aimed at computing solvation properties with a reasonable compromise between accuracy and speed. The first GB model, called NSR6, is based on a numerically surface integration over the standard molecular surface. When applied to a set of small drug-like molecules, NSR6 produced an accuracy, with respect to experiments, that is essentially at the same level as that of the expensive explicit solvent treatment. Furthermore, we developed an analytic GB model, called AR6, based on an approximation of the volume integral over the standard molecular volume. The accuracy of the AR6 model is tested relative to the numerically exact NSR6. Overall AR6 produces a good accuracy and is suitable for Molecular Dynamics simulations which is the main intended application. Advisors/Committee Members: Onufriev, Alexey V. (committeechair), Bajaj, Chandrajit L. (committee member), Sandu, Adrian (committee member), Cao, Yang (committee member), Bevan, David R. (committee member).

Subjects/Keywords: Molecular Modeling; Implicit solvents; Generalized Born Model

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APA (6^th Edition):

Aguilar Huacan, B. A. (2014). Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/64409

Chicago Manual of Style (16^th Edition):

Aguilar Huacan, Boris Abner. “Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling.” 2014. Doctoral Dissertation, Virginia Tech. Accessed March 04, 2021. http://hdl.handle.net/10919/64409.

MLA Handbook (7^th Edition):

Aguilar Huacan, Boris Abner. “Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling.” 2014. Web. 04 Mar 2021.

Vancouver:

Aguilar Huacan BA. Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling. [Internet] [Doctoral dissertation]. Virginia Tech; 2014. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10919/64409.

Council of Science Editors:

Aguilar Huacan BA. Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling. [Doctoral Dissertation]. Virginia Tech; 2014. Available from: http://hdl.handle.net/10919/64409

Virginia Tech

21. Donato, Adam Armido. Multiscale Modeling and Uncertainty Quantification of Multiphase Flow and Mass Transfer Processes.

Degree: PhD, Mechanical Engineering, 2015, Virginia Tech

URL: http://hdl.handle.net/10919/51246

► Most engineering systems have some degree of uncertainty in their input and operating parameters. The interaction of these parameters leads to the uncertain nature of… (more)

▼ Most engineering systems have some degree of uncertainty in their input and operating parameters. The interaction of these parameters leads to the uncertain nature of the system performance and outputs. In order to quantify this uncertainty in a computational model, it is necessary to include the full range of uncertainty in the model. Currently, there are two major technical barriers to achieving this: (1) in many situations -particularly those involving multiscale phenomena-the stochastic nature of input parameters is not well defined, and is usually approximated by limited experimental data or heuristics; (2) incorporating the full range of uncertainty across all uncertain input and operating parameters via conventional techniques often results in an inordinate number of computational scenarios to be performed, thereby limiting uncertainty analysis to simple or approximate computational models. This first objective is addressed through combining molecular and macroscale modeling where the molecular modeling is used to quantify the stochastic distribution of parameters that are typically approximated. Specifically, an adsorption separation process is used to demonstrate this computational technique. In this demonstration, stochastic molecular modeling results are validated against a diverse range of experimental data sets. The stochastic molecular-level results are then shown to have a significant role on the macro-scale performance of adsorption systems. The second portion of this research is focused on reducing the computational burden of performing an uncertainty analysis on practical engineering systems. The state of the art for uncertainty analysis relies on the construction of a meta-model (also known as a surrogate model or reduced order model) which can then be sampled stochastically at a relatively minimal computational burden. Unfortunately these meta-models can be very computationally expensive to construct, and the complexity of construction can scale exponentially with the number of relevant uncertain input parameters. In an effort to dramatically reduce this effort, a novel methodology "QUICKER (Quantifying Uncertainty In Computational Knowledge Engineering Rapidly)" has been developed. Instead of building a meta-model, QUICKER focuses exclusively on the output distributions, which are always one-dimensional. By focusing on one-dimensional distributions instead of the multiple dimensions analyzed via meta-models, QUICKER is able to handle systems with far more uncertain inputs. Advisors/Committee Members: Pitchumani, Ranga (committeechair), Huxtable, Scott T. (committee member), Achenie, Luke E. K. (committee member), Tafti, Danesh K. (committee member), Ekkad, Srinath (committee member).

Subjects/Keywords: Multiphase Transport Phenomena; Adsorption Separation; Multiscale Modeling; Molecular Modeling; Uncertainty Quantification

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APA (6^th Edition):

Donato, A. A. (2015). Multiscale Modeling and Uncertainty Quantification of Multiphase Flow and Mass Transfer Processes. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/51246

Chicago Manual of Style (16^th Edition):

Donato, Adam Armido. “Multiscale Modeling and Uncertainty Quantification of Multiphase Flow and Mass Transfer Processes.” 2015. Doctoral Dissertation, Virginia Tech. Accessed March 04, 2021. http://hdl.handle.net/10919/51246.

MLA Handbook (7^th Edition):

Donato, Adam Armido. “Multiscale Modeling and Uncertainty Quantification of Multiphase Flow and Mass Transfer Processes.” 2015. Web. 04 Mar 2021.

Vancouver:

Donato AA. Multiscale Modeling and Uncertainty Quantification of Multiphase Flow and Mass Transfer Processes. [Internet] [Doctoral dissertation]. Virginia Tech; 2015. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/10919/51246.

Council of Science Editors:

Donato AA. Multiscale Modeling and Uncertainty Quantification of Multiphase Flow and Mass Transfer Processes. [Doctoral Dissertation]. Virginia Tech; 2015. Available from: http://hdl.handle.net/10919/51246

Duquesne University

22. Raghavan, Sudhir. Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin.

Degree: PhD, Medicinal Chemistry, 2013, Duquesne University

URL: https://dsc.duq.edu/etd/1080

► The results from this work are reported into two sections listed below: Synthesis: Following structural classes of compounds have been designed, synthesized and studied as… (more)

▼ The results from this work are reported into two sections listed below: Synthesis: Following structural classes of compounds have been designed, synthesized and studied as inhibitors of pjDHFR, RTKs and tubulin: 1. 2,4-Diamino-6-(substituted-arylmethyl)pyrido[2,3-d]pyrimidines 2. 4-((3-Bromophenyl)linked)-6-(substituted-benzyl)-7H-pyrrolo[2,3-d]pyrimidin-2-amines 3. 6-Methyl-5-((substitutedphenyl)thio)-7H-pyrrolo[2,3-d]pyrimidin-2-amines A total of 35 new compounds (excluding intermediates) were synthesized, characterized and submitted for biological evaluation. Results from these studies will be presented in due course. Bulk synthesis of the potent lead compound 170 was carried out to facilitate in vivo evaluation. Docking Studies Docking studies were performed using LeadIT, MOE, Sybyl or Flexx for target compounds listed above and for other compounds reported by Gangjee et al. against the following targets: 1. Dihydrofolate reductase: human, P. carinii, P. jirovecii (pjDHFR) and T. gondii (tgDHFR) 2. Thymidylate synthase: human (hTS) and T. gondii (tgTS) 3. Receptor tyrosine kinases: VEGFR2, EGFR and PDGFR-β 4. Colchicine binding site of tublulin. Novel homology models were generated and validated for pjDHFR, tgDHFR, tgTS, PDGFR-β and the F36C L65P pjDHFR double mutant. The tgTS homology model generated in this study and employed to design novel inhibitors shows remarkable similarity with the recently published X-ray crystal structures. Docking studies were performed to provide a molecular basis for the observed activity of target compounds against DHFR, RTKs or tubulin. Results from these studies support structure-based and ligand-based medicinal chemistry efforts in order to improve potency and/or selectivity of analogs of the docked compounds against these targets. Novel topomer CoMFA models were developed for tgTS and hTS using a set of 85 bicyclic inhibitors and for RTKs using a set of 60 inhibitors reported by Gangjee et al. The resultant models could be used to explain the potency and/or selectivity differences for selected molecules for tgTS over hTS. Topomer CoMFA maps show differences in steric and/or electronic requirements among the three RTKs, and could be used, in conjuction with other medicinal chemistry approaches, to modulate the selectivity and/or potency of inhibitors with multiple RTK inhibitory potential. Drug design efforts that involve virtual library screening using these topomer CoMFA models in conjunction with traditional medicinal chemistry techniques and docking are currently underway. Advisors/Committee Members: Aleem Gangjee, Marc Harrold, Patrick Flaherty, David Lapinsky, Lawrence Block, James Drennen, J. Douglas Bricker.

Subjects/Keywords: Cancer; Docking; Homology modeling; Molecular modeling; Opportunistic infections

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APA (6^th Edition):

Raghavan, S. (2013). Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin. (Doctoral Dissertation). Duquesne University. Retrieved from https://dsc.duq.edu/etd/1080

Chicago Manual of Style (16^th Edition):

Raghavan, Sudhir. “Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin.” 2013. Doctoral Dissertation, Duquesne University. Accessed March 04, 2021. https://dsc.duq.edu/etd/1080.

MLA Handbook (7^th Edition):

Raghavan, Sudhir. “Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin.” 2013. Web. 04 Mar 2021.

Vancouver:

Raghavan S. Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin. [Internet] [Doctoral dissertation]. Duquesne University; 2013. [cited 2021 Mar 04]. Available from: https://dsc.duq.edu/etd/1080.

Council of Science Editors:

Raghavan S. Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin. [Doctoral Dissertation]. Duquesne University; 2013. Available from: https://dsc.duq.edu/etd/1080

University of Texas – Austin

23. Moldenhauer, Theodore Gerald 1970-. Implementing inquiry based computational modeling curriculum in the secondary science classroom.

Degree: MA, Science Education, 2012, University of Texas – Austin

URL: http://hdl.handle.net/2152/26629

► Better visualization of micro-level structures and processes can greatly enhance student understanding of key biological functions such as the central dogma. Previous research has demonstrated… (more)

Subjects/Keywords: Molecular modeling; Central-dogma; Secondary science education; Computational modeling programs

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APA (6^th Edition):

Moldenhauer, T. G. 1. (2012). Implementing inquiry based computational modeling curriculum in the secondary science classroom. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/26629

Chicago Manual of Style (16^th Edition):

Moldenhauer, Theodore Gerald 1970-. “Implementing inquiry based computational modeling curriculum in the secondary science classroom.” 2012. Masters Thesis, University of Texas – Austin. Accessed March 04, 2021. http://hdl.handle.net/2152/26629.

MLA Handbook (7^th Edition):

Moldenhauer, Theodore Gerald 1970-. “Implementing inquiry based computational modeling curriculum in the secondary science classroom.” 2012. Web. 04 Mar 2021.

Vancouver:

Moldenhauer TG1. Implementing inquiry based computational modeling curriculum in the secondary science classroom. [Internet] [Masters thesis]. University of Texas – Austin; 2012. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2152/26629.

Council of Science Editors:

Moldenhauer TG1. Implementing inquiry based computational modeling curriculum in the secondary science classroom. [Masters Thesis]. University of Texas – Austin; 2012. Available from: http://hdl.handle.net/2152/26629

University of California – San Diego

24. Li, Amanda. Noncovalent Interactions: Evaluation of computational methods and characterization of molecular binding.

Degree: Bioeng w/Spec Multi-ScaleBio, 2016, University of California – San Diego

URL: http://www.escholarship.org/uc/item/6rj6x5md

► Noncovalent interactions are of central importance to biochemical phenomena. This dissertation includes both evaluations of the methods used to compute noncovalent interactions and analyses of… (more)

Subjects/Keywords: Chemistry; molecular dynamics; molecular modeling; noncovalent interactions; polarization; quantum mechanical methods

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APA (6^th Edition):

Li, A. (2016). Noncovalent Interactions: Evaluation of computational methods and characterization of molecular binding. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/6rj6x5md

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):

Li, Amanda. “Noncovalent Interactions: Evaluation of computational methods and characterization of molecular binding.” 2016. Thesis, University of California – San Diego. Accessed March 04, 2021. http://www.escholarship.org/uc/item/6rj6x5md.

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

MLA Handbook (7^th Edition):

Li, Amanda. “Noncovalent Interactions: Evaluation of computational methods and characterization of molecular binding.” 2016. Web. 04 Mar 2021.

Vancouver:

Li A. Noncovalent Interactions: Evaluation of computational methods and characterization of molecular binding. [Internet] [Thesis]. University of California – San Diego; 2016. [cited 2021 Mar 04]. Available from: http://www.escholarship.org/uc/item/6rj6x5md.

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

Council of Science Editors:

Li A. Noncovalent Interactions: Evaluation of computational methods and characterization of molecular binding. [Thesis]. University of California – San Diego; 2016. Available from: http://www.escholarship.org/uc/item/6rj6x5md

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

25. Nagurniak, Gláucio Regis. Análise da relação entre a estrutura química e a atividade biológica de antagonistas moleculares do receptor μ-opióide.

Degree: Mestrado, Físico-Química, 2013, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/75/75134/tde-30072013-093119/ ;

►

Desde os tempos antigos, o leite de papoula é usado como sedativo e poderoso analgésico. Hoje, na terapêutica, a morfina - a qual se encontra… (more)

▼

Desde os tempos antigos, o leite de papoula é usado como sedativo e poderoso analgésico. Hoje, na terapêutica, a morfina - a qual se encontra em grande proporção no leite da papoula - continua sendo utilizada como analgésico em casos de dor moderada e severa. Concomitantemente, drogas derivadas da morfina têm sido amplamente utilizadas; sendo a heroína uma das drogas com maior potencial viciante conhecido. O desenvolvimento de antagonistas do receptor alvo da morfina/heroína (receptor μ-opioide) pode auxiliar tanto no desenvolvimento de medicamentos analgésicos mais seguros e potentes, bem como no desenvolvimento de medicamentos que podem ter utilidade no tratamento da dependência por drogas opiáceas. Com o intuito de criar a relação entre a atividade biológica de um conjunto de 51 moléculas e sua respectiva ação antagonista ao receptor μ-opioide, foram selecionadas, da literatura, moléculas que apresentam interações biológicas contra o receptor μ-opioide. As moléculas selecionadas tiveram suas geometrias otimizadas e suas propriedades calculadas pelo método DFT/B3LYP, com um conjunto de funções de base 6-31g++(d,p). Os dados obtidos, como informações sobre a estrutura eletrônica, propriedades topológicas e físico-químicas, foram relacionados com os valores de pKi. Para a correta análise das variáveis que são úteis na descrição da atividade biológica, métodos de análise estatística como PCA, HCA, SIMCA e KNN foram utilizados, além do método de PLS para a construção do modelo matemático de relação entre atividade biológica e as variáveis. Os resultados mostram que variáveis como a energia do orbital LUMO, a quantidade de nitrogênios na cadeia da molécula, o volume de alguns substituintes e o valor das variáveis E1p e E3u (mensuradas respectivamente pela polarizabilidade molecular e peso atômico) têm grande relação com a atividade biológica. O modelo criado é útil na previsão da atividade biológica de outras moléculas, bem como ao fornecer ideias para uma síntese planejada de novos compostos com atividade antagonista promissora.

Since antiquity, the poppy\'s milk has been used as sedative and powerful analgesic. Nowadays, in the therapy, the morphine - that is found in large proportion in poppy\'s milk - is still being used as painkiller in cases of moderate and severe pain. Concurrently, drugs made from morphine have been widely used; being the heroin the drug with the highest known addictive potential. The development of the antagonists of the morphine/heroine target receptor (μ-opiate receptor) can help on more safety and powerful medicine developments, and also to develop medicines that can be useful in treating opiate drugs addiction. In order to create the relationship between biological activity of a set of 51 molecules and their respective antagonist action by μ-opiate receptor, was selected, from the literature, molecules that show biological interaction against μ-opiate receptor. The selected molecules had their geometries optimized…

Advisors/Committee Members: Silva, Albérico Borges Ferreira da.

Subjects/Keywords: µ; -opiate; µ; -opióide; modelagem molecular; molecular modeling; QSAR; QSAR

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APA (6^th Edition):

Nagurniak, G. R. (2013). Análise da relação entre a estrutura química e a atividade biológica de antagonistas moleculares do receptor μ-opióide. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/75/75134/tde-30072013-093119/ ;

Chicago Manual of Style (16^th Edition):

Nagurniak, Gláucio Regis. “Análise da relação entre a estrutura química e a atividade biológica de antagonistas moleculares do receptor μ-opióide.” 2013. Masters Thesis, University of São Paulo. Accessed March 04, 2021. http://www.teses.usp.br/teses/disponiveis/75/75134/tde-30072013-093119/ ;.

MLA Handbook (7^th Edition):

Nagurniak, Gláucio Regis. “Análise da relação entre a estrutura química e a atividade biológica de antagonistas moleculares do receptor μ-opióide.” 2013. Web. 04 Mar 2021.

Vancouver:

Nagurniak GR. Análise da relação entre a estrutura química e a atividade biológica de antagonistas moleculares do receptor μ-opióide. [Internet] [Masters thesis]. University of São Paulo; 2013. [cited 2021 Mar 04]. Available from: http://www.teses.usp.br/teses/disponiveis/75/75134/tde-30072013-093119/ ;.

Council of Science Editors:

Nagurniak GR. Análise da relação entre a estrutura química e a atividade biológica de antagonistas moleculares do receptor μ-opióide. [Masters Thesis]. University of São Paulo; 2013. Available from: http://www.teses.usp.br/teses/disponiveis/75/75134/tde-30072013-093119/ ;

University of Texas – Austin

26. Zhang, Jiajing. Insight into biomolecular structure, interaction and energetics from modeling and simulation.

Degree: PhD, Biomedical Engineering, 2011, University of Texas – Austin

URL: http://hdl.handle.net/2152/20672

► A central goal of computational biophysics and biochemistry is to understand the behavior, interactions, and reactions of molecules, and to interpret and facilitate experimental design.… (more)

Subjects/Keywords: Molecular modeling; Molecular dynamics simulation; Protein-ligand binding free energy calculation

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

APA (6^th Edition):

Zhang, J. (2011). Insight into biomolecular structure, interaction and energetics from modeling and simulation. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/20672

Chicago Manual of Style (16^th Edition):

Zhang, Jiajing. “Insight into biomolecular structure, interaction and energetics from modeling and simulation.” 2011. Doctoral Dissertation, University of Texas – Austin. Accessed March 04, 2021. http://hdl.handle.net/2152/20672.

MLA Handbook (7^th Edition):

Zhang, Jiajing. “Insight into biomolecular structure, interaction and energetics from modeling and simulation.” 2011. Web. 04 Mar 2021.

Vancouver:

Zhang J. Insight into biomolecular structure, interaction and energetics from modeling and simulation. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2011. [cited 2021 Mar 04]. Available from: http://hdl.handle.net/2152/20672.

Council of Science Editors:

Zhang J. Insight into biomolecular structure, interaction and energetics from modeling and simulation. [Doctoral Dissertation]. University of Texas – Austin; 2011. Available from: http://hdl.handle.net/2152/20672

27. RABELLO, Marcelo Montenegro. Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica .

Degree: 2016, Universidade Federal de Pernambuco

URL: https://repositorio.ufpe.br/handle/123456789/17588

► Este trabalho apresenta uma metodologia in silico para o estudo de complexos de inclus o utilizados na inova o terap utica. Um complexo de inclus… (more)

Subjects/Keywords: Bioinform tica.Terap utica.Ciclodextrinas. CycloMolder, complexos de inclus o, ciclodextrina, modelagem molecular, docking molecular; CycloMolder, inclusion Complex, cyclodextrin, molecular modeling, Molecular docking.

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

APA (6^th Edition):

RABELLO, M. M. (2016). Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica . (Doctoral Dissertation). Universidade Federal de Pernambuco. Retrieved from https://repositorio.ufpe.br/handle/123456789/17588

Chicago Manual of Style (16^th Edition):

RABELLO, Marcelo Montenegro. “Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica .” 2016. Doctoral Dissertation, Universidade Federal de Pernambuco. Accessed March 04, 2021. https://repositorio.ufpe.br/handle/123456789/17588.

MLA Handbook (7^th Edition):

RABELLO, Marcelo Montenegro. “Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica .” 2016. Web. 04 Mar 2021.

Vancouver:

RABELLO MM. Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica . [Internet] [Doctoral dissertation]. Universidade Federal de Pernambuco; 2016. [cited 2021 Mar 04]. Available from: https://repositorio.ufpe.br/handle/123456789/17588.

Council of Science Editors:

RABELLO MM. Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica . [Doctoral Dissertation]. Universidade Federal de Pernambuco; 2016. Available from: https://repositorio.ufpe.br/handle/123456789/17588

Miami University

28. Caudle, Miranda. Molecular Modeling of Ionic Liquids for Potential Applications in the Desulfurization of Diesel Fuel.

Degree: MS, Chemical, Paper & Biomedical Engineering, 2018, Miami University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=miami1543863786081448

► The sulfur compounds in diesel fuel produce harmful environmental pollutants during combustion. Hydrodesulfurization (HDS) is the most common technique to reduce the sulfur content of… (more)

Subjects/Keywords: Chemical Engineering; Chemistry; Molecular Chemistry; Molecular Physics; ionic liquids; ILs; desulfurization; diesel fuel; molecular modeling; molecular dynamic simulations

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

APA (6^th Edition):

Caudle, M. (2018). Molecular Modeling of Ionic Liquids for Potential Applications in the Desulfurization of Diesel Fuel. (Masters Thesis). Miami University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=miami1543863786081448

Chicago Manual of Style (16^th Edition):

Caudle, Miranda. “Molecular Modeling of Ionic Liquids for Potential Applications in the Desulfurization of Diesel Fuel.” 2018. Masters Thesis, Miami University. Accessed March 04, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=miami1543863786081448.

MLA Handbook (7^th Edition):

Caudle, Miranda. “Molecular Modeling of Ionic Liquids for Potential Applications in the Desulfurization of Diesel Fuel.” 2018. Web. 04 Mar 2021.

Vancouver:

Caudle M. Molecular Modeling of Ionic Liquids for Potential Applications in the Desulfurization of Diesel Fuel. [Internet] [Masters thesis]. Miami University; 2018. [cited 2021 Mar 04]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=miami1543863786081448.

Council of Science Editors:

Caudle M. Molecular Modeling of Ionic Liquids for Potential Applications in the Desulfurization of Diesel Fuel. [Masters Thesis]. Miami University; 2018. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=miami1543863786081448

Penn State University

29. Rudzinski, Joseph F. Hierarchical Coarse-graining via a Generalized yvon-born-green Framework: Many-body Correlations, mappings, and Structural Accuracy.

Degree: 2014, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/23368

► Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible… (more)

▼ Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible molecular insight, these simulations are insufficient for investigating complex biological processes, e.g., protein folding or molecular aggregation, on relevant length and time scales. The increasing scope and sophistication of atomically-detailed models has motivated the development of “hierarchical” approaches, which parameterize a low resolution, coarse-grained (CG) model based on simulations of an atomically-detailed model. The utility of hierarchical CG models depends on their ability to accurately incorporate the correct physics of the underlying model. One approach for ensuring this “consistency” between the models is to parame- terize the CG model to reproduce the structural ensemble generated by the high resolution model. The many-body potential of mean force is the proper CG energy function for reproducing all structural distri- butions of the atomically-detailed model, at the CG level of resolution. However, this CG potential is a configuration-dependent free energy function that is generally too complicated to represent or simulate. The multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to directly determine a variationally optimal approximation to the many-body potential of mean force. The MS-CG/g-YBG method provides a convenient and transparent framework for investigating the equilibrium structure of the system, at the CG level of resolution. In this work, we investigate the fundamental limitations and approximations of the MS-CG/g-YBG method. Throughout the work, we propose several theoretic con- structs to directly relate the the MS-CG/g-YBG method to other popular structure-based CG approaches. We investigate the physical interpretation of the MS-CG/g-YBG correlation matrix, the quantity responsible for disentangling the various contributions to the average force on a CG site. We then employ an iterative extension of the MS-CG/g-YBG method that improves the accuracy of a particular set of low order correla- tion functions relative to the original MS-CG/g-YBG model. We demonstrate that this method provides a powerful framework for identifying the precise source of error in an MS-CG/g-YBG model. We then propose a method for identifying an optimal CG representation, prior to the development of the CG model. We employ these techniques together to demonstrate that in the cases where the MS-CG/g-YBG method fails to determine an accurate model, a fundamental problem likely exists with the chosen CG representation or interaction set. Additionally, we explicitly demonstrate that while the iterative model successfully improves the accuracy of the low order structure, it does so by distorting the higher order structural correlations relative to the underlying model. Finally, we apply these methods to investigate the utility of the MS-CG/g- YBG method for developing… Advisors/Committee Members: William George Noid, Dissertation Advisor/Co-Advisor, William George Noid, Committee Chair/Co-Chair, Barbara Jane Garrison, Committee Member, David D Boehr, Committee Member, Janna Kay Maranas, Committee Member, Janna Kay Maranas, Special Member.

Subjects/Keywords: molecular simulations; multiscale modeling; coarse-grained modeling; generalized Yvon-Born-Green; many-body correlations

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

APA (6^th Edition):

Rudzinski, J. F. (2014). Hierarchical Coarse-graining via a Generalized yvon-born-green Framework: Many-body Correlations, mappings, and Structural Accuracy. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/23368

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):

Rudzinski, Joseph F. “Hierarchical Coarse-graining via a Generalized yvon-born-green Framework: Many-body Correlations, mappings, and Structural Accuracy.” 2014. Thesis, Penn State University. Accessed March 04, 2021. https://submit-etda.libraries.psu.edu/catalog/23368.

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

MLA Handbook (7^th Edition):

Rudzinski, Joseph F. “Hierarchical Coarse-graining via a Generalized yvon-born-green Framework: Many-body Correlations, mappings, and Structural Accuracy.” 2014. Web. 04 Mar 2021.

Vancouver:

Rudzinski JF. Hierarchical Coarse-graining via a Generalized yvon-born-green Framework: Many-body Correlations, mappings, and Structural Accuracy. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Mar 04]. Available from: https://submit-etda.libraries.psu.edu/catalog/23368.

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

Council of Science Editors:

Rudzinski JF. Hierarchical Coarse-graining via a Generalized yvon-born-green Framework: Many-body Correlations, mappings, and Structural Accuracy. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/23368

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

30. Smith, David Joseph. A multiscale biophysical platform for charting design-specific interactions of nanoparticles with model cellular membranes.

Degree: 2018, University of California – eScholarship, University of California

URL: http://www.escholarship.org/uc/item/07p934v3

► In this thesis, we outline the development of a multiscale physics-based platform for exploring and ultimately predicting the design-specific interaction of ~1-10 nm particles with… (more)

▼ In this thesis, we outline the development of a multiscale physics-based platform for exploring and ultimately predicting the design-specific interaction of ~1-10 nm particles with model cellular membranes. Nanoparticles (NP) are ever-present in foods and beverages, cosmetics, packaging, cooking products, fertilizers, pesticides, and novel pharmaceuticals, and pose significant challenges related to their increased consumer, occupational, and environmental exposure and their unique bioactivity relative to small molecules and large colloids. Thanks to rapidly advancing fabrication and characterization techniques, NPs are highly tunable in physicochemical properties such as size, surface chemistry, shape, elasticity, roughness, and crystallinity. Currently, however, the influence of these NP design parameters is highly underdeveloped, and difficult to reproducibly demonstrate in in vivo, in vitro, and even model experiments. Specifically, NP interactions with and passive transport across cellular membranes play a significant role in pharmacological and consumer product performance (biodistribution) as well as adverse outcome pathways in toxicology. We thus focus on the fundamental problem of design-specific interactions between NPs and cellular membranes, modeled to a first approximation as lipid bilayers.To provide accurate, efficient, and robust predictions for a range of NP designs, we construct a first-of-its kind, multiscale physics-based platform linking detailed molecular dynamics (MD) simulations, continuum mechanical theory, and multi-compartment modeling. Using this platform, we examine the two most influential design parameters – size and surface chemistry – and through two main case studies: (1) the membrane permeability of sub-nanometer particles and (2) the thermodynamic stability of larger-scale, ~1-10 nm particle-membrane interactions. Within (1), we first simulate the NP-membrane interactions and transport in full detail to test the validity of Overton's Rule, a longstanding structure-property relationship, and the inhomogeneous solubility-diffusion (ISD) model, a microscopic mechanistic continuum model for transport. We show that Overton's Rule is overly simplified for describing transport across a fluctuating lipid bilayer membrane, yet that ISD model holds for small enough particles. Within this range of particles where the solubility-diffusion mechanism holds, we directly link the impact of particle chemistry in the MD simulations to transient (time-dependent) transport outcomes in the macroscopic multi-compartmental models. This allows us to both compare with and evaluate models used in experimental permeability assays and close the orders of magnitude gap between simulation-predicted and experimentally-calculated permeabilities. We also leverage our platform to construct improved structure-property relationships for the steady-state membrane permeability and structure-kinetic relationships, accounting for a wider range of particle chemistries and highlighting the imperative of time in dictating the…

Subjects/Keywords: Computational physics; Biophysics; Continuum mechanics; Lipid membranes; Molecular dynamics; Multiscale modeling; Nanoparticles; Systems modeling

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

Smith, D. J. (2018). A multiscale biophysical platform for charting design-specific interactions of nanoparticles with model cellular membranes. (Thesis). University of California – eScholarship, University of California. Retrieved from http://www.escholarship.org/uc/item/07p934v3

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):

Smith, David Joseph. “A multiscale biophysical platform for charting design-specific interactions of nanoparticles with model cellular membranes.” 2018. Thesis, University of California – eScholarship, University of California. Accessed March 04, 2021. http://www.escholarship.org/uc/item/07p934v3.

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

MLA Handbook (7^th Edition):

Smith, David Joseph. “A multiscale biophysical platform for charting design-specific interactions of nanoparticles with model cellular membranes.” 2018. Web. 04 Mar 2021.

Vancouver:

Smith DJ. A multiscale biophysical platform for charting design-specific interactions of nanoparticles with model cellular membranes. [Internet] [Thesis]. University of California – eScholarship, University of California; 2018. [cited 2021 Mar 04]. Available from: http://www.escholarship.org/uc/item/07p934v3.

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

Council of Science Editors:

Smith DJ. A multiscale biophysical platform for charting design-specific interactions of nanoparticles with model cellular membranes. [Thesis]. University of California – eScholarship, University of California; 2018. Available from: http://www.escholarship.org/uc/item/07p934v3

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

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Open Access Theses and Dissertations