subject:(Molecular dynamics simulations)

University of Iowa

1. Lay, Wesley K. Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level.

Degree: PhD, Biochemistry, 2018, University of Iowa

URL: https://ir.uiowa.edu/etd/6603

► Computer simulations allow researchers to study the dynamics and interactions of biological molecules in ways that cannot be currently achieved in experiments. In this… (more)

▼ Computer simulations allow researchers to study the dynamics and interactions of biological molecules in ways that cannot be currently achieved in experiments. In this work, I have used computer simulations to study the following systems: (1) carbohydrate-carbohydrate and carbohydrate-amino acid interactions using all-atom molecular dynamics simulations, and (2) protein-protein interactions using coarse-grained implicit solvent models. My first studies involved simulating carbohydrate and amino acid systems using atomistic force fields. During my initial simulations, I observed that carbohydrates were interacting too favorably leading them to aggregate in conditions under which they experimentally remain soluble. To alleviate this issue, I surgically modified the carbohydrate-carbohydrate interaction parameters in order to match osmotic pressure data from experiment. This approach was successful while preserving many of the correct features of the original force field. Next, I observed similar issues in carbohydrate-amino acid simulations and used the same methodology to correct carbohydrate-amino acid parameters. I showed that the modified parameters also worked well in simulations of much larger systems, allowing realistic simulations to be performed on polymeric sugars such as dextran and the peptidoglycan layer of the cell wall. In a more recent and separate study, I have attempted to parameterize very coarse-grained models of proteins (for eventual use in cellular scale simulations) using experimental osmotic second virial coefficients. I found that a 10 residue-per-bead model including electrostatic interactions could approximately match most of the second virial coefficient data obtained from experiment. In contrast, a more simplified, spherical model of proteins could not adequately reproduce experiment. Although more work will be required to establish a better quantitative agreement with experiment, my results indicate that even very coarse models of proteins can produce reasonably accurate simulations of protein-protein interactions. Advisors/Committee Members: Elcock, Adrian H. (supervisor).

Subjects/Keywords: Computer Simulations; Molecular Dynamics; Biochemistry

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APA (6^th Edition):

Lay, W. K. (2018). Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level. (Doctoral Dissertation). University of Iowa. Retrieved from https://ir.uiowa.edu/etd/6603

Chicago Manual of Style (16^th Edition):

Lay, Wesley K. “Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level.” 2018. Doctoral Dissertation, University of Iowa. Accessed March 06, 2021. https://ir.uiowa.edu/etd/6603.

MLA Handbook (7^th Edition):

Lay, Wesley K. “Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level.” 2018. Web. 06 Mar 2021.

Vancouver:

Lay WK. Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level. [Internet] [Doctoral dissertation]. University of Iowa; 2018. [cited 2021 Mar 06]. Available from: https://ir.uiowa.edu/etd/6603.

Council of Science Editors:

Lay WK. Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level. [Doctoral Dissertation]. University of Iowa; 2018. Available from: https://ir.uiowa.edu/etd/6603

University of Illinois – Chicago

2. Sharma, Priyanka O. Simulated Permeation of Nanoparticles with Size, Shape, and Functional Diversity Through a Model Membrane.

Degree: 2016, University of Illinois – Chicago

URL: http://hdl.handle.net/10027/21524

► Molecular dynamics simulations are particularly useful in providing details that permit understanding of phenomena occurring at surfaces, phenomena characterized by surface-sensitive experimental methods yielding average… (more)

▼ Molecular dynamics simulations are particularly useful in providing details that permit understanding of phenomena occurring at surfaces, phenomena characterized by surface-sensitive experimental methods yielding average properties. The coarse-grained simulation approach methods that we consider here reveal how the characteristics of the surface and the permeant affect penetration events at the surface of phospholipid bilayer membranes. We use molecular dynamics simulations to investigate permeation of lipid bilayer membranes by surface-functionalized nanoparticles and to provide molecular-level detailed mechanisms that are otherwise not readily available via most experimental means. Permeation of small molecules through lipid bilayer membranes is a fundamental biological process that is important to understand in developing therapeutic applications. Nanoparticles have recently become important carriers for drug delivery in such therapeutic applications. We describe coarse-grained simulation methods applicable to such large systems and use examples where the permeants are bare gold nanocrystals, gold-core nanoparticles with hydrophobic ligands (alkanethiol ligands of various lengths), and gold-core nanoparticles with hydrophilic ligands (methyl-terminated polyethylene glycol ligands of various lengths). In addition to spherical gold nanoparticles, we also examine the characteristic permeation mechanisms of the differently shaped gold nanorods with polyethylene glycol ligands, where the aspect ratio different from 1 makes the permeation event dependent on the angle of the nanorod axis relative to the membrane surface. This thesis examines the phenomena associated with the interaction of these various permeants with the phospholipid bilayer that serves as our model membrane. We consider adsorption at the interface, the permeant within the top lipid leaflet, in the middle of the membrane within the lipid tail region, and finally exiting the membrane on the way to recovery, for the various permeants. As a consequence of nanocarrier permeation, we observe the formation of a water pore, occasional transport of ions across the lipid bilayer, lipid translocation, and lipid displacement from the membrane. We investigate the rotational behavior of PEGylated nanorods during the permeation process and the available pathways for these nanorods in completing the permeation. These events differ depending on the chemical nature (hydrophobic or hydrophilic) of the ligands, their length, the surface coverage density on the gold surface, and the aspect ratio of the gold nanocarrier core. This thesis, which highlights comparisons of permeation of nanoparticles with size, shape, and functional diversity, should aid experimentalists who are designing desirable candidates for drug delivery applications. Advisors/Committee Members: Murad, Sohail (advisor), Chaplin, Brian (committee member), Jameson, Cynthia (committee member), Nitsche, Ludwig (committee member), Sharma, Vivek (committee member), Murad, Sohail (chair).

Subjects/Keywords: Drug delivery; molecular dynamics simulations

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APA (6^th Edition):

Sharma, P. O. (2016). Simulated Permeation of Nanoparticles with Size, Shape, and Functional Diversity Through a Model Membrane. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/21524

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):

Sharma, Priyanka O. “Simulated Permeation of Nanoparticles with Size, Shape, and Functional Diversity Through a Model Membrane.” 2016. Thesis, University of Illinois – Chicago. Accessed March 06, 2021. http://hdl.handle.net/10027/21524.

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

MLA Handbook (7^th Edition):

Sharma, Priyanka O. “Simulated Permeation of Nanoparticles with Size, Shape, and Functional Diversity Through a Model Membrane.” 2016. Web. 06 Mar 2021.

Vancouver:

Sharma PO. Simulated Permeation of Nanoparticles with Size, Shape, and Functional Diversity Through a Model Membrane. [Internet] [Thesis]. University of Illinois – Chicago; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/10027/21524.

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

Council of Science Editors:

Sharma PO. Simulated Permeation of Nanoparticles with Size, Shape, and Functional Diversity Through a Model Membrane. [Thesis]. University of Illinois – Chicago; 2016. Available from: http://hdl.handle.net/10027/21524

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

Laurentian University

3. Mangiardi, Chris. Moleclar-dynamics simulations using spatial decomposition and task-based parallelism .

Degree: 2016, Laurentian University

URL: https://zone.biblio.laurentian.ca/handle/10219/2618

► Molecular Dynamics (MD) simulations are an integral method in the computational studies of materials. This thesis discusses an algorithm for large-scale MD simulations using modern… (more)

Subjects/Keywords: Molecular Dynamics (MD); simulations

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APA (6^th Edition):

Mangiardi, C. (2016). Moleclar-dynamics simulations using spatial decomposition and task-based parallelism . (Thesis). Laurentian University. Retrieved from https://zone.biblio.laurentian.ca/handle/10219/2618

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):

Mangiardi, Chris. “Moleclar-dynamics simulations using spatial decomposition and task-based parallelism .” 2016. Thesis, Laurentian University. Accessed March 06, 2021. https://zone.biblio.laurentian.ca/handle/10219/2618.

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

MLA Handbook (7^th Edition):

Mangiardi, Chris. “Moleclar-dynamics simulations using spatial decomposition and task-based parallelism .” 2016. Web. 06 Mar 2021.

Vancouver:

Mangiardi C. Moleclar-dynamics simulations using spatial decomposition and task-based parallelism . [Internet] [Thesis]. Laurentian University; 2016. [cited 2021 Mar 06]. Available from: https://zone.biblio.laurentian.ca/handle/10219/2618.

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

Council of Science Editors:

Mangiardi C. Moleclar-dynamics simulations using spatial decomposition and task-based parallelism . [Thesis]. Laurentian University; 2016. Available from: https://zone.biblio.laurentian.ca/handle/10219/2618

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

Cornell University

4. Ackerman, David. Molecular Dynamics Simulations Of Lipid Membranes: The Effects Of Probes, Lipid Composition And Peptides.

Degree: PhD, Biophysics, 2015, Cornell University

URL: http://hdl.handle.net/1813/40908

► The cell plasma membrane is comprised of hundreds of different lipid species as well as a variety of integral and peripheral proteins. The diversity of… (more)

▼ The cell plasma membrane is comprised of hundreds of different lipid species as well as a variety of integral and peripheral proteins. The diversity of molecular constituents leads to the formation of functional lateral heterogeneities within the plane of the membrane, known as lipid rafts, which are distinct from the surrounding membrane. Given the complexity of the plasma membrane, and the importance of rafts in the life of a cell, simplified model mixtures capturing the characteristics of the plasma membrane have been essential for unraveling its underlying behavior. In this work, we use molecular dynamics simulations to study model membranes at resolutions not possible with experimental techniques. We first investigated a fundamental assumption in model membrane experiments: that extrinsic probes added to the membrane do not disrupt membrane behavior. We addressed this issue by simulating single component model membranes that contained commonly used fluorescent lipid analogs. We found that the probes are able to disorder the bilayer and reorient lipid headgroups due to the probes' large, positively charged headgroups and long, interdigitating acyl chains. Importantly though, these effects die off within a couple of nanometers of the probe. This means that the probes do not disrupt large-scale membrane behavior and can effectively be used for experimental membrane studies. However, the short-ranged perturbations also indicate that probes may provide incorrect information if they report directly on their local, disrupted, environment. Next, we studied the behavior of more complex model membranes containing multiple lipid species. Experimentally, model membranes comprised of four lipid components can yield coexisting phases, mimicking raft and non-raft environments, ranging in size from nanometers to microns. Through simulations, we found that domain size and alignment are highly coupled and that they both change abruptly at certain lipid compositions. We also found that the phase interface between domains was only a couple of nanometers wide regardless of the properties of the two coexisting phases. Addition of transmembrane [alpha]-helical peptides of various lengths to the lipid-only mixtures significantly increased both domain size and alignment. These effects were largest for the shortest peptides and increased with peptide concentration. Thus cells may be able to control raft size and alignment, and in turn a variety of cellular processes, simply by altering lipid and protein concentrations. Advisors/Committee Members: Feigenson,Gerald W (chair), Brady Jr,John Woodbury (committee member), Zipfel,Warren R. (committee member).

Subjects/Keywords: molecular dynamics simulations; lipid bilayer; phase behavior

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APA (6^th Edition):

Ackerman, D. (2015). Molecular Dynamics Simulations Of Lipid Membranes: The Effects Of Probes, Lipid Composition And Peptides. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/40908

Chicago Manual of Style (16^th Edition):

Ackerman, David. “Molecular Dynamics Simulations Of Lipid Membranes: The Effects Of Probes, Lipid Composition And Peptides.” 2015. Doctoral Dissertation, Cornell University. Accessed March 06, 2021. http://hdl.handle.net/1813/40908.

MLA Handbook (7^th Edition):

Ackerman, David. “Molecular Dynamics Simulations Of Lipid Membranes: The Effects Of Probes, Lipid Composition And Peptides.” 2015. Web. 06 Mar 2021.

Vancouver:

Ackerman D. Molecular Dynamics Simulations Of Lipid Membranes: The Effects Of Probes, Lipid Composition And Peptides. [Internet] [Doctoral dissertation]. Cornell University; 2015. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1813/40908.

Council of Science Editors:

Ackerman D. Molecular Dynamics Simulations Of Lipid Membranes: The Effects Of Probes, Lipid Composition And Peptides. [Doctoral Dissertation]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/40908

Syracuse University

5. Okoroafor, Kelechi. MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION.

Degree: PhD, Biomedical and Chemical Engineering, 2018, Syracuse University

URL: https://surface.syr.edu/etd/929

► Micellar structures have been proposed for potential application in hydrotropy, biomimetics, dispersion and emulsification, enhanced oil recovery, detergency, templating, drug delivery, personal care products,… (more)

▼ Micellar structures have been proposed for potential application in hydrotropy, biomimetics, dispersion and emulsification, enhanced oil recovery, detergency, templating, drug delivery, personal care products, drag reduction, nanoscale reaction vessels, therapeutic gene delivery, bio-catalysis and so on. Though several studies exist, there still remains a gap in the current knowledge on structural response of single micelles in solution to uniaxial extensional flow deformation. These knowledge gaps are possibly due to the inability of traditional experimental studies to investigate micellar properties at the time- and length-scale pertinent to self-assembly and micellar dynamics. To this end, this work aims to utilise coarse-grained molecular dynamics simulations to investigate the dynamics and structural response of various infinitely dilute micellar solutions under the influence of uniaxial extensional flow. Spherical vesicles formed from hexacosanoate anion and octyltrimethylammonium cation; rod-like and worm-like micelles formed from hexacosanoate and palmitate anions; and branched worm-like micelles formed from cetyltrimethylammonium cation and sodium salicylate anion have been parametrised according to the Martini force field formalism. These structures were simulated in equilibrium; under uniaxial extensional flow; and in cessation of uniaxialextensional flow. Changes in micellar structure in uniaxial extensional flow and subsequent stress responses are presented for each micellar system at varying deformation rates. It is observed that structural changes and stress response are dependent on micellar stress relaxation ability whilst undergoing uniaxial deformation. The nature and varying influence of stress relaxation as a function of deformation rate is studied for each structure. Deformation of these structures in a direction normal to their principal orientation is also investigated. It is shown that orientation has a short-term effect on the dynamics and structural evolution of non-isotropic micellar structures. Finally, structural and stress responses following cessation of uniaxial extensional flow are presented. Advisors/Committee Members: Radhakhrishna Sureshkumar.

Subjects/Keywords: micelle; molecular dynamics (MD) simulations; rheology; Engineering

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APA (6^th Edition):

Okoroafor, K. (2018). MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION. (Doctoral Dissertation). Syracuse University. Retrieved from https://surface.syr.edu/etd/929

Chicago Manual of Style (16^th Edition):

Okoroafor, Kelechi. “MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION.” 2018. Doctoral Dissertation, Syracuse University. Accessed March 06, 2021. https://surface.syr.edu/etd/929.

MLA Handbook (7^th Edition):

Okoroafor, Kelechi. “MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION.” 2018. Web. 06 Mar 2021.

Vancouver:

Okoroafor K. MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION. [Internet] [Doctoral dissertation]. Syracuse University; 2018. [cited 2021 Mar 06]. Available from: https://surface.syr.edu/etd/929.

Council of Science Editors:

Okoroafor K. MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION. [Doctoral Dissertation]. Syracuse University; 2018. Available from: https://surface.syr.edu/etd/929

Wesleyan University

6. Storey, Amber Nicole. Effects of Molecular Architecture on the Structure and Dynamics of Supported Ultrathin Polymer Films.

Degree: Physics, 2019, Wesleyan University

URL: https://wesscholar.wesleyan.edu/etd_mas_theses/260

► Polymers are ubiquitous in our everyday lives and have uses in a wide range of industries, from electronics to food goods. Understanding properties of… (more)

▼ Polymers are ubiquitous in our everyday lives and have uses in a wide range of industries, from electronics to food goods. Understanding properties of ultra-thin films has become a major interest in polymer science due to their use in semiconductors, adhesives, and artificial tissues. There has been a sustained interest in confinement since work by Keddie et al. (1994 EPL 27 59) published over 20 years ago suggesting the reduction in the glass transition temperature, T_g, is due to the presence of a \liquid-like" layer at the air-polymer interface. Confinement effects result from a difference in the dynamics at the interfaces or the interference of a characteristic length scale; therefore, it is our aim to understand how confinement effects work in conjunction with complex polymer structures, which also affect dynamic properties like T_g and fragility. Dynamic fragility is key feature to know about polymer glasses for both their processing and application. However, there is still much debate on what polymer properties specifically contribute to the fragility. Much work has been done investigating this challenge using simulations, however prior studies have focused primarily on bead-spring type models instead of models that are more molecularly realistic. In this thesis, we employ molecular dynamics (MD) simulations of a coarse-grained polymer models that are chemically specific to polyethylene oxide (PEO) and polymethyl methacrylate (PMMA) with the aim to understand the role of molecular architecture on the structure and dynamics of bulk polymers and supported thin films. Our results show that when film thickness is reduced to 50 Å near T_g, there are minor reductions in T_g for PEO and PMMA indicating the dynamics are only weakly impacted by the differing molecular architecture. The structure, however, is highly affected due to the presence of the side group in PMMA. We also probe the film sensitivity to changes in the substrate interaction strength and observe that PMMA is more sensitive to changes of the substrate interaction strength because of the resulting disruption in monomer organization persisting nearly completely throughout the film. Advisors/Committee Members: Francis Starr, Meng-Ju Sher, George Paily.

Subjects/Keywords: Polymers; Molecular Dynamics simulations; Polymers in confinement

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APA (6^th Edition):

Storey, A. N. (2019). Effects of Molecular Architecture on the Structure and Dynamics of Supported Ultrathin Polymer Films. (Masters Thesis). Wesleyan University. Retrieved from https://wesscholar.wesleyan.edu/etd_mas_theses/260

Chicago Manual of Style (16^th Edition):

Storey, Amber Nicole. “Effects of Molecular Architecture on the Structure and Dynamics of Supported Ultrathin Polymer Films.” 2019. Masters Thesis, Wesleyan University. Accessed March 06, 2021. https://wesscholar.wesleyan.edu/etd_mas_theses/260.

MLA Handbook (7^th Edition):

Storey, Amber Nicole. “Effects of Molecular Architecture on the Structure and Dynamics of Supported Ultrathin Polymer Films.” 2019. Web. 06 Mar 2021.

Vancouver:

Storey AN. Effects of Molecular Architecture on the Structure and Dynamics of Supported Ultrathin Polymer Films. [Internet] [Masters thesis]. Wesleyan University; 2019. [cited 2021 Mar 06]. Available from: https://wesscholar.wesleyan.edu/etd_mas_theses/260.

Council of Science Editors:

Storey AN. Effects of Molecular Architecture on the Structure and Dynamics of Supported Ultrathin Polymer Films. [Masters Thesis]. Wesleyan University; 2019. Available from: https://wesscholar.wesleyan.edu/etd_mas_theses/260

University of Manchester

7. Nawaz, Selina. Molecular dynamics simulations of amphiphilic macromolecules at interfaces.

Degree: PhD, 2013, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-amphiphilic-macromolecules-at-interfaces(227bd442-2935-40c8-8601-9016d925db3d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.570305

► The aim of this thesis is to investigate the structural and thermodynamic properties of biologically and technological relevant macromolecules when placed at soft interfaces. In… (more)

▼ The aim of this thesis is to investigate the structural and thermodynamic properties of biologically and technological relevant macromolecules when placed at soft interfaces. In particular two amphiphilic macromolecules characterized by different topologies have been investigated namely amphiphilic dendrimers and linear block copolymers. This goal is achieved using a multiscale approach which includes all-atom, united atom and coarse grained models by means of molecular dynamic simulations.Amphiphilic dendrimers have shown to be promising building blocks for a range of interfacial materials and can be used in applications such as surface-base sensors or surface nanopatterning. In this part of the thesis by means of all-atom molecular dynamics simulations, we investigated the structure and stability of alkyl-modified polyamido-amide (PAMAM) dendrimers at the air/water interface as a function of the number and the relative position of the modified end groups. We found that the PAMAM dendrimer with all terminal groups functionalized is more stable at the interface than the Janus dendrimer, where only half the amine groups are modified. These results indicate that monolayers of fully functionalized molecules could be as stable as (or more stable than) those self-assembled from Janus molecules.The second part of the thesis is devoted to model a particular family of amphiphilic triblock copolymer sold as Pluronics, consisting of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO) arranged as PEO–PPO–PEO. There is evidence that this class of amphiphilic materials can be used for different biological applications. A fuller understanding of the molecular mechanisms underpinning their interactions with living cells is essential for ensuring the polymers safety and efficacy in biomedical applications. Using united-atom molecular dynamics simulations and membrane lysis assays, we investigated the relationship between the molecular conformations of a subset of the Pluronic copolymers (L31, L61, L62 and L64) and their haemolytic activity. Our computational studies suggest that the hydrophilic blocks in these copolymers interact with the polar head groups of lipid molecules, resulting in a predicted modification of the structure of the membranes. Parallel membrane lysis assays in human erythrocytes indicate differences in the rates of haemolysis, as a result of incubation with these polymers, which correlate well with the predicted interactions from the atomistic simulations. The computational data thus provide a putative mechanism to rationalize the available experimental data on membrane lysis by these copolymers. The data quantitatively agree with haemoglobin release endpoints measured when copolymers with the same molecular weight and structure as of those modelled are incubated with erythrocytes. The data further suggest some new structure– function relationships at the nanoscale that are likely to be of importance in determining the biological activity of these otherwise inert copolymers.In order to visualise the…

Subjects/Keywords: 541; Molecular Dynamics; Simulations; Amphiphilic; Macromolecules; Interfaces

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APA (6^th Edition):

Nawaz, S. (2013). Molecular dynamics simulations of amphiphilic macromolecules at interfaces. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-amphiphilic-macromolecules-at-interfaces(227bd442-2935-40c8-8601-9016d925db3d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.570305

Chicago Manual of Style (16^th Edition):

Nawaz, Selina. “Molecular dynamics simulations of amphiphilic macromolecules at interfaces.” 2013. Doctoral Dissertation, University of Manchester. Accessed March 06, 2021. https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-amphiphilic-macromolecules-at-interfaces(227bd442-2935-40c8-8601-9016d925db3d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.570305.

MLA Handbook (7^th Edition):

Nawaz, Selina. “Molecular dynamics simulations of amphiphilic macromolecules at interfaces.” 2013. Web. 06 Mar 2021.

Vancouver:

Nawaz S. Molecular dynamics simulations of amphiphilic macromolecules at interfaces. [Internet] [Doctoral dissertation]. University of Manchester; 2013. [cited 2021 Mar 06]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-amphiphilic-macromolecules-at-interfaces(227bd442-2935-40c8-8601-9016d925db3d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.570305.

Council of Science Editors:

Nawaz S. Molecular dynamics simulations of amphiphilic macromolecules at interfaces. [Doctoral Dissertation]. University of Manchester; 2013. Available from: https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-amphiphilic-macromolecules-at-interfaces(227bd442-2935-40c8-8601-9016d925db3d).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.570305

University of Southern California

8. Lin, Chih-Ying. Molecular dynamics simulation study of initial protein unfolding induced by the photo-responsive surfactants, azoTAB.

Degree: PhD, Chemical Engineering, 2014, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/364713/rec/4186

► How proteins fold and unfold has been a great focus for decades. Techniques of molecular dynamics simulations provide the atomic insight of protein folding/unfolding. Proteins… (more)

Subjects/Keywords: molecular dynamics; simulations; protein; surfactants; folding; unfolding

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APA (6^th Edition):

Lin, C. (2014). Molecular dynamics simulation study of initial protein unfolding induced by the photo-responsive surfactants, azoTAB. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/364713/rec/4186

Chicago Manual of Style (16^th Edition):

Lin, Chih-Ying. “Molecular dynamics simulation study of initial protein unfolding induced by the photo-responsive surfactants, azoTAB.” 2014. Doctoral Dissertation, University of Southern California. Accessed March 06, 2021. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/364713/rec/4186.

MLA Handbook (7^th Edition):

Lin, Chih-Ying. “Molecular dynamics simulation study of initial protein unfolding induced by the photo-responsive surfactants, azoTAB.” 2014. Web. 06 Mar 2021.

Vancouver:

Lin C. Molecular dynamics simulation study of initial protein unfolding induced by the photo-responsive surfactants, azoTAB. [Internet] [Doctoral dissertation]. University of Southern California; 2014. [cited 2021 Mar 06]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/364713/rec/4186.

Council of Science Editors:

Lin C. Molecular dynamics simulation study of initial protein unfolding induced by the photo-responsive surfactants, azoTAB. [Doctoral Dissertation]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/364713/rec/4186

Clemson University

9. Aryal, Dipak. Computational Insight into Structured Ionic Co-polymers from Molecule to Membrane.

Degree: PhD, Chemistry, 2017, Clemson University

URL: https://tigerprints.clemson.edu/all_dissertations/1984

► Impact of ionizable blocks on structure and dynamics of structured ionic co-polymers in solutions, melts, and thin films has been studied using atomistic molecular dynamics… (more)

▼ Impact of ionizable blocks on structure and dynamics of structured ionic co-polymers in solutions, melts, and thin films has been studied using atomistic molecular dynamics simulations. Much of the interest in ionic block co-polymers derives from their inherent tendency to phase segregate into hydrophobic and hydrophilic domains. Ionic domains in ionic block co-polymers serve as physical cross-linkers and form a long-range percolated cluster assembly, which is a crucial component to transport ions or solvents for varieties of applications from clean energy to biotechnology. One of such ionic co-polymers, where ionic blocks facilitate the transport and other non-ionic blocks provide chemical and mechanical stability, is pentablock (ABCBA) co-polymer. It consists of randomly sulfonated polystyrene (C) in the center, tethered to poly-ethylene-r-propylene (B), terminated on both sides by poly-t-butyl styrene (A). This dissertation focuses on the studies of these co-polymers in their different forms, including the single chains to micelles in solutions, membrane, and followed by water penetration into their thin films. Single chains were studied as a function of nature of solvents including the 1:1 mixture of cyclohexane/heptane and water. This specific hydrophobic solvent is used in industrial casting processing. Water is a highly prevalent substance in the environment and is a by-product of many eletrochemical reactions. We find that a single molecule of the ionic co-block polymer even undergo internal segregation into ionic and non-nonic blocks in both solvents. We then probed the assembly of the pentablock copolymer in solutions to understand the structural diffrences between the micelles formed by the ionic copolymer and van der Waals polymers. Micelles are the building blocks of a membrane, and a key step to engineer controlled polymeric ion transport systems. We find that the ionic network serves as a long lived skeleton of the assembled co-polymers where the hydrophobic blocks are able to migrate in and out of this structure depending on the nature of the solvents. Following the understanding of micellizaion of polymers we moved to melts. We find that the melts form intertwined networks of t-b-PS and center PS blocks. These networks are independent of the degree of sulfonation and have no long-range ordering. The sulfonated groups form different size of clusters where their cohesiveness and morphology affect both collective and segmental dynamics of all the blocks. Studies have been further exteneded to focus on the interfacial behaviour of complex copolymer thin films in solvent environments. We find that inerfacial response of hydropbobic and hydrophilic blocks including their dynamcis differs from the bulk ones. We aslo observe a multi-steps water penetration process. Onset of slow penetration is observed at the early stage where water molecules first transverse the hydrophobic rich surface before reaching to the hydrophilic regime. Water molecules then diffuse along the… Advisors/Committee Members: Dr. Dvora Perahia, Committee Chair, Dr. Gary S. Grest, Dr. Brian Dominy, Dr. Steven J. Stuart.

Subjects/Keywords: Ionic Block Copolymer; Molecular Dynamics Simulations

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APA (6^th Edition):

Aryal, D. (2017). Computational Insight into Structured Ionic Co-polymers from Molecule to Membrane. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/1984

Chicago Manual of Style (16^th Edition):

Aryal, Dipak. “Computational Insight into Structured Ionic Co-polymers from Molecule to Membrane.” 2017. Doctoral Dissertation, Clemson University. Accessed March 06, 2021. https://tigerprints.clemson.edu/all_dissertations/1984.

MLA Handbook (7^th Edition):

Aryal, Dipak. “Computational Insight into Structured Ionic Co-polymers from Molecule to Membrane.” 2017. Web. 06 Mar 2021.

Vancouver:

Aryal D. Computational Insight into Structured Ionic Co-polymers from Molecule to Membrane. [Internet] [Doctoral dissertation]. Clemson University; 2017. [cited 2021 Mar 06]. Available from: https://tigerprints.clemson.edu/all_dissertations/1984.

Council of Science Editors:

Aryal D. Computational Insight into Structured Ionic Co-polymers from Molecule to Membrane. [Doctoral Dissertation]. Clemson University; 2017. Available from: https://tigerprints.clemson.edu/all_dissertations/1984

University of Edinburgh

10. Naithani, Ankita. Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway.

Degree: PhD, 2015, University of Edinburgh

URL: http://hdl.handle.net/1842/16201

► There is a growing body of interest to understand the regulation of allosteric proteins. Allostery is a phenomenon of protein regulation whereby binding of an… (more)

▼ There is a growing body of interest to understand the regulation of allosteric proteins. Allostery is a phenomenon of protein regulation whereby binding of an effector molecule at a remote site affects binding and activity at the protein‟s active site. Over the years, these sites have become popular drug targets as they provide advantages in terms of selectivity and saturability. Both experimental and computational methods are being used to study and identify allosteric sites. Although experimental methods provide us with detailed structures and have been relatively successful in identifying these sites, they are subject to time and cost limitations. In the present dissertation, Molecular Dynamics Simulations (MDS) and Principal Component Analysis (PCA) have been employed to enhance our understanding ofallostery and protein dynamics. MD simulations generated trajectories which were then qualitatively assessed using PCA. Both of these techniques were applied to two important trypanosomatid drug targets and controlling enzymes of the glycolytic pathway - pyruvate kinase (PYK) and phosphofructokinase (PFK). Molecular Dynamics simulations were first carried out on both the effector bound and unbound forms of the proteins. This provided a framework for direct comparison and inspection of the conformational changes at the atomic level. Following MD simulations, PCA was run to further analyse the motions. The principal components thus captured are in quantitative agreement with the previously published experimental data which increased our confidence in the reliability of our simulations. Also, the binding of FBP affects the allosteric mechanism of PYK in a very interesting way. The inspection of the vibrational modes reveals interesting patterns in the movement of the subunits which differ from the conventional symmetrical pattern. Also, lowering of B-factors on effector binding provides evidence that the effector is not only locking the R-state but is also acting as a general heat-sink to cool down the whole tetramer. This observation suggests that protein rigidity and intrinsic heat capacity are important factors in stabilizing allosteric proteins. Thus, this work also provides new and promising insights into the classical Monod-Wyman-Changeux model of allostery.

Subjects/Keywords: 572; allostery; molecular dynamics simulations; pyruvate kinase

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

APA (6^th Edition):

Naithani, A. (2015). Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/16201

Chicago Manual of Style (16^th Edition):

Naithani, Ankita. “Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed March 06, 2021. http://hdl.handle.net/1842/16201.

MLA Handbook (7^th Edition):

Naithani, Ankita. “Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway.” 2015. Web. 06 Mar 2021.

Vancouver:

Naithani A. Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1842/16201.

Council of Science Editors:

Naithani A. Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/16201

University of North Texas

11. Hilbig, Travis. Scratch Modeling of Polymeric Materials with Molecular Dynamics.

Degree: 2012, University of North Texas

URL: https://digital.library.unt.edu/ark:/67531/metadc149608/

► It is impossible to determine the amount of money that is spent every replacing products damaged from wear, but it is safe to assume that… (more)

Subjects/Keywords: Molecular dynamics; computer simulations; polymer; scratch

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APA (6^th Edition):

Hilbig, T. (2012). Scratch Modeling of Polymeric Materials with Molecular Dynamics. (Thesis). University of North Texas. Retrieved from https://digital.library.unt.edu/ark:/67531/metadc149608/

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):

Hilbig, Travis. “Scratch Modeling of Polymeric Materials with Molecular Dynamics.” 2012. Thesis, University of North Texas. Accessed March 06, 2021. https://digital.library.unt.edu/ark:/67531/metadc149608/.

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

MLA Handbook (7^th Edition):

Hilbig, Travis. “Scratch Modeling of Polymeric Materials with Molecular Dynamics.” 2012. Web. 06 Mar 2021.

Vancouver:

Hilbig T. Scratch Modeling of Polymeric Materials with Molecular Dynamics. [Internet] [Thesis]. University of North Texas; 2012. [cited 2021 Mar 06]. Available from: https://digital.library.unt.edu/ark:/67531/metadc149608/.

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

Council of Science Editors:

Hilbig T. Scratch Modeling of Polymeric Materials with Molecular Dynamics. [Thesis]. University of North Texas; 2012. Available from: https://digital.library.unt.edu/ark:/67531/metadc149608/

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

Texas A&M University

12. Kim, Doyong. Monitorying the Desolvaiton of Ions and Create Candidate Structure for the Ions Detected by Ion Mobility-Mass Spectrometry Study by Molecular Dynamics Simulations.

Degree: PhD, Chemistry, 2016, Texas A&M University

URL: http://hdl.handle.net/1969.1/158098

► Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has emerged in recent years as a tool to separate heterogeneous conformer populations and determine ion-neutral collision cross… (more)

▼ Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has emerged in recent years as a tool to separate heterogeneous conformer populations and determine ion-neutral collision cross sections (CCS). However, IM cannot provide specific structural information such as atomic coordinates obtained from X-ray crystallography or nuclear magnetic resonance (NMR) experiments. In this work, molecular dynamics simulations (MDS), and quantum mechanical simulations were used to provide structural information for three families of peptides previously characterized by IM: substance P (SP) and its mutants, phosphopeptides with various phosphorylation locations and mutants, and polyprolines. The simulated structure’s theoretical CCS was calculated by using the MOBCAL trajectory method. CCS values from ESI-IM-MS experiments provided boundary conditions to filter simulated structures to within ±3% of experimental CCS values. Additional experimental results, such as electron capture dissociation (ECD) and proline cis/trans conformation results, were also used to filter simulated structures which enhanced further the validity of simulated structure. The electrospray process was also investigated by utilizing MDS for the ultimate goal to understand the structure evolution of ions from solution to the gas phase. A series of conditioning simulations determined the optimum droplet size to be ~2400 water molecules, and the temperature of desolvation simulation was determined to be 360 K, which is consistent with the previously reported ESI-cryo-IM-MS heated capillary temperature. The net charge of the droplet was determined to be +15. Using these determined conditions, three desolvation simulations were performed with SP as model. The desolvation results showed evaporation and droplet fission which were consistent with other simulations. A further desolvation study incorporated Cl- in the droplet containing SP3+ as counter ions. The structural evolution of the SP3+ ion during the desolvation process was monitored via CCS calculations. The calculated CCS of the SP3+ ion during the later stages of desolvation was consistent with the previously determined ESI-IM-MS value. This simulation indicates that the droplet desolvation follows the process best described as the combined charge residue-field emission model. Advisors/Committee Members: Russell, David H. (advisor), Hilty, Christian (committee member), Schweikert, Emile A. (committee member), Scholtz, Martin J. (committee member).

Subjects/Keywords: Mass Spectrometry; Ion Mobility; Molecular Dynamics Simulations; Simulated Annealing Molecular Dynamics Simulations; Desolvation; MDS

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

APA (6^th Edition):

Kim, D. (2016). Monitorying the Desolvaiton of Ions and Create Candidate Structure for the Ions Detected by Ion Mobility-Mass Spectrometry Study by Molecular Dynamics Simulations. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/158098

Chicago Manual of Style (16^th Edition):

Kim, Doyong. “Monitorying the Desolvaiton of Ions and Create Candidate Structure for the Ions Detected by Ion Mobility-Mass Spectrometry Study by Molecular Dynamics Simulations.” 2016. Doctoral Dissertation, Texas A&M University. Accessed March 06, 2021. http://hdl.handle.net/1969.1/158098.

MLA Handbook (7^th Edition):

Kim, Doyong. “Monitorying the Desolvaiton of Ions and Create Candidate Structure for the Ions Detected by Ion Mobility-Mass Spectrometry Study by Molecular Dynamics Simulations.” 2016. Web. 06 Mar 2021.

Vancouver:

Kim D. Monitorying the Desolvaiton of Ions and Create Candidate Structure for the Ions Detected by Ion Mobility-Mass Spectrometry Study by Molecular Dynamics Simulations. [Internet] [Doctoral dissertation]. Texas A&M University; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1969.1/158098.

Council of Science Editors:

Kim D. Monitorying the Desolvaiton of Ions and Create Candidate Structure for the Ions Detected by Ion Mobility-Mass Spectrometry Study by Molecular Dynamics Simulations. [Doctoral Dissertation]. Texas A&M University; 2016. Available from: http://hdl.handle.net/1969.1/158098

NSYSU

13. Huang, Yu-Ren. A Computational Study of Graphene Composites.

Degree: PhD, Chemistry, 2017, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-1121117-100922

► In this dissertation, we studied thermal conduction and electron transfer of graphene-related compounds mixed with polymer systems by molecular dynamics simulations. This work can be… (more)

Subjects/Keywords: Electron transport; Thermal dynamics; wrinkles; Molecular dynamics simulations; Graphene-oxide

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APA (6^th Edition):

Huang, Y. (2017). A Computational Study of Graphene Composites. (Doctoral Dissertation). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-1121117-100922

Chicago Manual of Style (16^th Edition):

Huang, Yu-Ren. “A Computational Study of Graphene Composites.” 2017. Doctoral Dissertation, NSYSU. Accessed March 06, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-1121117-100922.

MLA Handbook (7^th Edition):

Huang, Yu-Ren. “A Computational Study of Graphene Composites.” 2017. Web. 06 Mar 2021.

Vancouver:

Huang Y. A Computational Study of Graphene Composites. [Internet] [Doctoral dissertation]. NSYSU; 2017. [cited 2021 Mar 06]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-1121117-100922.

Council of Science Editors:

Huang Y. A Computational Study of Graphene Composites. [Doctoral Dissertation]. NSYSU; 2017. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-1121117-100922

14. Ding, Minxia. Molecular simulations of reverse osmosis membranes : Simulations moléculaires de membranes d'osmose inverse.

Degree: Docteur es, Chimie, 2015, Rennes 1

URL: http://www.theses.fr/2015REN1S058

►

L'osmose inverse (OI) est actuellement le procédé le plus utilisé mondialement pour le dessalement des eaux saumâtres et de l’eau de mer. Cette thèse s'est… (more)

▼

L'osmose inverse (OI) est actuellement le procédé le plus utilisé mondialement pour le dessalement des eaux saumâtres et de l’eau de mer. Cette thèse s'est intéressée à la simulation moléculaire de membranes d'OI afin d'améliorer la compréhension des propriétés structurales, dynamiques et de transport de l'eau et d'ions à l'intérieur de ces matériaux. La membrane d'OI étudiée dans ce travail est une membrane de polyamide aromatique, matériau le plus utilisé actuellement en OI. Dans la première partie de ce travail, une méthodologie a été développée pour construire un modèle atomique en trois dimensions d'une membrane polyamide fortement réticulé. Des simulations de dynamique moléculaire à l’équilibre (EMD) et hors-équilibre (NEMD) ont été réalisées pour étudier le comportement de l'eau et des ions Na+ et Cl- à travers la membrane. Les simulations EMD ont montré que les caractéristiques structurales de la membrane modèle étaient en bon accord avec celles d'une membrane typique d'OI. Les propriétés dynamiques et diélectriques de l'eau confinée dans la membrane ont également été étudiées et il a été montré que celles-ci étaient fortement modifiées par rapport à une phase volumique. Deux types de techniques NEMD ont été utilisés pour étudier le transport baromembranaire à travers la membrane modèle. La perméabilité à l'eau pure a été trouvée en très bon accord avec les données expérimentales rapportées dans la littérature et les deux méthodes NEMD ont révélé une très forte rétention saline, confirmant ainsi la pertinence du modèle de membrane d'OI développé dans ce travail.

Reverse osmosis (RO) is currently the leading process used worldwide for both brackish and seawater desalination. This thesis focuses on the molecular simulation of RO membranes in order to improve the understanding of structure, dynamics and transport of water and ions inside these materials. The RO membrane studied in this work is a typical polyamide RO membrane. In the first step of this work, a methodology for building a fully atomic and three-dimensional model of a highly cross-linked polyamide membrane was developed. Both equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD) simulations were further performed to investigate the behavior of water and ions (Na+ and Cl-) through the membrane. EMD simulations showed that the structural characteristics of the model polyamide membrane were in good agreement with those of a typical RO membrane. The dynamics and dielectric properties of water confined in the RO membrane were also studied and have shown to be dramatically modified with respect to the bulk phase. Two types of NEMD techniques were employed to investigate pressure-driven transport through the model membrane. Pure water permeability was found to be in very good agreement with experimental data reported in the literature for similar membrane materials and both NEMD methods highlighted very high salt rejection properties, thus confirming the relevance of the model membrane developed in this work.

Advisors/Committee Members: Szymczyk, Anthony (thesis director).

Subjects/Keywords: Simulations; Dynamique moléculaire; Membranes d'osmose inverse; Polyamide; Simulations; Molecular dynamics; Reverse osmosis membranes; Polyamide

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

APA (6^th Edition):

Ding, M. (2015). Molecular simulations of reverse osmosis membranes : Simulations moléculaires de membranes d'osmose inverse. (Doctoral Dissertation). Rennes 1. Retrieved from http://www.theses.fr/2015REN1S058

Chicago Manual of Style (16^th Edition):

Ding, Minxia. “Molecular simulations of reverse osmosis membranes : Simulations moléculaires de membranes d'osmose inverse.” 2015. Doctoral Dissertation, Rennes 1. Accessed March 06, 2021. http://www.theses.fr/2015REN1S058.

MLA Handbook (7^th Edition):

Ding, Minxia. “Molecular simulations of reverse osmosis membranes : Simulations moléculaires de membranes d'osmose inverse.” 2015. Web. 06 Mar 2021.

Vancouver:

Ding M. Molecular simulations of reverse osmosis membranes : Simulations moléculaires de membranes d'osmose inverse. [Internet] [Doctoral dissertation]. Rennes 1; 2015. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2015REN1S058.

Council of Science Editors:

Ding M. Molecular simulations of reverse osmosis membranes : Simulations moléculaires de membranes d'osmose inverse. [Doctoral Dissertation]. Rennes 1; 2015. Available from: http://www.theses.fr/2015REN1S058

University of Edinburgh

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

Degree: PhD, 2020, University of Edinburgh

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

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

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

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

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

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

Chicago Manual of Style (16^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Doctoral Dissertation, University of Edinburgh. Accessed March 06, 2021. http://hdl.handle.net/1842/37111.

MLA Handbook (7^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Web. 06 Mar 2021.

Vancouver:

Patrick L. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. [Internet] [Doctoral dissertation]. University of Edinburgh; 2020. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1842/37111.

Council of Science Editors:

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

University of Edinburgh

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

Degree: PhD, 2020, University of Edinburgh

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

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

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

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

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

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

Chicago Manual of Style (16^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Doctoral Dissertation, University of Edinburgh. Accessed March 06, 2021. https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132.

MLA Handbook (7^th Edition):

Patrick, Lisa. “Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation.” 2020. Web. 06 Mar 2021.

Vancouver:

Patrick L. Development of an information theory based computational framework for the analysis of molecular dynamics simulations of proteins under allosteric regulation. [Internet] [Doctoral dissertation]. University of Edinburgh; 2020. [cited 2021 Mar 06]. Available from: https://doi.org/10.7488/era/412 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806132.

Council of Science Editors:

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

17. Marín Aguilar, Susana. Local structure and dynamics of dense colloidal systems : from patchy particles to hard spheres : Structure locale et dynamique des systèmes colloïdaux à densité élevée.

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

URL: http://www.theses.fr/2020UPASP052

►

Le rôle de la structure dans la dynamique colloïdale vitreuse est encore un sujet de débat. Cependant, il existe des preuves d'un lien direct entre… (more)

▼

Le rôle de la structure dans la dynamique colloïdale vitreuse est encore un sujet de débat. Cependant, il existe des preuves d'un lien direct entre les changements de la dynamique et les propriétés structurelles du système. Nous explorons l'interaction de la structure et de la dynamique locales en utilisant des particules à patchs. Pour ce faire, nous utilisons des simulations de dynamique moléculaire. Nous montrons qu'en renforçant la géométrie icosaédrique, le dynamique du système présente un ralentissement extrême. Grâce à ces résultats, nous fournissons une voie pour contrôler la dynamique vitreuse par l'utilisation de particules à patchs. De plus, il est intéressant de savoir si nous pouvons extraire des informations sur la dynamique en utilisant uniquement des informations structurelles. Afin d'explorer ce point, nous simulons une grande variété de mélanges de sphères dures. Nous montrons que la dynamique globale de ces systèmes peut être prédite avec précision en introduisant un nouveau paramètre d'ordre appelé tétraédralité de la structure locale qui compte le nombre de tétraèdres auxquels chaque particule participe. Les prédictions de ce paramètre d'ordre restent valables pour dans une grande variété de densités, ce qui prouve son universalité dans cette famille de précurseurs de verre. De plus, il est également capable de saisir les changements sur la dynamique locale, car les régions à forte tétraédralité sont fortement corrélées avec les régions à dynamique lente. Enfin, nous explorons l'utilisation de techniques d'apprentissage machine non supervisé pour classer les particules ayant des environnements structurels différents.

The role played by the structure in determining the dynamics of glassy colloidal systems is still a subject of debate. However, there is compelling evidence of a direct link between changes in the local structure and the dynamical slowdown in glassy systems. Here, we explore the interplay between local structure and dynamics by using patchy particles as glass formers. This is done by making use of molecular dynamics simulations. We show that reinforcing icosahedral geometry causes, the system to exhibit an extreme slowdown in its dynamics. With these results, we provide a route for controlling glassy dynamics through the use of patchy particles. Additionally, an interesting point is whether we can extract information about dynamics from only structural information. In order to explore this point, we simulate a wide variety of hard-sphere mixtures. We show that global dynamics of these systems can be precisely predicted by quantifying the tetrahedrality of the local structure: an order parameter that consists of counting the number of tetrahedra each particle participates in. The predictions of this order parameter maintain their accuracy over a wide variety of densities proving its universality in this family of glass formers. Moreover, it is also capable of capturing the changes in the local dynamics, as regions with high tetrahedrality are strongly correlated with regions with…

Advisors/Committee Members: Foffi, Giuseppe (thesis director).

Subjects/Keywords: Dynamique vitreuse; Particules à patchs; Simulations moléculaires; Colloïdes; Glassy dynamics; Patchy particles; Molecular simulations; Colloids

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APA (6^th Edition):

Marín Aguilar, S. (2020). Local structure and dynamics of dense colloidal systems : from patchy particles to hard spheres : Structure locale et dynamique des systèmes colloïdaux à densité élevée. (Doctoral Dissertation). université Paris-Saclay. Retrieved from http://www.theses.fr/2020UPASP052

Chicago Manual of Style (16^th Edition):

Marín Aguilar, Susana. “Local structure and dynamics of dense colloidal systems : from patchy particles to hard spheres : Structure locale et dynamique des systèmes colloïdaux à densité élevée.” 2020. Doctoral Dissertation, université Paris-Saclay. Accessed March 06, 2021. http://www.theses.fr/2020UPASP052.

MLA Handbook (7^th Edition):

Marín Aguilar, Susana. “Local structure and dynamics of dense colloidal systems : from patchy particles to hard spheres : Structure locale et dynamique des systèmes colloïdaux à densité élevée.” 2020. Web. 06 Mar 2021.

Vancouver:

Marín Aguilar S. Local structure and dynamics of dense colloidal systems : from patchy particles to hard spheres : Structure locale et dynamique des systèmes colloïdaux à densité élevée. [Internet] [Doctoral dissertation]. université Paris-Saclay; 2020. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2020UPASP052.

Council of Science Editors:

Marín Aguilar S. Local structure and dynamics of dense colloidal systems : from patchy particles to hard spheres : Structure locale et dynamique des systèmes colloïdaux à densité élevée. [Doctoral Dissertation]. université Paris-Saclay; 2020. Available from: http://www.theses.fr/2020UPASP052

University of Rochester

18. Li, Zhi. Frontiers in the atomistic modeling of molecular junctions: bringing theory closer to experiment.

Degree: PhD, 2019, University of Rochester

URL: http://hdl.handle.net/1802/35235

► This thesis focuses on advancing the theory and simulation needed to atomistically understand molecular junction experiments where a single molecule acts as a bridge between… (more)

▼ This thesis focuses on advancing the theory and simulation needed to atomistically understand molecular junction experiments where a single molecule acts as a bridge between two metal electrodes. In this class of experiments, a molecular junction is mechanically elongated while measuring its conductance, or its conductance and the applied force. The interest in this class of experiments is that they provide a versa- tile platform to investigate chemistry and physics at the nanoscale. To atomistically understand experiments and guide experimental progress, in this thesis we introduce new simulation tools and strategies that establish a contact between theory and experiment. We use such those technical advances to provide atomistic understanding of key experiments in the area, and to propose new frontiers for future experimental progress. In particular, we developed a non-reactive classical force field that accurately cap- tures metal-molecule interactions. Such force field opens the possibility to perform classical molecular dynamics simulations of molecules on surfaces on experimentally relevant system size and time scales. Using it, we developed atomistic understand- ing of two state-of-the-art low temperature scanning tunneling microscopy (STM) experiments that measure the conductance of a single molecular wire (composed of polyfluorenes or graphene nanoribbons) as a continuous function of its length. Then we turned our attention to the problem of how to compare theory and experiments in STM break junction (STM-BJ) experiments where the conductance is measured on thousands of freshly formed molecular junctions to generate a reproducible conductance histogram. For this, we introduced a modeling strategy to model the STM-BJ experiments with statistics that takes into account uncertainties in junction geometries in and between experiments. Using such a strategy, we computationally examined possible contributing factors to the wide conductance dispersion encountered in the experiments and developed an atomistic understanding of the key effects. Last, we computationally proposed a new route - the mechanical route - to tune the degree of quantum coherence in transport of molecular junctions.

Subjects/Keywords: Molecular electronics; Molecular junctions; Molecular dynamics; Metal-molecule interactions; Electronic transport; Break junction simulations

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APA (6^th Edition):

Li, Z. (2019). Frontiers in the atomistic modeling of molecular junctions: bringing theory closer to experiment. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/35235

Chicago Manual of Style (16^th Edition):

Li, Zhi. “Frontiers in the atomistic modeling of molecular junctions: bringing theory closer to experiment.” 2019. Doctoral Dissertation, University of Rochester. Accessed March 06, 2021. http://hdl.handle.net/1802/35235.

MLA Handbook (7^th Edition):

Li, Zhi. “Frontiers in the atomistic modeling of molecular junctions: bringing theory closer to experiment.” 2019. Web. 06 Mar 2021.

Vancouver:

Li Z. Frontiers in the atomistic modeling of molecular junctions: bringing theory closer to experiment. [Internet] [Doctoral dissertation]. University of Rochester; 2019. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1802/35235.

Council of Science Editors:

Li Z. Frontiers in the atomistic modeling of molecular junctions: bringing theory closer to experiment. [Doctoral Dissertation]. University of Rochester; 2019. Available from: http://hdl.handle.net/1802/35235

Indian Institute of Science

19. Katagi, Gurunath M. Analysis of Molecular Dynamics Trajectories of Proteins Performed using Different Forcefields and Identifiction of Mobile Segments.

Degree: MSc Engg, Faculty of Engineering, 2018, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/3327

► The selection of the forcefield is a crucial issue in any MD related work and there is no clear indication as to which of the… (more)

▼ The selection of the forcefield is a crucial issue in any MD related work and there is no clear indication as to which of the many available forcefields is the best for protein analysis. Many recent literature surveys indicate that MD work may be hindered by two limitations, namely conformational sampling and forcefields used (inaccuracies in the potential energy function may bias the simulation toward incorrect conformations). However, the advances in computing infrastructures, theoretical and computing aspects of MD have paved the way to carry out a sampling on a sufficiently longtime scale, putting a need for the accuracies in the forcefield. Because there are established differences in MD results when using forcefields, we have sought to ask how we could assess common mobility segments from a protein by analysis of trajectories using three forcefields in a similar environment. This is important because, disparate fluctuations appear to be more at flexible regions compared to stiff regions; in particular, flexible regions are more relevant to functional activities of the protein molecule. Therefore, we have tried to assess the similarity in the dynamics using three well-known forcefields ENCAD, CHARMM27 and AMBERFF99SB for 61 monomeric proteins and identify the properties of dynamic residues, which may be important for function. The comparison of popular forcefields with different parameterization philosophy may give hints to improve some of the currently existing agnostics in forcefields and characterization of mobile regions based on dynamics of proteins with diverse folds. These may also give some signature on the proteins at the level of dynamics in relation to function, which can be used in protein engineering studies. Nanosecond level MD simulation(30ns) on 61 monomeric proteins were carried out using CHARMM and AMBER forcefields and the trajectories with ENCAD forcefield obtained from Dynameomics database. The trajectories were first analyzed to check whether structural and dynamic properties from the three forcefields similar choosing few parameters in each case. The gross dynamic properties calculated (root mean square deviation (RMSD), TM-score derived RMSD, radius of gyration and accessible surface area) indicated similarity in many proteins. Flexibility index analysis on 17 proteins, which showed a notable difference in the flexibility, indicated that tertiary interactions (fraction of nonnative stable hydrogen bonds and salt bridges) might be responsible for the difference in the flexibility index. The normalized subspace overlap and shape overlap score taken based on the covariance matrices derived from trajectories indicated that majority of the proteins show a range between 0.3-0.5 indicating that the first principal components from these proteins in different combinations may not match well. These results indicate that although dynamic properties in general are similar in many proteins. However, flexibility index and normalized subspace overlap score indicate that subspaces on the first… Advisors/Committee Members: Pal, Debnath (advisor).

Subjects/Keywords: Protein Structures; Protein Dynamics; Protein Functions; Proteins - Analysis; Proteins - Molecular Dynamics Simulations; Protein Flexibility; Protein Simulation Trajectories; Forcefields - Protein Analysis; Protein Structure - Computation; Molecular Dynamics Simulations; MD Simulations; Biochemistry

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APA (6^th Edition):

Katagi, G. M. (2018). Analysis of Molecular Dynamics Trajectories of Proteins Performed using Different Forcefields and Identifiction of Mobile Segments. (Masters Thesis). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/3327

Chicago Manual of Style (16^th Edition):

Katagi, Gurunath M. “Analysis of Molecular Dynamics Trajectories of Proteins Performed using Different Forcefields and Identifiction of Mobile Segments.” 2018. Masters Thesis, Indian Institute of Science. Accessed March 06, 2021. http://etd.iisc.ac.in/handle/2005/3327.

MLA Handbook (7^th Edition):

Katagi, Gurunath M. “Analysis of Molecular Dynamics Trajectories of Proteins Performed using Different Forcefields and Identifiction of Mobile Segments.” 2018. Web. 06 Mar 2021.

Vancouver:

Katagi GM. Analysis of Molecular Dynamics Trajectories of Proteins Performed using Different Forcefields and Identifiction of Mobile Segments. [Internet] [Masters thesis]. Indian Institute of Science; 2018. [cited 2021 Mar 06]. Available from: http://etd.iisc.ac.in/handle/2005/3327.

Council of Science Editors:

Katagi GM. Analysis of Molecular Dynamics Trajectories of Proteins Performed using Different Forcefields and Identifiction of Mobile Segments. [Masters Thesis]. Indian Institute of Science; 2018. Available from: http://etd.iisc.ac.in/handle/2005/3327

NSYSU

20. Chang, Shao-Heng. Modeling of nano-particle motion: subjected to press of two moving bodies.

Degree: PhD, Mechanical and Electro-Mechanical Engineering, 2012, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905112-112610

► This dissertation aims to establish a mathematical model to predict the steady-state (stationary) motion of a nano-particle that is suppressed between two parallel moving objects.… (more)

▼ This dissertation aims to establish a mathematical model to predict the steady-state (stationary) motion of a nano-particle that is suppressed between two parallel moving objects. The main purpose of this study intends to find an appropriate means to reduce surface damage caused by moving nano-paricle. This study will show that, via the molecular dynamics (MD) analysis, the surface will result in different sizes of damaged layer and surface roughness when a nano-particle moves in a distinct way on it. Therefore, it has a significant value in the applications of high precision polishing and surface cleaning to identify the dominant factors in affecting the motion of nano-particle. The proposed model is to find the steady-state motion by meeting the conditions of force and torque balances on a moving nano-particle. Several hypotheses are suggested to derive the interaction force occurred at the interface between particle and each object. The hypothesis starts from the energy point of view. It is claimed that the potential and kinetic energies of object atoms will increase when nano-particle moves relative to the object. Because of the relative motion, some of the object atoms will be pushed or driven away, depending on the manner of motion. The increment of potential or kinetic energies is assumed to be proportional to the number of pushed or driven atoms. The increase of energy is supplied from the works done by the normal stress and shear stress at the interface of particle. The interaction at the front end of particle is very different from that at the rear end when particle rolls on object surface. There is a pushing action at the front end while a pulling action occurs at the rear end. The magnitudes of both actions are dominated and proportional to the adhesive strength between particle and object. The computer simulations show that the particle motion is mainly affected by the relative adhesive strength among particle and two objects. If the adhesive strength between particle and one object increase, the particle will increase the sliding speed relative to another object. On the other hand, if the adhesive strength between particle and one object is close to that of another object, the particle tends to have significant rolling motion relative to two objects. The suppressed loading between particle and objects has little effect on the qualitative trend of particle motion. The validity of proposed model is evaluated by the molecular dynamics simulation. It indicates that the predicted behaviors of proposed model are consistent with that from the analysis of molecular dynamics simulations. Advisors/Committee Members: Y.T. Sheen (chair), C.T. Pan (chair), Jung-Shu Wu (chair), Y.T.Su (committee member), KUANG-HUA FUH (chair).

Subjects/Keywords: adhesive strength; steady-state motion; molecular dynamics simulations

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APA (6^th Edition):

Chang, S. (2012). Modeling of nano-particle motion: subjected to press of two moving bodies. (Doctoral Dissertation). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905112-112610

Chicago Manual of Style (16^th Edition):

Chang, Shao-Heng. “Modeling of nano-particle motion: subjected to press of two moving bodies.” 2012. Doctoral Dissertation, NSYSU. Accessed March 06, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905112-112610.

MLA Handbook (7^th Edition):

Chang, Shao-Heng. “Modeling of nano-particle motion: subjected to press of two moving bodies.” 2012. Web. 06 Mar 2021.

Vancouver:

Chang S. Modeling of nano-particle motion: subjected to press of two moving bodies. [Internet] [Doctoral dissertation]. NSYSU; 2012. [cited 2021 Mar 06]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905112-112610.

Council of Science Editors:

Chang S. Modeling of nano-particle motion: subjected to press of two moving bodies. [Doctoral Dissertation]. NSYSU; 2012. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0905112-112610

University of California – Irvine

21. Parry, Krista Monique. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions.

Degree: Chemical and Material Physics, 2017, University of California – Irvine

URL: http://www.escholarship.org/uc/item/42g2g920

► Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy (AP-XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the… (more)

Subjects/Keywords: Chemistry; Molecular Dynamics Simulations; X-ray Photoelectron Spectroscopy

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APA (6^th Edition):

Parry, K. M. (2017). Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/42g2g920

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):

Parry, Krista Monique. “Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions.” 2017. Thesis, University of California – Irvine. Accessed March 06, 2021. http://www.escholarship.org/uc/item/42g2g920.

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

MLA Handbook (7^th Edition):

Parry, Krista Monique. “Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions.” 2017. Web. 06 Mar 2021.

Vancouver:

Parry KM. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions. [Internet] [Thesis]. University of California – Irvine; 2017. [cited 2021 Mar 06]. Available from: http://www.escholarship.org/uc/item/42g2g920.

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

Council of Science Editors:

Parry KM. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions. [Thesis]. University of California – Irvine; 2017. Available from: http://www.escholarship.org/uc/item/42g2g920

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

Mississippi State University

22. Bowman, Andrew Lee. Multiscale damage and fracture modeling of polyethylene using molecular dynamics simulations and continuum internal state variable theory.

Degree: PhD, Mississippi State University, 2019, Mississippi State University

URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03212019-113345/ ;

► A multiscale model using simulated nanoscale damage (free volume) evolution and continuum damage evolution equations (void nucleation, growth, and coalescence) for the amorphous phase… (more)

Subjects/Keywords: voids; polymers; internal state variable theory; damage modeling; molecular dynamics simulations

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APA (6^th Edition):

Bowman, A. L. (2019). Multiscale damage and fracture modeling of polyethylene using molecular dynamics simulations and continuum internal state variable theory. (Doctoral Dissertation). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-03212019-113345/ ;

Chicago Manual of Style (16^th Edition):

Bowman, Andrew Lee. “Multiscale damage and fracture modeling of polyethylene using molecular dynamics simulations and continuum internal state variable theory.” 2019. Doctoral Dissertation, Mississippi State University. Accessed March 06, 2021. http://sun.library.msstate.edu/ETD-db/theses/available/etd-03212019-113345/ ;.

MLA Handbook (7^th Edition):

Bowman, Andrew Lee. “Multiscale damage and fracture modeling of polyethylene using molecular dynamics simulations and continuum internal state variable theory.” 2019. Web. 06 Mar 2021.

Vancouver:

Bowman AL. Multiscale damage and fracture modeling of polyethylene using molecular dynamics simulations and continuum internal state variable theory. [Internet] [Doctoral dissertation]. Mississippi State University; 2019. [cited 2021 Mar 06]. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03212019-113345/ ;.

Council of Science Editors:

Bowman AL. Multiscale damage and fracture modeling of polyethylene using molecular dynamics simulations and continuum internal state variable theory. [Doctoral Dissertation]. Mississippi State University; 2019. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-03212019-113345/ ;

University of Minnesota

23. Nikiforov, Ilia A. A study of bending deformations in carbon nanotubes using the objective molecular dynamics method.

Degree: MS, Mechanical Engineering, 2010, University of Minnesota

URL: http://purl.umn.edu/102693

►

University of Minnesota M.S. thesis. September 2010. Major: Mechanical Engineering. Advisor: Prof. Traian Dumitrica. 1 computer file (PDF); x, 65 pages, appendix A.

Bending of… (more)

Subjects/Keywords: Nanotoxicology; Nanotubes; Atomistic simulations; Molecular dynamics; Elastic bending; Multi-walled tubes

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APA (6^th Edition):

Nikiforov, I. A. (2010). A study of bending deformations in carbon nanotubes using the objective molecular dynamics method. (Masters Thesis). University of Minnesota. Retrieved from http://purl.umn.edu/102693

Chicago Manual of Style (16^th Edition):

Nikiforov, Ilia A. “A study of bending deformations in carbon nanotubes using the objective molecular dynamics method.” 2010. Masters Thesis, University of Minnesota. Accessed March 06, 2021. http://purl.umn.edu/102693.

MLA Handbook (7^th Edition):

Nikiforov, Ilia A. “A study of bending deformations in carbon nanotubes using the objective molecular dynamics method.” 2010. Web. 06 Mar 2021.

Vancouver:

Nikiforov IA. A study of bending deformations in carbon nanotubes using the objective molecular dynamics method. [Internet] [Masters thesis]. University of Minnesota; 2010. [cited 2021 Mar 06]. Available from: http://purl.umn.edu/102693.

Council of Science Editors:

Nikiforov IA. A study of bending deformations in carbon nanotubes using the objective molecular dynamics method. [Masters Thesis]. University of Minnesota; 2010. Available from: http://purl.umn.edu/102693

University of Michigan

24. Ghanakota, Phani. Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design.

Degree: PhD, Medicinal Chemistry, 2015, University of Michigan

URL: http://hdl.handle.net/2027.42/113593

► Hotspots are defined as regions on the protein surface that disproportionately contribute to binding free energy. Mixed-solvent molecular dynamics (MixMD) is a hotspot mapping technique… (more)

▼ Hotspots are defined as regions on the protein surface that disproportionately contribute to binding free energy. Mixed-solvent molecular dynamics (MixMD) is a hotspot mapping technique that relies on molecular dynamics simulations of binary solvent mixtures. Previous work in the group on MixMD has established the technique’s effectiveness in capturing binding sites of small organic compounds. The MixMD approach embraces full protein flexibility while allowing for competition between probes and water. Sites preferentially mapped by probe molecules are more likely to be hotspots. First, we establish a rigorous protocol for the identification of hotspots on the binding surface. There are two important requirements: 1) the high-ranking hotspots must be mapped at very high signal-to-noise ratio and 2) the hotspots must be mapped by multiple probes. We have focused our probe molecule repertoire to include acetonitrile, isopropanol, and pyrimidine as these probes allowed us to capture a range of interaction types that include hydrophilic, hydrophobic, hydrogen-bonding and aromatic interactions. Second, we use MixMD to identify both competitive and allosteric sites on proteins. The test cases include Abl Kinase, Androgen Receptor, Chk1 Kinase, Glucokinase, Pdk1 Kinase, Protein-Tyrosine Phosphatase 1B, and Farnesyl Pyrophosphate Synthase. The success of the technique is demonstrated by the fact that the top four sites map the competitive and allosteric sites. We then present methodological developments for characterizing the free energies and entropies of binding sites identified by MixMD. Finally, the significance of these findings is strengthened by a successful prospective application of MixMD on Heat Shock Protein 27. Taken together, these studies demonstrate the powerful utility of MixMD in structure based drug design. Advisors/Committee Members: Carlson, Heather A. (committee member), Mosberg, Henry I. (committee member), Brooks Iii, Charles L. (committee member), Grant, Barry (committee member).

Subjects/Keywords: Computational Chemistry; Structure Based Drug Design; Molecular Dynamics Simulations; Chemistry; Science

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APA (6^th Edition):

Ghanakota, P. (2015). Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/113593

Chicago Manual of Style (16^th Edition):

Ghanakota, Phani. “Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design.” 2015. Doctoral Dissertation, University of Michigan. Accessed March 06, 2021. http://hdl.handle.net/2027.42/113593.

MLA Handbook (7^th Edition):

Ghanakota, Phani. “Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design.” 2015. Web. 06 Mar 2021.

Vancouver:

Ghanakota P. Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design. [Internet] [Doctoral dissertation]. University of Michigan; 2015. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/2027.42/113593.

Council of Science Editors:

Ghanakota P. Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design. [Doctoral Dissertation]. University of Michigan; 2015. Available from: http://hdl.handle.net/2027.42/113593

Cornell University

25. Stolzenberg, Sebastian. Multi-Scale Computational Studies Of Molecular Mechanisms In The Function Of Membrane-Proteins In The Family Of Neurotransmitter Transporters.

Degree: PhD, Physics, 2014, Cornell University

URL: http://hdl.handle.net/1813/36182

► In my thesis work, I investigate functional mechanisms of complex molecular machines in the cell membrane that carry out the transport (reuptake) of neurotransmitter molecules… (more)

Subjects/Keywords: Substrate Transport Mechanism; Molecular Dynamics Simulations; Motion Planning

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APA (6^th Edition):

Stolzenberg, S. (2014). Multi-Scale Computational Studies Of Molecular Mechanisms In The Function Of Membrane-Proteins In The Family Of Neurotransmitter Transporters. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/36182

Chicago Manual of Style (16^th Edition):

Stolzenberg, Sebastian. “Multi-Scale Computational Studies Of Molecular Mechanisms In The Function Of Membrane-Proteins In The Family Of Neurotransmitter Transporters.” 2014. Doctoral Dissertation, Cornell University. Accessed March 06, 2021. http://hdl.handle.net/1813/36182.

MLA Handbook (7^th Edition):

Stolzenberg, Sebastian. “Multi-Scale Computational Studies Of Molecular Mechanisms In The Function Of Membrane-Proteins In The Family Of Neurotransmitter Transporters.” 2014. Web. 06 Mar 2021.

Vancouver:

Stolzenberg S. Multi-Scale Computational Studies Of Molecular Mechanisms In The Function Of Membrane-Proteins In The Family Of Neurotransmitter Transporters. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1813/36182.

Council of Science Editors:

Stolzenberg S. Multi-Scale Computational Studies Of Molecular Mechanisms In The Function Of Membrane-Proteins In The Family Of Neurotransmitter Transporters. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/36182

Texas A&M University

26. Smith, Taylor William. Effects of Electrolyte Composition and Polysulfide Species on the Reactivity of Lithium Anodes in Lithium-Sulfur Batteries.

Degree: MS, Materials Science and Engineering, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/156452

► In attempting to develop energy storage systems possessing superior properties to traditional lithium ion batteries (LIBs), numerous alternative chemistries have undergone study and development. Of… (more)

▼ In attempting to develop energy storage systems possessing superior properties to traditional lithium ion batteries (LIBs), numerous alternative chemistries have undergone study and development. Of these, the lithium-sulfur battery seems one of the more promising contenders for replacing LIBs, particularly for applications like electric vehicles. Nevertheless, a variety of limitations have prevented lithium-sulfur battery introduction to the marketplace, in spite of almost fifty years of research, including polysulfide shuttle, reactivity of the electrolyte, and anodic microstructure evolution. This thesis will explore the use of first-principles computational techniques in understanding the impact of electrolyte composition, polysulfide molecules, and lithium crystal structure on the reactions taking place near the lithium anode in order to better address the problems facing lithium-sulfur batteries. Using ab initio molecular dynamics simulations (AIMD), in conjunction with static density functional theory (DFT) optimizations, Bader charge analysis, and additional analytical techniques, the interactions and impacts of the different components of the typical lithium-sulfur battery can be examined on a molecular basis. It is the author’s hope that a better theoretical understanding of how these species behave will enable design and implementation of real-world lithium-sulfur systems capable of meeting and overcoming the difficulties facing their commercialization. In order to test the effects of lithium crystal structure on electrolyte stability and surface morphology evolution, both a (100) and (110) lithium metal surface were created and tested using AIMD simulations. There was a minimal difference in the results for each structure, in both the surface morphology and ratio of solvent molecules reduced by the lithium. In testing the effects and stability of various solvents, it was found that ethylene carbonate reduced readily, while dioxolane, dimethoxyethane, and fluorinated ether molecules were quite stable in the presence of the anode. AIMD simulations of polysulfide molecules in the vicinity of the lithium surface show high reactivity, as seen experimentally, and subsequent DFT calculations indicate the reduction of long-chain polysulfide molecules in the presence of Li atoms is a thermodynamically favorable reaction pathway. Finally, it was observed that high molarity salt systems have properties capable of improving cell performance. Advisors/Committee Members: Balbuena, Perla B (advisor), Mukherjee, Partha P (committee member), Shamberger, Patrick J (committee member).

Subjects/Keywords: Batteries; Lithium-Sulfur; Simulations; Polysulfide Shuttle; Battery Anode; Molecular Dynamics

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APA (6^th Edition):

Smith, T. W. (2015). Effects of Electrolyte Composition and Polysulfide Species on the Reactivity of Lithium Anodes in Lithium-Sulfur Batteries. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/156452

Chicago Manual of Style (16^th Edition):

Smith, Taylor William. “Effects of Electrolyte Composition and Polysulfide Species on the Reactivity of Lithium Anodes in Lithium-Sulfur Batteries.” 2015. Masters Thesis, Texas A&M University. Accessed March 06, 2021. http://hdl.handle.net/1969.1/156452.

MLA Handbook (7^th Edition):

Smith, Taylor William. “Effects of Electrolyte Composition and Polysulfide Species on the Reactivity of Lithium Anodes in Lithium-Sulfur Batteries.” 2015. Web. 06 Mar 2021.

Vancouver:

Smith TW. Effects of Electrolyte Composition and Polysulfide Species on the Reactivity of Lithium Anodes in Lithium-Sulfur Batteries. [Internet] [Masters thesis]. Texas A&M University; 2015. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1969.1/156452.

Council of Science Editors:

Smith TW. Effects of Electrolyte Composition and Polysulfide Species on the Reactivity of Lithium Anodes in Lithium-Sulfur Batteries. [Masters Thesis]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/156452

Penn State University

27. Hong, Sung Wook. ATOMISTIC-SCALE INVESTIGATION OF THE GROWTH KINETICS OF ALUMINUM OXIDE LAYERS ON ALUMINUM NANOPARTICLES AND GERMANIUM-BASED SEMICONDUCTORS USING THE REAXFF REACTIVE FORCE FIELD.

Degree: 2016, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/ft848q60n

► In this dissertation, the ReaxFF potential was employed to investigate the complex surface chemistry of two nano-scale systems, including growth of aluminum oxide (Al2O3) layers… (more)

▼ In this dissertation, the ReaxFF potential was employed to investigate the complex surface chemistry of two nano-scale systems, including growth of aluminum oxide (Al2O3) layers on aluminum nanoparticles (ANPs) and Ge-based semiconductors. ANPs have been considered “energetic materials” due to their high enthalpy of oxidation and potentially applicable to rocket propellant formulations. In addition, there is a growing interest in using the Ge-based semiconductors to replace conventional Si-based semiconductors. However, a quantitative and comprehensive understanding of kinetic mechanisms associated with the above-mentioned systems has not yet been fully achieved, primarily due to complexities of their reaction processes in nature. Given this, the present work is motivated by two research questions: (1) What are the dominant factors that give a higher degree of energy efficiency during the oxidation process of ANPs, and (2) What is the optimal guidance for manufacturing Ge-based semiconductors? As such, this study aims to gain atomistic-scale insights into growth kinetics of passivation layers on ANPs and Ge surfaces using the ReaxFF reactive force field method. To achieve these aims, research strategies included: (a) application of the ReaxFF potential for Al/O system being chosen as a means of understanding the mechanism of the oxidation of ANPs; (b) development and application of a ReaxFF reactive force field for Al/C/H/O interactions to study the effects of surface modification on the oxidation kinetics of the ANPs; and (c) extension of the ReaxFF potential to Ge/Al/C/H/O systems to directly model an Al2O3 atomic layer deposition (ALD) process on Ge surfaces, and comparing computational results with experimental work. Our findings from combined ReaxFF and experimental studies offer very promising options and systematic strategies for the ANPs and the Ge-based semiconductors to be used in the combustion and the ALD applications, respectively. In summary, this dissertation clarifies mechanisms for growth kinetics of passivation layers (i.e., Al2O3 layer) on ANPs and Ge surfaces and suggests future directions for studying the reaction kinetics of a wide range of complex nano-scale systems from an atomistic-scale viewpoint. Advisors/Committee Members: Adri C.T. van Duin, Dissertation Advisor/Co-Advisor, Adri C.T. van Duin, Committee Chair/Co-Chair, Yuan Xuan, Committee Member, Richard A Yetter, Committee Member, Roman Engel-Herbert, Outside Member.

Subjects/Keywords: ReaxFF; Molecular Dynamics Simulations; Aluminum oxide layer; Aluminum nanoparticles; Ge slab

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

APA (6^th Edition):

Hong, S. W. (2016). ATOMISTIC-SCALE INVESTIGATION OF THE GROWTH KINETICS OF ALUMINUM OXIDE LAYERS ON ALUMINUM NANOPARTICLES AND GERMANIUM-BASED SEMICONDUCTORS USING THE REAXFF REACTIVE FORCE FIELD. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/ft848q60n

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):

Hong, Sung Wook. “ATOMISTIC-SCALE INVESTIGATION OF THE GROWTH KINETICS OF ALUMINUM OXIDE LAYERS ON ALUMINUM NANOPARTICLES AND GERMANIUM-BASED SEMICONDUCTORS USING THE REAXFF REACTIVE FORCE FIELD.” 2016. Thesis, Penn State University. Accessed March 06, 2021. https://submit-etda.libraries.psu.edu/catalog/ft848q60n.

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

MLA Handbook (7^th Edition):

Hong, Sung Wook. “ATOMISTIC-SCALE INVESTIGATION OF THE GROWTH KINETICS OF ALUMINUM OXIDE LAYERS ON ALUMINUM NANOPARTICLES AND GERMANIUM-BASED SEMICONDUCTORS USING THE REAXFF REACTIVE FORCE FIELD.” 2016. Web. 06 Mar 2021.

Vancouver:

Hong SW. ATOMISTIC-SCALE INVESTIGATION OF THE GROWTH KINETICS OF ALUMINUM OXIDE LAYERS ON ALUMINUM NANOPARTICLES AND GERMANIUM-BASED SEMICONDUCTORS USING THE REAXFF REACTIVE FORCE FIELD. [Internet] [Thesis]. Penn State University; 2016. [cited 2021 Mar 06]. Available from: https://submit-etda.libraries.psu.edu/catalog/ft848q60n.

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

Council of Science Editors:

Hong SW. ATOMISTIC-SCALE INVESTIGATION OF THE GROWTH KINETICS OF ALUMINUM OXIDE LAYERS ON ALUMINUM NANOPARTICLES AND GERMANIUM-BASED SEMICONDUCTORS USING THE REAXFF REACTIVE FORCE FIELD. [Thesis]. Penn State University; 2016. Available from: https://submit-etda.libraries.psu.edu/catalog/ft848q60n

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

Boston University

28. Lascaris, Erik. Liquid-liquid phase transitions and water-like anomalies in liquids.

Degree: PhD, Physics, 2014, Boston University

URL: http://hdl.handle.net/2144/15303

► In this thesis we employ computer simulations and statistical physics to understand the origin of liquid-liquid phase transitions and their relationship with anomalies typical of… (more)

▼ In this thesis we employ computer simulations and statistical physics to understand the origin of liquid-liquid phase transitions and their relationship with anomalies typical of liquid water. Compared with other liquids, water has many anomalies. For example the density anomaly: when water is cooled below 4 C the density decreases rather than increases. This and other anomalies have also been found to occur in a few other one-component liquids, sometimes in conjunction with the existence of a liquid-liquid phase transition (LLPT) between a low-density liquid (LDL) and a high-density liquid (HDL). Using simple models we explain how these anomalies arise from the presence of two competing length scales. As a specific example we investigate the cut ramp potential, where we show the importance of "competition" in this context, and how one length scale can sometimes be zero. When there is a clear energetic preference for either LDL or HDL for all pressures and temperatures, then there is insufficient competition between the two liquid structures and no anomalies occur. From the simple models it also follows that anomalies can occur without the presence of a LLPT and vice versa. It remains therefore unclear if water has a LLPT that ends in a liquid-liquid critical point (LLCP), a hypothesis that was first proposed based on simulations of the ST2 water model. We confirm the existence of a LLCP in this model using finite size scaling and the Challa-Landau-Binder parameter, and show that the LLPT is not a liquid-crystal transition, as has recently been suggested. Previous research has indicated the possible existence of a LLCP in liquid silica. We perform a detailed analysis of two different silica models (WAC and BKS) at temperatures much lower than was previously simulated. Within the accessible temperature range we find no LLCP in either model, although in the case of WAC potential it is closely approached. We compare our results with those obtained for other tetrahedral liquids and conclude that insufficient "stiffness" in the Si-O-Si bond angle might be responsible for the absence of a LLCP.

Subjects/Keywords: Physics; Liquid-liquid critical points; Molecular dynamics simulations; Silica; Water

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

APA (6^th Edition):

Lascaris, E. (2014). Liquid-liquid phase transitions and water-like anomalies in liquids. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/15303

Chicago Manual of Style (16^th Edition):

Lascaris, Erik. “Liquid-liquid phase transitions and water-like anomalies in liquids.” 2014. Doctoral Dissertation, Boston University. Accessed March 06, 2021. http://hdl.handle.net/2144/15303.

MLA Handbook (7^th Edition):

Lascaris, Erik. “Liquid-liquid phase transitions and water-like anomalies in liquids.” 2014. Web. 06 Mar 2021.

Vancouver:

Lascaris E. Liquid-liquid phase transitions and water-like anomalies in liquids. [Internet] [Doctoral dissertation]. Boston University; 2014. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/2144/15303.

Council of Science Editors:

Lascaris E. Liquid-liquid phase transitions and water-like anomalies in liquids. [Doctoral Dissertation]. Boston University; 2014. Available from: http://hdl.handle.net/2144/15303

Virginia Commonwealth University

29. Al-Nsour, Rawan. MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS.

Degree: PhD, Mechanical and Nuclear Engineering, 2014, Virginia Commonwealth University

URL: https://doi.org/10.25772/Q9FZ-X547 ; https://scholarscompass.vcu.edu/etd/3845

► Fluoropolymers are employed in countless end-user applications across several industries. One such fluoropolymer is polytetrafluoroethylene. This research is concerned with studying and understanding the… (more)

Subjects/Keywords: Molecular Dynamics Simulations; Polytetrafluoroethylene; Glassy Transition Temperature; Mechanical Engineering

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

APA (6^th Edition):

Al-Nsour, R. (2014). MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS. (Doctoral Dissertation). Virginia Commonwealth University. Retrieved from https://doi.org/10.25772/Q9FZ-X547 ; https://scholarscompass.vcu.edu/etd/3845

Chicago Manual of Style (16^th Edition):

Al-Nsour, Rawan. “MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS.” 2014. Doctoral Dissertation, Virginia Commonwealth University. Accessed March 06, 2021. https://doi.org/10.25772/Q9FZ-X547 ; https://scholarscompass.vcu.edu/etd/3845.

MLA Handbook (7^th Edition):

Al-Nsour, Rawan. “MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS.” 2014. Web. 06 Mar 2021.

Vancouver:

Al-Nsour R. MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS. [Internet] [Doctoral dissertation]. Virginia Commonwealth University; 2014. [cited 2021 Mar 06]. Available from: https://doi.org/10.25772/Q9FZ-X547 ; https://scholarscompass.vcu.edu/etd/3845.

Council of Science Editors:

Al-Nsour R. MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS. [Doctoral Dissertation]. Virginia Commonwealth University; 2014. Available from: https://doi.org/10.25772/Q9FZ-X547 ; https://scholarscompass.vcu.edu/etd/3845

University of Western Ontario

30. Martin, Leanne. Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations.

Degree: 2020, University of Western Ontario

URL: https://ir.lib.uwo.ca/etd/7336

► Electrospray ionization mass spectrometry (ESI-MS) is a powerful technique to investigate proteins and many other analytes. However, many fundamental aspects of ESI remain poorly understood.… (more)

Subjects/Keywords: Proteins; Electrospray Ionization Mass Spectrometry; Supercharging; Molecular Dynamics Simulations; Salt Clusters

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

APA (6^th Edition):

Martin, L. (2020). Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/7336

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):

Martin, Leanne. “Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations.” 2020. Thesis, University of Western Ontario. Accessed March 06, 2021. https://ir.lib.uwo.ca/etd/7336.

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

MLA Handbook (7^th Edition):

Martin, Leanne. “Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations.” 2020. Web. 06 Mar 2021.

Vancouver:

Martin L. Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations. [Internet] [Thesis]. University of Western Ontario; 2020. [cited 2021 Mar 06]. Available from: https://ir.lib.uwo.ca/etd/7336.

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

Council of Science Editors:

Martin L. Mechanistic Insights into Analyte Charge Enhancement using Mass Spectrometry and Molecular Dynamics Simulations. [Thesis]. University of Western Ontario; 2020. Available from: https://ir.lib.uwo.ca/etd/7336

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

Open Access Theses and Dissertations