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Large-scale molecular dynamics simulations of semiconductor nanostructures
Title
Large-scale molecular dynamics simulations of semiconductor nanostructures.
Creator
Cornwell, Charles F., Florida Atlantic University, Wille, Luc T.
Abstract/Description
Classical trajectory molecular dynamics methods are used to investigate the critical strain of single-walled carbon nanotubes ("SWT") and the strength and extent of the interactions between 3D Ge structures on the surface of Si(001). The discrete model is capable of giving some insight into the critical strain of the SWT's beyond the limits of the continuous model and allow us to investigate the effects of lattice distortion due to the placement of Ge structures on the surface of a Si...
Show moreClassical trajectory molecular dynamics methods are used to investigate the critical strain of single-walled carbon nanotubes ("SWT") and the strength and extent of the interactions between 3D Ge structures on the surface of Si(001). The discrete model is capable of giving some insight into the critical strain of the SWT's beyond the limits of the continuous model and allow us to investigate the effects of lattice distortion due to the placement of Ge structures on the surface of a Si substrate. Total energy calculations performed using classical three-body interatomic potentials with appropriate boundary conditions for each case are used to investigate the two systems. We discuss the development of a parallel code to simulate short-ranged empirical potentials such as those of Stillinger and Weber, Tersoff, and Tersoff-Brenner. We then use the Tersoff potential to model C and Si/Ge system. Data collected are used to examine the behavior of the two systems.
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Date Issued
1999
PURL
http://purl.flvc.org/fcla/dt/12614
Subject Headings
Molecular dynamics--Computer simulation, Nanostructured materials, Semiconductors
Format
Document (PDF)
Effects of small molecule modulators and Phospholipid Liposomes on βeta-amyloid (1-40) Amyloidogenesis
Title
Effects of small molecule modulators and Phospholipid Liposomes on βeta-amyloid (1-40) Amyloidogenesis.
Creator
Morris, Clifford, Du, Deguo, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
Beta-Amyloid (1-40) (Aβ40) is an aggregation prone protein, which undergoes a nucleation-dependent aggregation process causing the pathological neurodegeneration by amyloid plaque formation implicated in Alzheimer’s disease. In this thesis, we investigated the effects of small molecule modulators extracted from the marine invertebrate Pseudopterogorgia elisabethae on the Aβ40 amyloidogenic process using in- vitro ThT fluorescence assay and atomic force microscopy. We also investigated the...
Show moreBeta-Amyloid (1-40) (Aβ40) is an aggregation prone protein, which undergoes a nucleation-dependent aggregation process causing the pathological neurodegeneration by amyloid plaque formation implicated in Alzheimer’s disease. In this thesis, we investigated the effects of small molecule modulators extracted from the marine invertebrate Pseudopterogorgia elisabethae on the Aβ40 amyloidogenic process using in- vitro ThT fluorescence assay and atomic force microscopy. We also investigated the effects of neutral and anionic phospholipid liposomes on Aβ40 aggregation. Our results show that a marine natural product Pseudopterosin-A and its derivatives can suppress and modulate the Aβ40 aggregation process. Furthermore, our results demonstrate that a neutral phospholipid liposome inhibits Aβ40 fibril formation, whereas the anionic liposomes promote it.
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Date Issued
2015
PURL
http://purl.flvc.org/fau/fd/FA00004453, http://purl.flvc.org/fau/fd/FA00004453
Subject Headings
Aggregation (Chemistry), Alzheimer's disease -- Pathogenesis, Alzheimer's disease -- Research, Amyloid beta protein, Molecular biology, Molecular dynamics, Prions, Proteins -- Metabolism -- Disorders
Format
Document (PDF)
Studies of Site-Specific Dynamics of Aβ Amyloid Formation and Effect of Macromolecules on Aβ Amyloidogenesis
Title
Studies of Site-Specific Dynamics of Aβ Amyloid Formation and Effect of Macromolecules on Aβ Amyloidogenesis.
Creator
Liu, Haiyang, Du, Deguo, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
The aim of this dissertation was 1) to explore early stage aggregation kinetic behavior of Amyloid-β 1-40 (Aβ1-40) by incorporation of unnatural amino acid pcyanophenylalanine as a site-specific fluorescence reporter, 2) to explore the effect of macromolecules on the aggregation of Aβ1-40. Chapter One provides an introduction of Alzheimer’s disease as an amyloidogenic disease, amyloidogenic peptide and amyloid formation. Details were shown about the research progress of Aβ1-40 aggregation and...
Show moreThe aim of this dissertation was 1) to explore early stage aggregation kinetic behavior of Amyloid-β 1-40 (Aβ1-40) by incorporation of unnatural amino acid pcyanophenylalanine as a site-specific fluorescence reporter, 2) to explore the effect of macromolecules on the aggregation of Aβ1-40. Chapter One provides an introduction of Alzheimer’s disease as an amyloidogenic disease, amyloidogenic peptide and amyloid formation. Details were shown about the research progress of Aβ1-40 aggregation and Aβ1-40’s interaction with polyelectrolytes, and how treatments studies were designed. In Chapter two, using Aβ1-23 as a model molecule, the distinct site-specific dynamics was identified, during amyloid formation, and the structural characteristics of amyloid fibrils were defined by using an unnatural amino acid, p-cyanophenylalanine, as a sensitive fluorescent and Raman probe. The results reveal distinct local environmental changes of specific residues during the aggregation of Aβ1-23. The results also suggest that an edge-to-face aromatic interaction between the F4 and F19 residues from the adjacent in-register β-strands plays a key role in the conformational conversion to form and stabilize β-sheet structure. In Chapter Three, p-cyanophenylalanine was incorporated in the full sequence of Aβ1-40. Site-specific information from p-cyanophenylalanine fluorescence was studied and summarized. In Chapter Four, the inhibiting effect of an anionic polyelectrolyte poly(4- styrenesulfonate) (PSS) on the aggregation of Aβ1-40 peptide was reported. The results demonstrate the strong inhibition potential of PSS on the aggregation of Aβ1-40. Additional studies indicate that the presence of both aliphatic backbone as well as aromatic side chain group in PSS is essential for its inhibition activity. In Chapter Five, it was investigated the effect of two polyelectrolytes, chitosan (CHT) and N-trimethyl chitosan chloride (TMC), on the aggregation of Aβ1-40. Results show that both CHT and TMC exhibit a concentration-dependent decrease of amyloid aggregation suggesting their application as amyloid assembly inhibitors. Their binding mechanism was investigated by computational modeling which shows that Aβ1-40 monomer was primarily stabilized by electrostatic interactions with charged amine and quaternary amines of CHT and TMC respectively. Chapter Six, describes all experimental procedures and instrument setup in detail.
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Date Issued
2016
PURL
http://purl.flvc.org/fau/fd/FA00004769, http://purl.flvc.org/fau/fd/FA00004769
Subject Headings
Alzheimer's disease--Research., Alzheimer's disease--Pathogenesis., Molecular biology., Molecular dynamics., Prions., Amyloid beta-protein.
Format
Document (PDF)
Visualization tool for molecular dynamics simulation
Title
Visualization tool for molecular dynamics simulation.
Creator
Garg, Meha., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description
A study of Molecular Dynamics using computational methods and modeling provides the understanding on the interaction of the atoms, properties, structure, and motion and model phenomenon. There are numerous commercial tools available for simulation, analysis and visualization. However any particular tool does not provide all the functionalities. The main objective of this work is the development of the visualization tool customized for our research needs to view the three dimensional...
Show moreA study of Molecular Dynamics using computational methods and modeling provides the understanding on the interaction of the atoms, properties, structure, and motion and model phenomenon. There are numerous commercial tools available for simulation, analysis and visualization. However any particular tool does not provide all the functionalities. The main objective of this work is the development of the visualization tool customized for our research needs to view the three dimensional orientation of the atom, process the simulation results offline, able to handle large volume of data, ability to display complete frame, atomic trails, and runtime response to the researchers' query with low processing time. This thesis forms the basis for the development of such an in-house tool for analysis and display of simulation results based on Open GL and MFC. Advantages, limitations, capabilities and future aspects are also discussed. The result is the system capable of processing large amount of simulation result data in 11 minutes and query response and display in less than 1 second.
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Date Issued
2010
PURL
http://purl.flvc.org/FAU/1927308
Subject Headings
Molecular dynamics, Computer simulation, Condensed matter, Computer simulation, Intermolecular forces, Computer simulation, Molecules, Mathematical models
Format
Document (PDF)
Pattern mining and visualization for molecular dynamics simulation
Title
Pattern mining and visualization for molecular dynamics simulation.
Creator
Kong, Xue, Zhu, Xingquan, Florida Atlantic University, College of Computer Science and Engineering, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description
Molecular dynamics is a computer simulation technique for expressing the ultimate details of individual particle motions and can be used in many fields, such as chemical physics, materials science, and the modeling of biomolecules. In this thesis, we study visualization and pattern mining in molecular dynamics simulation. The molecular data set has a large number of atoms in each frame and range of frames. The features of the data set include atom ID; frame number; position in x, y, and z...
Show moreMolecular dynamics is a computer simulation technique for expressing the ultimate details of individual particle motions and can be used in many fields, such as chemical physics, materials science, and the modeling of biomolecules. In this thesis, we study visualization and pattern mining in molecular dynamics simulation. The molecular data set has a large number of atoms in each frame and range of frames. The features of the data set include atom ID; frame number; position in x, y, and z plane; charge; and mass. The three main challenges of this thesis are to display a larger number of atoms and range of frames, to visualize this large data set in 3-dimension, and to cluster the abnormally shifting atoms that move with the same pace and direction in different frames. Focusing on these three challenges, there are three contributions of this thesis. First, we design an abnormal pattern mining and visualization framework for molecular dynamics simulation. The proposed framework can visualize the clusters of abnormal shifting atom groups in a three-dimensional space, and show their temporal relationships. Second, we propose a pattern mining method to detect abnormal atom groups which share similar movement and have large variance compared to the majority atoms. We propose a general molecular dynamics simulation tool, which can visualize a large number of atoms, including their movement and temporal relationships, to help domain experts study molecular dynamics simulation results. The main functions for this visualization and pattern mining tool include atom number, cluster visualization, search across different frames, multiple frame range search, frame range switch, and line demonstration for atom motions in different frames. Therefore, this visualization and pattern mining tool can be used in the field of chemical physics, materials science, and the modeling of biomolecules for the molecular dynamic simulation outcomes.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00004212, http://purl.flvc.org/fau/fd/FA00004212
Subject Headings
Data mining, Information visualization, Molecular dynamics -- Computer simulation, Molecules -- Mathematical models, Pattern perception
Format
Document (PDF)