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Molecular modeling and dynamics of sphinogomyelin phosphodiesterase D LISicTox-alphalll1i
Title
Molecular modeling and dynamics of sphinogomyelin phosphodiesterase D LISicTox-alphalll1i.
Creator
Jordan, Autumn, Snyder, Patricia Ann
Date Issued
2013-04-05
PURL
http://purl.flvc.org/fcla/dt/3361099
Subject Headings
Molecular models, Molecules--Models--Computer simulation, Computational chemistry
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)
Structure-function relationships in eukaryotic and prokaryotic family 6 glycosyltransferases
Title
Structure-function relationships in eukaryotic and prokaryotic family 6 glycosyltransferases.
Creator
Tumbale, Percy., Charles E. Schmidt College of Medicine, Department of Biomedical Science
Abstract/Description
Carbohydrate Active Enzyme family 6 (CA6) glycosyltransferases (GTs) are type II transmembrane proteins localized in the Golgi apparatus. CA6 GTs have a GT-A fold, a type of structure that resembles the Rossman fold and catalyze the transfer either galactose (Gal) or N-acetylgalactosamine (GalNAc) from the UDP nucleotide sugar to an non-reducing terminal Gal or GalNAc on an acceptor via an a-1,3 linkage. In this reaction, the anomeric configuration of the sugar moiety of the donor is retained...
Show moreCarbohydrate Active Enzyme family 6 (CA6) glycosyltransferases (GTs) are type II transmembrane proteins localized in the Golgi apparatus. CA6 GTs have a GT-A fold, a type of structure that resembles the Rossman fold and catalyze the transfer either galactose (Gal) or N-acetylgalactosamine (GalNAc) from the UDP nucleotide sugar to an non-reducing terminal Gal or GalNAc on an acceptor via an a-1,3 linkage. In this reaction, the anomeric configuration of the sugar moiety of the donor is retained in the product. CA6 GTs includes the histo-blood group A and B GTs, a-galactosyltransferase (a3GT), Forssman glycolipid synthase (FS), isogloboside 3 synthase (iGb3) in mammals. a3GT and its products (a-Gal epitode) are present in most mammals but are absent in humans and old world primates because of inactivating mutations. The absence of a3GT and its products results in the production of anti-a-Gal epitope natural antibodies in these species., Up to date, the catalytic mechanisms of the CA6 GTs are not well understood. Based on previous structural and mutagenesis studies of bovine aB3GT, we investigated active site residues (His315, Asp316, Ser318, His319, and Lys359) that are highly conserved among CA6 GTs. We have also investigated the role of the C-terminal region by progressive C-terminal truncations. Findings from these studies clarify the functional roles of these residues in structure, catalysis, and specificity in these enzymes and have implications for their catalytic mechanisms. GTs are useful tools in synthesis of glycans for various applications in science and medicine. Methods for the large scale production of pure glycans are continuously being developed. We created a limited randomized combinatorial library based on knowledge of structural information and sequence analysis of the enzyme and its mammalian homologues., Two GalNAc-specific variants were identified from the library and one Glc-specific variant was identified by site-direct mutagenesis. The glycosyltransferase activities of these variants are expected to be improved by further screens of libraries which are designed using the variants as templates. The mammalian CA6 GTs that have been characterized to date are metal-independent and require the divalent cation, Mn2+ for activity. In some recently-discovered bacterial CA6 GTs, the DXD sequence that is present in eukaryotic GTs is replaced by NXN. We cloned and expressed one of these proteins from Bacteroides ovatus, a bacterium that has been linked with inflammatory bowel disease. Functional characterization shows it is a metal-independent monomeric GT that efficiently catalyzes the synthesis of oligosaccharides similar to human blood group A glycan., Mutational studies indicated that despite the lack of a metal cofactor there are similarities in structure-function relationships between the bacterial and vertebrate family 6 GTs.
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Date Issued
2009
PURL
http://purl.flvc.org/FAU/186686
Subject Headings
Molecular biology, Mathematical models, Glycotransferase genes, Biological transport, Proteins, Synthesis, Evolutionary genetics
Format
Document (PDF)
Reduced representation of neural networks
Title
Reduced representation of neural networks.
Creator
Stefanescu, Roxana A., Charles E. Schmidt College of Science, Department of Physics
Abstract/Description
Experimental and computational investigations addressing how various neural functions are achieved in the brain converged in recent years to a unified idea that the neural activity underlying most of the cognitive functions is distributed over large scale networks comprising various cortical and subcortical areas. Modeling approaches represent these areas and their connections using diverse models of neurocomputational units engaged in graph-like or neural field-like structures. Regardless of...
Show moreExperimental and computational investigations addressing how various neural functions are achieved in the brain converged in recent years to a unified idea that the neural activity underlying most of the cognitive functions is distributed over large scale networks comprising various cortical and subcortical areas. Modeling approaches represent these areas and their connections using diverse models of neurocomputational units engaged in graph-like or neural field-like structures. Regardless of the manner of network implementation, simulations of large scale networks have encountered significant difficulties mainly due to the time delay introduced by the long range connections. To decrease the computational effort, it is common to assume severe approximations to simplify the descriptions of the neural dynamics associated with the system's units. In this dissertation we propose an alternative framework allowing the prevention of such strong assumptions while efficiently representing th e dynamics of a complex neural network. First, we consider the dynamics of small scale networks of globally coupled non-identical excitatory and inhibitory neurons, which could realistically instantiate a neurocomputational unit. We identify the most significant dynamical features the neural population exhibits in different parametric configuration, including multi-cluster dynamics, multi-scale synchronization and oscillator death. Then, using mode decomposition techniques, we construct analytically low dimensional representations of the network dynamics and show that these reduced systems capture the dynamical features of the entire neural population. The cases of linear and synaptic coupling are discussed in detail. In chapter 5, we extend this approach for spatially extended neural networks., We consider the dynamical behavior of a neural field-like network, which incorporates many biologically realistic characteristics such as heterogeneous local and global connectivity as well as dispersion in the neural membrane excitability. We show that in this case as well, we can construct a reduced representation, which may capture well the dynamical features of the full system. The method outlined in this dissertation provides a consistent way to represent complex dynamical features of various neural networks in a computationally efficient manner.
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Date Issued
2009
PURL
http://purl.flvc.org/FAU/369387
Subject Headings
Molecular neurobiology, Neural networks (Neurobiology), Brain, Mathematical models, Cognitive neuroscience, Recognition (Psychology)
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)
Hurst analysis applied to the study of single calcium-activated potassium channel kinetics
Title
Hurst analysis applied to the study of single calcium-activated potassium channel kinetics.
Creator
Liebovitch, Larry S., Figueiroa, Josed N., Nogueira, Romildo A., Varanda, Wamberto A.
Date Issued
2000-10-07
PURL
http://purl.flvc.org/FAU/165249
Subject Headings
Ion channels-Mathematical models, Memory, Chemical kinetics, Calcium channels, Fractals, Markov processes, Leydig cells, Molecular biology--Statistical methods
Format
Document (PDF)
Myofibril-Inducing RNA (MIR) is essential for tropomyosin expression and myofibrillogenesis in axolotl hearts
Title
Myofibril-Inducing RNA (MIR) is essential for tropomyosin expression and myofibrillogenesis in axolotl hearts.
Creator
Zhang, Chi, Jia, Pingping, Huang, Xupei, Sferrazza, Gian Franco, Athauda, Gagani, Achary, Mohan P., Wang, Jikui, Lemanski, Sharon L., Lemanski, Larry F.
Date Issued
2009-09-03
PURL
http://purl.flvc.org/fcla/dt/3327272
Subject Headings
Ambystoma mexicanum --embryology, Ambystoma mexicanum --genetics, Base Sequence, DNA, Complementary --genetics, Endoderm --physiology, Exons --genetics, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Genes, Recessive, Heart --embryology, Models, Genetic, Molecular Sequence Data, Muscle Proteins --biosynthesis, Muscle Proteins --genetics, Myocardial Contraction --physiology, Protein Isoforms, Reverse Transcriptase Polymerase Chain Reaction, Tropomyosin
Format
Document (PDF)