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Articles 1 - 4 of 4
Full-Text Articles in Computational Chemistry
Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers
Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers
Legacy Theses & Dissertations (2009 - 2024)
Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …
An Ims-Ms/Md Workflow For Determining Higher Order Structure And Dynamics Of Nucleic Acids, Rebecca D'Esposito
An Ims-Ms/Md Workflow For Determining Higher Order Structure And Dynamics Of Nucleic Acids, Rebecca D'Esposito
Legacy Theses & Dissertations (2009 - 2024)
Ion mobility spectrometry - mass spectrometry (IMS-MS) has potential for the investigation of structure and dynamics in large biopolymers, which will come to full fruition only with a firmer understanding of how to interpret the experimental data. Numerous studies have employed elements of nucleic acid (NA) secondary structure, such as duplexes and hairpins, to explore the relationships between structure, experimental conditions, and actual observations. When combined with molecular dynamics simulations (MDS), IMS-MS can be effectively employed to perform structural elucidation of biomolecules that are not readily amenable to established techniques employed for structural analysis.
Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi
Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi
Legacy Theses & Dissertations (2009 - 2024)
MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …
Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan
Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan
Legacy Theses & Dissertations (2009 - 2024)
Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …