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Full-Text Articles in Physical Sciences and Mathematics
The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess
The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess
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The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions 1. The experimental data1 evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …
Elucidation Of Active Site And Mechanism Of Metal Catalysts Supported In Nu-1000, Hafeera Shabbir
Elucidation Of Active Site And Mechanism Of Metal Catalysts Supported In Nu-1000, Hafeera Shabbir
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Advances in extraction of shale oil and gas has increased the production of geographically stranded natural gas (primarily consisting of methane (C1) and ethane (C2)) that is burned on site. A potential utilization strategy for shale gas is to convert it into fuel range hydrocarbons by catalytic dehydrogenation followed by oligomerization by direct efficient catalysts. This work focuses on understanding metal cation catalysts supported on metal-organic framework (MOF) NU-1000 that will actively and selectively do this transformation under mild reaction conditions, while remaining stable to deactivation (via metal agglomeration or sintering). I built computational models validated by experimental methods to …
Computational And Experimental Investigations Of Alkali Cation Interactions At The Rutile – Water Interface, Isaac Johnston
Computational And Experimental Investigations Of Alkali Cation Interactions At The Rutile – Water Interface, Isaac Johnston
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Overall, the objective of this dissertation was to investigate the degree of sorption for the alkali cations on rutile to ascertain the impact of different cation properties, such as ion size and charge density, on sorption mechanics as well as probe how the ion may alter the surface – aqueous interface. Initial molecular dynamic simulations and batch experiments showed minimal surface sorption for any alkali cation at relatively low concentrations while simultaneously suggesting the enthalpy of deprotonation shifts slightly in the presence of the alkali cations at different ionic strengths. The cations are likely causing small reorientations of the near-surface …
Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal
Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal
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Molecular dynamics (MD) simulations were carried out for aqueous dipeptides, water over self-assembled monolayer (SAM) surfaces, and the nicotinic acetylcholine receptor (nAChR) ion channel. The main goal is to use advanced methods to increase the accuracy of molecular dynamics simulations while seeking solutions to problems relevant to chemistry, biophysics and materials science. In addition, activation energies of several cyclodimerization reactions were studied quantum mechanically. The simulations of the aqueous dipeptides and SAM surfaces involve modeling and detailed analysis of interfacial water, which is of interest to a range of fields from biology to materials science. For example, water has a …
Hybrid Bond-Order Potential For Silicon, Suleiman Oloriegbe
Hybrid Bond-Order Potential For Silicon, Suleiman Oloriegbe
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ABSTRACT
A new hybrid bond-order potential for silicon is developed. The functional form of the potential is derived from hybrid of expressions from empirical bond-order formalism and first principles approximations. The total energy is expressed as the sum of attractive, repulsive and promotion energies. By introducing a screening function derived from approximations to first principles expressions, the potential is made long-ranged by allowing covalent interactions beyond the first nearest neighbor shell of atoms in agreement with quantum mechanical descriptions of the bonding in silicon. Environment-dependent promotion energy is introduced that accurately accounts for energetic interactions due to changes in hybridization …