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Showing 1 to 20 of 22 for “"CHARMM"”.
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Investigating the effects of different force fields on spring-based normal mode analysis
… step. In the previous work on sbNMA, only the CHARMM force field was explored. In this work, we extend the analyses to AMBER, another widely-used force field. We investigate the dependence of sbNMA's performance on force fields. This work provides also insightful understandings of the …
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Green fluorescent protein as a mechanical sensor
… Implicit solvent molecular dynamics CHARMM simulations demonstrated details inaccessible by AFM and OT methods, such as the linkage dependency of fluorophore environment changes and the energy exchanges between protein components during protein unfolding. Theoretical considerations …
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Reactive Sieving With M-Phenylene Ethynylene Foldamers: Effects of Structural Modification on Reactivity
… the methylsulfonate guests were developed for CHARMM-based molecular dynamics simulations. A total of 14 simulations were performed (500 ps each) and the dihedral angles of the guest alkyl chains were monitored. It was found that many of the dihedral angles could adopt and maintain a gauche …
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FEARCF: Graph-based software library for multidimensional free energy simulations
… this method was restricted to usage within the CHARMM MD software package. Taking inspiration from graph theory and object-orientated design, a successful software library implementation will be demonstrated by presenting results from a range of theories including: classical, ab initio and …
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A computational and synthetic study of poly(benzyl phenyl ether) dendrimers
… and molecular dynamics techniques. The existing CHARMm polymer force field was extended to include parameters for the tricarbonylchromium moiety. The two crystal structures solved as part of the synthetic effort, were used in this regard. The accuracy of the new parameters was assessed by …
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Toward Hydrogenase mimicry : subjecting the problem to three different approaches
… was successfully implemented and validated for CHARMM. After the deprotection of the thiol group in the bioorganometallic approach, the free SH groups were coordinated with iron-carbonyl, so as to mimic the Fe-only Hydrogenase active site. The complexes thus obtained were comprehensively …
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Run-time parallelization: A framework for parallel computation
… quantum mechanical simulation of molecules, and CHARMM for molecular dynamics simulation of organic systems. Therefore, since irregular programs represent a large and important fraction of applications, an automatable framework for run-time parallelization is needed to complement existing and …
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Scope: A Protein Force Field With An Artificial Neural Network Approach to Protein Refinement
… force fields such as those implemented in CHARMM, AMBER, NAMD, and Xplor-NIH have many individual force terms that include bonded and non-bonded energies. While deemed complete, the use of these traditional force fields in ab initio approaches to protein structure determination has been …
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Towards the Understanding of Fluorescence Quenching Mechanisms : Molecular Dynamics Simulations of Dye-Quencher Interactions in Biomolecular Systems
… quantum chemical calculations. Using this method CHARMM force field parameters for the two dyes were derived. The parameters were then used to perform MD simulations on two simplified, but realistic dye quencher systems: MR121/TRP and R6G/TRP. Results of these simulations have given important …
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Structure and Dynamics of Biomembranes containing Cholesterol and other Biologically-Important Sterols : a computational perspective
… and lanosterol, for the program package CHARMM are derived. Subsequently, MD simulations of hydrated sterol:DPPC lipid systems are performed at a biologically-relevant concentration (40\% mol.) at 309K and 323K. The simulations are compared with control simulations of the gel and liquid …
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Development of a force field with condensed phase consistent charges for N,N' - dialkylimidazolium room temperature ionic liquids
… mechanics/Molecular mechanics (QM/MM) methods in CHARMM 35 interfaced with GAMESS-UK was propose. The atomic charges were derived from liquid phase calculations using an iterative procedure. This was carried out for individual ions and cation-anion pairs, for the analysis of charge transfer, …
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Force Field Parameters and Atomistic Surface Models forHydroxyapatite and Analysis of Biomolecular Adsorption at Aqueous Interfaces
… into the polymer consistent force field (PCFF), CHARMM, and AMBER. In addition, models of hydrated HAP surfaces are critical under physiological conditions and have rarely been addressed in previous simulation studies. The proposed force field parameters and surface models of HAP are validated by …
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Accelerator-based look-up table for coarse-grained molecular dynamics computations
… molecule. Many fully atomistic systems such as CHARMM and NAMD have been refined over the years to improve their efficiency. But, simulating complex long-time events such as protein folding remains out reach for atomistic simulations. The consensus view amongst computational chemists and …
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The effect of macromolecular crowding on the structure of the protein complex superoxide dismutase
… modeled using an all atom MD simulation with the CHARMM forcefield and the crystallographically resolved structures of SOD and PEG. Two parallel MD simulations were performed for SOD in water and SOD in 40% PEG for over 150~ns. Over the period of the simulation the SOD structure in 40% PEG did not …
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Molecular Dynamics and Quantum Chemistry Studies of the Protein Bacteriorhodopsin
… by molecular dynamics simulations using a CHARMM force field with special parameters for retinal torsions. Spectral calculations successfully reproduce a shift in absorption maxima between native bacteriorhodopsin and its D85N mutant and demonstrate that the broad absorption spectrum of …
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From Dye Sensitized Solar Cells to Organic Field Effect Transistors: A Computational Investigation into the Structural and Electronic Properties of Novel Phthalocyanines
… a molecular dynamics forcefield within the CHARMM parameterization model was developed specific to these Pcs. This also allows for the simulation of bulk and thin film properties important to various application areas. Finally, we propose a completely solid state dye sensitized solar cell …
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Prediction of Physicochemical Properties For Fe3+ Chelating Agents
… novel Chemistry at HARvard Molecular Mechanics (CHARMM) force fields specifically for use in HPO simulations were developed. These new force fields were validated using Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) MD simulations of the chelators’ behaviour in aqueous solution
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Measuring the effects of reaction coordinate and electronic treatments in the QM/MM reaction dynamics of Trypanosoma cruzi trans-sialidase
… dynamics package. The resulting B3LYP/6-31G/CHARMM crossing trajectory provides a molecular orbital description of the glycosylation reaction. Direct investigation of the underlying potential energy functions for B3LYP/6-31G(d), B3LYP/6-31G and SCC-DFTB/MIO point to the minimal basis set as …
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Evolution and assembly of the ribosome
… the framework of the all-atom molecular dynamics CHARMM force field, with which hundreds of simultaneous folding and binding events between the rRNA and r-protein are captured. Comparison between these simulations with the smFRET experiments reveals folding pathways constructed upon distinct …
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The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
… 34X is achieved. QSL/GAMESS-UK coupled to the CHARMM molecular dynamics package was then used in order to perform accelerated molecular dynamics simulations. Benchmark QM and QM/MM molecular dynamics simulations were performed on cellobiose in vacuo and in a water sphere (45 QM atoms and 24843 …
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