Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 344 for “"Molecular Dynamics (MD)"”.
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GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained Molecular Dynamics Simulations
Molecular Dynamics (MD) simulations provide a molecular-resolution picture of
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ASSESSING MUTATIONS IN A ZINC FINGER DOMAIN OF NF-κB ESSENTIAL MODULATOR (NEMO) USING MOLECULAR DYNAMICS SIMULATIONS
Molecular dynamics (MD) simulations permit the probing of biomolecular systems in
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Ion Implantation Damage in Solids
… and roughening processes were studied using Molecular Dynamics (MD) computer simulation. The simulations on self-ion bombarded W showed the effect of the surface on defect production and the roughening of the surface. The simulations on the CuTi, Ag and Ni with amorphous and crystalline …
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Theoretical Studies of the Solvation, Dynamics, and Photochemistry of Ethylene, Retinal Protonated Schiff Base, Oligocellulose, and Gd(III) Clusters
The solution dynamics of an anomerically pure series of cellulose oligomers have been studied by 13C NMR relaxation techniques and compared to molecular dynamics (MD) simulations. We found evidence of anisotropic motion across the series, with experimentally determined order parameters (S 2) …
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Nanoscale Patterning of Chemical Order Introduced by Displacement Cascades in Irradiated Alloys
… predictions on the Ni3Al compound by combining molecular dynamics (MD) and KMC simulations. For 1MeV Kr and 70keV He ions, MD simulations are used to simulate the disordered zones, which are then incorporated into KMC simulations to reach long irradiation times. These simulations indicate that …
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Computer simulations of Fréchet dendrimers in solutions
The structure and dynamics of dendrimers in solution are studied through nanosecond atomistic Molecular Dynamics (MD) simulations of explicitly solvated Fréchet dendrimers, generations G1 to G5. The properties of these dendrimers are investigated in four solvent invironments: vacuum and water …
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Molecular dynamics modeling of normal shock waves in monatomic and polyatomic gas mixtures.
Large-scale molecular dynamics (MD) simulations using the Lennard-Jones potential are performed to study the structure of normal shock waves in dilute Nitrogen and mixtures of Helium-Argon and Helium-Xenon. The use of realistic MD simulations of normal shock waves promises to provide a more …
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Molecular Dynamic Simulation of Bio-molecular Dynamics, Folding, and Assembly
A major goal in molecular biophysics is to understand how biomolecules fold into specific structures to carry out cellular processes to result in a functioning organism. Computational molecular dynamics (MD) simulations can characterize biomolecules at a microscopic level. These indispensable …
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Atomistic studies on irradiation damage in iron
… induced by radiation have been simulated using molecular dynamics (MD). The number and type of defects produced are compared for pure iron and iron with a small hydrogen concentration. Second, the inter- action energy between point defects and line dislocations has been calculated for a number …
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Molecular dynamics simulation of mechanical behavior of nanoporous copper foams
… behavior of nanoporous copper was simulated. Molecular dynamics (MD) simulations were performed at room temperature using the Mishin potential on tetrakaidecahedron foam structures. In closed-celled foams close agreement is observed between simulated Young's moduli and constitutive theory. …
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Model and analysis of MoS2 nanopore biomolecule detection via membrane current
… In combination with experimental study and molecular dynamics (MD) calculation, a comprehensive physical analysis of various resistive effects involved in the electronic detection of a single biomolecule in a nanopore of a MoS2 nanoribbon is presented. The analysis emphasizes the effects of …
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Molecular dynamics simulations of metallic friction and of its dependence on electric currents: development and first results
We have extended the HOLA molecular dynamics (MD) code to run slider-on-block friction experiments for Al and Cu. Both objects are allowed to evolve freely and show marked deformation despite the hardness difference. We recover realistic coefficients of friction and verify the importance of …
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Multiscale modeling of two-dimensional materials : structures, properties, and designs
… the development of a scaled-up model, e.g., molecular dynamics, from quantum mechanics, should be validated against the experiments. Two-dimensional (2D) materials provide excellent platforms to verify theoretical models by directly comparing atomic structures and properties with advanced …
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Atomistic engineering of fluid Structure at the fluid-solid interface
… scale is comparable to the fluid's internal (molecular) length scale. Elucidating the physical principles governing nanoconfined fluids is critical for many pursuits in nanoscale engineering. In this thesis, we present several theoretical and computational results on the structure and …
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FEARCF: Graph-based software library for multidimensional free energy simulations
… library, enabling it to be interfaced with other molecular dynamics (MD) software packages. There exist many methods to calculate the free energy of molecular systems, an important quantity when studying chemical reactions and molecular structures. One of these, FEARCF, was developed at the …
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Insight into the structure and reactivity at solid-liquid interfaces
… of Pt(111) as a catalytic surface, using Molecular Dynamics (MD) coupled with Density Functional Theory (DFT), to calculate the dynamics and energetics of the reacting systems. Whereas the last chapter deals with using high dimensional neural network (HDNN) potentials to describe the …
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Finite Opening of Propagating Shear Cracks
Molecular Dynamics (MD) simulations of shear-dominated crack propagation by Abraham and Gao (2000) showed that there was finite crack opening when the crack propagated at a sub-Rayleigh speed while the crack opening became negligible when the crack propagated faster than the shear wave speed. On …
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Techniques for identifying long-range residue correlations in the fifth binding module of LDLR
… Markov models (HMMs) and the other applying molecular dynamics (MD), were implemented to identify a comprehensive set of residue couplings, as well as provide possible explanations for the correlations. HMMs were employed to model the secondary structural elements of proteins in order to …
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Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations
… leading fields is computational biophysics where molecular dynamics (MD) simulations provide microscopic resolution details of how biomolecules move, fold, and assemble into intricate complexes that perform biological functions. However, it still remains a challenge to accurately perform MD …
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