Molecular dynamics is a technique in which the trajectories of a group of particles are calculated as a function of time by integrating the equations of motion. In this thesis we study the use of molecular dynamics for atoms in a crystal. A model is introduced which describes interactions of a physical system with an external heat reservoir in molecular dynamics simulations. This is accomplished by the addition of a "virtual variable" to the Hamiltonian which is used to scale time. Aspects of this model are discussed and examples are presented for a simple system. Similarly, a constant pressure model is introduced in which additional virtual volume variables are added to the Hamiltonian. The volume and shape of the molecular dynamics cell are now free to vary. Simple examples are discussed. Aspects of the computer programs and the algorithms are explained. Particular attention is focused on the methods used to integrate the equations of motion and to calculate the coulomb interactions. Examples of simulations using a zirconium oxide crystal are presented. We study the effects of heat bath and pressure bath simulations, both separately and in combination. Various features of the behavior are investigated with the primary focus on phase changes, numerical errors, and parameters describing the heat and pressure baths. / Graduation date: 1996

Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Ludovice, Pete; Committee Member: Chen, Rachel; Committee Member: Harvey, Steve; Committee Member: Sambanis, Athanassios; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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Polymer materials stand on a very significant position in the materials industry area. The presence of organoclay nanocomposites reinforces polymer materials on many properties like strength, tensile and so on. Most previous studies on the characteristics of organoclays and polymer nanocomposites were based on the experimental approaches such as XRD (X-ray Diffraction) and NMR (Nuclear Magnetic Resonance). These methods have achieved successfully on the basic analysis of chains and layering structures of polymer nanocomposites. However, information on the molecular level cannot be provided by those approaches. MD (Molecular Dynamic) simulation method could be employed to develop further information on the molecular level about organoclays and interlayer structure polymer nanocomposites. In the research of ODTMA-MMT (Octadecyltrimethylammonium-Montmorillonite) organoclay simulation, we find that the strong layering behaviour of interlayer ODTMA molecules is present with the same minimum distance between nitrogen atoms and MMT surface in different T/O (Tetrahedral vs. Octahedral) ratio cases. Nitrogen atoms sit right above the corresponding hexagonal cavities, which is in agreement with the previous research. The interaction energy between surfactants and MMT clay will reach the lowest point when substitution ratio of tetrahedral and octahedral (T/O) is equal to 1:1. Moreover, MSD (Mean Square Displacement) and diffusion coefficient of different models under same CEC (Charge Exchange Capacity) condition are inverse ratio to the T/O proportion. In nylon6 polymer nanocomposites, sodium cations which exist originally in ensemble as charge balancer are absorbed much closer to MMT surface than the organic components in the nylon 6 ODTMA-MMT ensemble. Sodium atoms or nitrogen atoms in surfactants both have higher MSD and coefficients than those atoms in the organic-modified clays. In the exfoliated nylon 6 ODTMA-MMT nanocomposites, pair correlation has been analysed instead of density profile. Layering packing structure is also shown through this analysis, which is also consistent with previous work.

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Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2008. / Committee Chair: Jianmin Qu; Committee Member: David McDowell; Committee Member: Elisa Riedo; Committee Member: Min Zhou; Committee Member: Mo Li.

The biological functions of proteins often rely on structural changes and the rates at which these conformational changes occur. Studies show that regions of a protein which are known to be involved in enzyme catalysis or in contact with the substrate are identifiable by NMR spectroscopy to be more flexible, evidenced through measuring order parameters of specific bond vectors. While generalized NMR can allow for detailed characterization of the extent and time scales of these conformational fluctuations, NMR cannot easily produce the structures of sparsely populated intermediates nor can it produce explicit complex atomistic-level mechanisms needed for the full understanding of such processes. Practically, preparing a protein with appropriate isotropic enrichment to study a set of specific bond vectors experimentally is challenging as well. Oftentimes, measuring the dynamics of neighboring bond vectors are necessitated. Detailed studies of the coupling interactions among specific residues and protein regions can be fulfilled by the use of molecular dynamics (MD) simulations. However, MD simulations rely on the ergodic hypothesis to mimic experimental conditions, requiring long simulation times. Simulations are additionally limited by the availability of accurate and reliable molecular mechanics force fields, which continue to be improved to better match experimental data. Much can also be learned from chemical theory and simulations to improve the methods in which experimental data is processed and analyzed. The overarching goals of this thesis are to improve upon the results generated by existing methods in NMR spin relaxation spectroscopy, whether that be through: (i) improving analytical techniques of raw NMR data or through (ii) supporting experimental results with atomistically-detailed MD simulations. The majority of this work is exemplified through the protein Escherichia coli ribonuclease HI (ecRNH). Ribonuclease HI (RNase H) is a conserved endonuclease responsible for cleaving the RNA strand of DNA/RNA hybrids in many biological processes, including reverse transcription of the viral genome in retroviral reverse transcriptases and Okazaki fragment processing during DNA replication of the lagging strand. RNase H belongs to a broader superfamily of nucleotidyl-transferases with conserved structure and mechanism, including retroviral integrases, Holliday junction resolvases, and transposases. RNase H has historically been the subject of many investigations in folding, structure, and dynamics. In support of the first aim, we discuss new methods of obtaining more precise experimental results for order parameters and time constants for the ILV methyl groups. Deuterium relaxation rate constants are determined by the spectral density function for reorientation of the C-D bond vector at zero, single-quantum, and double-quantum 2H frequencies. We interpolate relaxation rates measured at available NMR spectrometer frequencies in order to perform a joint single/double-quantum analysis. This yields approximately 10-15% more precise estimates of model-free parameters and consequently provides a general strategy for further interpolation and extrapolation of data gathered from existing NMR spectrometers for analysis of 2H spin relaxation data in biological macromolecules. In support of the second aim, we calculate autocorrelation functions and generalized order parameters for the ILV methyl side chain groups from MD simulation trajectories to assess the orientational motions of the side chain bond vectors. We demonstrate that motions of the side chain bond vectors can be separated into: (i) fluctuations within a given dihedral angle rotamer, (ii) jumps among the different rotamers, and (iii) motions from the protein backbone itself, through the C-alpha carbon. We are able to match order parameters of constitutive motions to conventionally calculated order parameters with an R2= 0.9962, 0.9708, and 0.9905 for Valine, Leucine, and Isoleucine residues, respectively. Some longer side chain residues such as Leucine and Isoleucine have correlated χ1 and χ2 dihedral angle rotational motions. This provides a method of evaluating the relative contributions of each constitutive motion towards the overall flexibility of a side chain. Multiple contributors of motion are possible for intermediate and low order parameters, signifying more flexible residues. While developing protocols for MD simulations, we evaluate the effects of running 1-microsecond long simulations and compare them to solution state NMR spectroscopy. If the overall tumbling time is removed from the simulation, then analysis blocks of 5-10 times the tumbling time is optimal to eliminate contributions from slower dynamics, which would not normally be measured in solution state NMR spectroscopy. We also assess the quality of the TIP4P(-EW) water model over TIP3P; although TIP4P simulates the isotropic tumbling time well for ecRNH, internal motions are equally not affected by either water model due to well-segregated motions. Additionally, the TIP4P water model does not appear to be able to replicate an axially symmetric shape for ecRNH (ecRNH is mostly spherical and only slightly axially symmetric). The final work of this thesis returns to the first overarching aim; we develop a specialized method that utilizes probability distribution functions to model spectral density functions. We derive the inverse Gaussian probability distribution function from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximum entropy. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. The approach is validated using 15N backbone relaxation data for the intrinsically disordered, DNA-binding region of the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA.

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 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. / by Meha Garg. / Thesis (M.S.C.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

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 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. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.