Digital Commons Network^™

A Polarizable Molecular Dynamics Potential For Molten Salt Property Prediction, Jared Thurgood

Theses and Dissertations

The present study attempts to find an alternate computational tool to model the complex physical interactions within the molten salt FLiNaK in a way that is both efficient and accurate. Additionally, this study seeks to describe the effects of several different types of impurities on the FLiNaK salt system. This study selects two different polarizable force fields, the AMOEBA polarizable approach and the polarizable ion model, to determine the density and the structure of the impure FLiNaK salt mixtures at typical operating temperatures in molten salt reactors (between 500-900 °C). This study conducts ab initio molecular dynamics (AIMD) simulations and …

Computational Modeling Of Energy Landscapes And Trajectory Studies Of Fundamental Organometallic Reactions, Joshua I. Wheeler

Theses and Dissertations

Organometallic reactions are a fundamental class of chemical transformations. The mechanisms of organometallic reactions are routinely modeled by calculating intermediates and transition-state structures on a potential energy surface with density functional theory (DFT). The translation of these calculated structures to a reaction mechanism is typically done under the umbrella of statistical transition state theory. This dissertation reports the use of DFT calculations and quasiclassical direct dynamics trajectories to explore the possibility of nonstatistical dynamic effects in organometallic reactions. Chapter 1 provides a brief review of potential energy surfaces, transition state theory, dynamics trajectories, and a review of previous dynamics studies …

Development Of The Tlvmie Force Field And A Standardized Methodology For Improved Pure-Component And Mixture Liquid Viscosity Predictions, Daniel J. Carlson

Theses and Dissertations

Existing viscosity prediction methods and relevant literature are reviewed. An exhaustive review of group contribution, corresponding states, and interpolative prediction methods finds that even the best of these models produces large prediction errors and often require significant experimental data. Molecular dynamics simulation techniques for viscosity prediction are evaluated and compared to one another to determine the best choice for this work. A thorough investigation finds that Equilibrium Molecular Dynamics (EMD) simulations are the best option for reproducible and reliable liquid viscosity predictions. The many tuning parameters available in molecular dynamics simulations are investigated for their effects on prediction uncertainty and …

Semiflexible Oligomers Crystallize Via A Cooperative Phase Transition, Pierre Kawak, Dakota S. Banks, Douglas R. Tree

Faculty Publications

Semicrystalline polymers are ubiquitous, yet despite their fundamental and industrial importance, the theory of homogeneous nucleation from a melt remains a subject of debate. A key component of the controversy is that polymer crystallization is a non-equilibrium process, making it difficult to distinguish between effects that are purely kinetic and those that arise from the underlying thermodynamics. Due to computational cost constraints, simulations of polymer crystallization typically employ non-equilibrium molecular dynamics techniques with large degrees of undercooling that further exacerbate the coupling between thermodynamics and kinetics. In a departure from this approach, in this study, we isolate the near-equilibrium nucleation …

Molecular Dynamics Of Organometallic Systems, Ryan Wayne Carlsen

Theses and Dissertations

Metal-mediated organometallic reactions are critical for both catalytic and synthetic chemistry. Density functional theory (DFT) potential-energy calculations are routinely used with a transition-state theory type of approach to understand and predict the reaction mechanisms of organometallic reactions. However, these calculations do not include atomic momentum and thus ignore dynamic effects. Molecular dynamics is a powerful tool for elucidating mechanistic details of chemical reactions. In this dissertation, quasiclassical molecular dynamics studies reveal key mechanistic details about several fundamental organometallic reactions. Chapter 1 provides a brief overview of key molecular dynamics details. Chapters 2-4 provide details on for three classic organometallic reactions …

Molecular Dynamic Simulation Of Protein Devices And The Parameterization Of Azides And Alkynes For Use In Unnatural Amino Acid Models, Addison Kyle Smith

Theses and Dissertations

Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device functionalization cannot be executed, and full-protein screens of all possible …

Molecular Dynamic Simulation Of Protein Devices And The Parameterization Of Azides And Alkynes For Use In Unnatural Amino Acid Models, Addison Kyle Smith

Theses and Dissertations

Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device functionalization cannot be executed, and full-protein screens of all possible …

Governing Dynamics Of Divalent Copper Binding By Influenza A Matrix Protein 2 His37 Imidazole, Kelly Lewis Mcguire

Theses and Dissertations

Influenza A is involved in hundreds of thousands of deaths globally every year resulting from viral infection-related complications. Previous efforts to subdue the virus by preventing proper function of wild-type (WT) neuraminidase (N), and M2 proteins using oseltamivir and amantadine (AMT) or rimantadine (RMT), respectively, exhibited success initially. Over time, these drugs began exhibiting mixed success as the virus developed drug resistance. M2 is a proton channel responsible for the acidification of the viral interior which facilitates release of the viral RNA into the host. M2 has a His37-tetrad that is the selective filter for protons. This protein has been …

An Atomistic Approach For The Survey Of Dislocation-Grain Boundary Interactions In Fcc Nickel, Devin William Adams

Theses and Dissertations

It is well known that grain boundaries (GBs) have a strong influence on mechanical properties of polycrystalline materials. Not as well-known is how different GBs interact with dislocations to influence dislocation movement. This work presents a molecular dynamics study of 33 different FCC Ni bicrystals subjected to mechanical loading to induce incident dislocation-GB interactions. The resulting simulations are analyzed to determine properties of the interaction that affect the likelihood of transmission of the dislocation through the GB in an effort to better inform mesoscale models of dislocation movement within polycrystals. It is found that the ability to predict the slip …

Computational Modelling Of Peptides Containing Non-Standard Amino Acids, David W. Kastner

Undergraduate Honors Theses

Peptides represent a class of abundant and potent pharmaceutic compounds. Despite their appeal, the design, synthesis, and engineering of biologically relevant peptides remain a challenge. Chapter 1 introduces the various computational methods that will be used. Chapter 2 focuses on the incorporation of a special class of amino acids called bulky dehydroamino acids into the turn of β-hairpins to proteolytically stabilize peptides. Our results suggest that dehydroamino acids confer proteolytic stability by favoring a more folded state. Chapter 3 describes the structural calculations of a rare anticancer peptide called Yaku’amide using a combined molecular mechanics/quantum mechanics hybrid method. The …

Stress Modulated Grain Boundary Mobility, Derek Michael Lontine

Theses and Dissertations

This thesis consists of a thermodynamically based kinetic model that more accurately predicts grain boundary mobility (GBM) over a large range of thermodynamic states including changes in temperature, pressure and shear stress. The form of the model was validated against calculated GBM values for Al bicrystals via molecular dynamics (MD) simulations. A total of 98,786 simulations were performed (164 different GBs, each with a minimum of 250 different thermodynamic states, and 2 different driving forces). Methodology for the computation of the GBM via MD simulations is provided. The model parameters are directly linked to extensive thermodynamic quantities and suggest potential …

Non-Schmid Effects And Criteria For Dislocation Nucleation On Different Slip Systems At Grain Boundaries, Richard Durtschi Wyman

Theses and Dissertations

Criteria for grain boundary dislocation nucleation are developed. A bicrystal containing two grain boundaries is placed under varying triaxial stress states using molecular dynamics. The local resolved shear, normal, and co-slip stresses needed for grain boundary dislocation nucleation are found. A framework is developed to detect the slip system grain boundary dislocation nucleation occurs on. A survey of the different ways grain boundary dislocation nucleation occurs in the sample shows a single grain boundary can nucleate dislocations in a rich variety of ways. Using the nucleation system and resolved stress values, criteria for grain boundary dislocation nucleation on different slip …

Verifying Molecular Dynamics Using Dielectric Spectroscopy, Joshua Dee Smith

Theses and Dissertations

The electrical properties of proteins in solution are important for their structure and function. Computational biophysics studies of proteins need accurate parameters to ensure that numerical simulations match physical reality. Past work in this eld has compared the electrical properties of proteins obtained from dielectric spectroscopy to numerical simulations of proteins in water with adjustment of pKa values to try to capture the inevitable changes in electrical conformation that will occur in a complex structure such as a folded protein. However, fundamental veri cation of the charge parameters of the amino acid building blocks in common molecular dynamics software packages …

Molecular Dynamics Of Nystatin Dimers, Brian Knudson, Dr. Dixon J. Woodbury

Journal of Undergraduate Research

As the original goal of the project was to investigate the channel-forming mechanism of Nystatin, I began the project as outlined in the proposal.

Developing A New Fluctuating-Charge Force Field For Charmm, Soren Harward, David Busath

Journal of Undergraduate Research

Molecular Dynamics (hereafter abbreviated MD) is a method of simulating on a computer the behavior of molecules. For over twenty years, it had been a valuable tool that has allowed chemists and physicists to observe chemical interactions that would are difficult or impossible to measure with standard laboratory equipment. The rapid growth of computing power has made feasible simulations of larger and larger systems, so that now biologists can use MD to study the complex chemistry of living organisms.

A Polarizable Reactive Force Field For Water To Enable Molecular Dynamics Simulations Of Proton Transport, Abhishek Asthana, Dean R. Wheeler

Faculty Publications

A new polarizable water model is developed for molecular dynamics (MD) simulations of the proton transport process. The interatomic potential model has three important submodels corresponding to electrostatic interactions, making and breaking of covalent bonds, and treatment of electron exchange and correlation through a van der Waals potential. A polarizable diffuse charge density function was used to describe Coulombic interactions between atoms. Most of the model parameters were obtained from ab initio data for a lone water molecule. Molecules respond realistically to their electrochemical environment by the use of coupled fluctuating charge and fluctuating dipole dynamics, which controlled the charge …

Liquid Dielectric Spectroscopy And Protein Simulation, Brett Lee Mellor

Theses and Dissertations

Protein electrical properties have been studied using dielectric relaxation measurements throughout the past century. These measurements have advanced both the theory and practice of liquid dielectric spectroscopy and have contributed to understanding of protein structure and function. In this dissertation, the relationship between permittivity measurements and underlying molecular mechanisms is explored. Also presented is a method to take molecular structures from the Protein Data Bank and subsequently estimate the charge distribution and dielectric relaxation properties of the proteins in solution. This process enables screening of target compounds for analysis by dielectric spectroscopy as well as better interpretation of protein relaxation …

Chemical Potential Perturbation: A Method To Predict Chemical Potential Using Molecular Simulations, Stan G. Moore

Theses and Dissertations

A new method, called chemical potential perturbation (CPP), has been developed to predict the chemical potential as a function of composition in molecular simulations. The CPP method applies a spatially varying external potential to the simulation, causing the composition to depend upon position in the simulation cell. Following equilibration, the homogeneous chemical potential as a function of composition can be determined relative to some reference state after correcting for the effects of the inhomogeneity of the system. The CPP method allows one to predict chemical potential for a wide range of composition points using a single simulation and works for …

Prediction Of Fluid Viscosity Through Transient Molecular Dynamic Simulations, Jason Christopher Thomas

Theses and Dissertations

A novel method of calculating viscosity from molecular dynamics simulations is developed, benchmarked, and tested. The technique is a transient method which has the potential to reduce CPU requirements for many conditions. An initial sinusoidal velocity profile is overlaid upon the peculiar velocities of the individual molecules in an equilibrated simulation. The transient relaxation of this initial velocity profile is then compared to the corresponding analytical solution of the momentum equation by adjusting the viscosity-related parameters in the constitutive equation that relate the shear rate to the stress tensor. The newly developed Transient Molecular Dynamics (TMD) method was tested for …

Mpsa Effects On Copper Electrodeposition Investigated By Molecular Dynamics Simulations, Clint G. Guymon, John N. Harb, Richard L. Rowley, Dean R. Wheeler

Faculty Publications

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulations to provide insight into the molecular function of an organic additive (3-mercaptopropanesulfonic acid or MPSA) important in superconformal electrodeposition. We also investigate how the presence of sodium chloride affects the surface adsorption and surface action of MPSA as well as the charge distribution in the system. We find that NaCl addition decreases the adsorption strength of MPSA at a simulated copper surface and attenuates …

Mpsa Effects On Copper Electrodeposition Investigated By Molecular Dynamics Simulations, John N. Harb, Richard L. Rowley, Dean R. Wheeler, Clint G. Guymon

Faculty Publications

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulation.

Transient Molecular Dynamics Simulations Of Viscosity For Simple Fluids, Richard L. Rowley, Jason C. Thomas

Faculty Publications

A transient molecular dynamics (TMD) method has been developed for simulation of fluid viscosity. In this method a sinusoidal velocity profile is instantaneously overlaid onto equilibrated molecular velocities, and the subsequent decay of that velocity profile is observed. The viscosity is obtained by matching in a least-squares sense the analytical solution of the corresponding momentum transport boundary-value problem to the simulated decay of the initial velocity profile. The method was benchmarked by comparing results obtained from the TMD method for a Lennard-Jones fluid with those previously obtained using equilibrium molecular dynamics (EMD) simulations. Two different constitutive models were used in …

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to average kinetic energy is …

Mpsa Effects On Copper Electrodeposition: Understanding Molecular Behavior At The Electrochemical Interface, Clint Gordon Guymon

Theses and Dissertations

In this work the structure of the electrochemical metal-liquid interface is determined through use of quantum mechanics, molecular simulation, and experiment. Herein are profiled the molecular dynamics details and results of solid-liquid interfaces at flat non-specific solid surfaces and copper metal electrodes. Ab initio quantum-mechanical calculations are reported and define the interatomic potentials in the simulations. Some of the quantum-mechanical calculations involve small copper clusters interacting with 3-mercaptopropanesulfonic acid (MPSA), sodium, chloride, bisulfate and cuprous ions. In connection with these I develop the electrode charge dynamics (ECD) routine to treat the charge mobility in a metal. ECD bridges the gap …

Effects Of Solvent Model Flexibility On Aqueous Electrolyte Behavior Between Electrodes, Richard L. Rowley, John N. Harb, Clint G. Guymon, Matthew L. Hunsaker, Douglas Henderson

Faculty Publications

Molecular dynamics simulations have been carried out for aqueous electrolyte solutions between model electrode surfaces. The effect of solvent model flexibility on bult and double layer properties was observed for electrode surface charge densities of 0, 0.1 and 0.2 and ion concentrations of 0, 0.5 and 1 M. Two flexible models were used to isolate the effects of flexibility from the effects of a change in the condensed-phase dipole moment. Model flexibility increases the pure water self-diffusion coefficient while a larger liquid diple moment substantially decreases it. There is an increase in ion contact adsorption and counter ion affinity with …

Slab-Geometry Molecular Dynamics Simulations: Development And Application To Calculation Of Activity Coefficients, Interfacial Electrochemistry, And Ion Channel Transport, Paul S. Crozier

Theses and Dissertations

Methods of slab-geometry molecular dynamics computer simulation were tested, compared, and applied to the prediction of activity coefficients, interfacial electrochemistry characterization, and ion transport through a model biological channel-membrane structure. The charged-sheets, 2-D Ewald, corrected 3-D Ewald, and corrected particle-particle-particle-mesh (P3M) methods were compared for efficiency and applicability to slab-geometry electrolyte systems with discrete water molecules. The P3M method was preferred for long-range force calculation in the problems of interest and was used throughout.

The osmotic molecular dynamics method (OMD) was applied to the prediction of liquid mixture activity coefficients for six binary systems: methanol/n-hexane, n-hexane/n-pentane, methanol/water, chloroform/acetone, n-hexane/chloroform, methanol/ …

Determination Of A Methane Intermolecular Potential Model For Use In Molecular Simulations From Ab Initio Calculations, Richard L. Rowley, Tapani A. Pakkanen

Faculty Publications

The possibility of obtaining an accurate site-site potential model suitable for use in molecular dynamics (MD) simulations of methane from ab initio calculations has been explored. Counterpoise-corrected (CPC), supermolecule, ab initio energies at the MP2/6-311 + G(2df,2pd) level were computed for eleven relative orientations of two methane molecules as a function of C-C separation distance. C-C, C-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for rigid methane molecules were regressed from the ab initio energies, and the resultant model accurately reproduced the ab initio energies. The model suggests that C-H attractions are dominant in weakly binding the …

Computer Simulations Of Branched Alkanes: The Effect Of Side Chain And Its Position On Rheological Behavior, Richard L. Rowley, Tapani A. Pakkanen, Maija Lahtela, Mikko Linnolahti

Faculty Publications

Nonequilibrium molecular dynamics simulations have been performed on model fluids representing eicosane isomers in order to investigate the effect of branching and side chain position on fluid rheology. A heterogeneous, united-atom model with 20 Lennard-Jones interaction sites located at carbon centers was used to model the fluids. Vibrations and bond rotations were frozen, but torsional rotation was included. It was found that viscosity increases significantly from the n-alkane structure to a branch on carbon 2, but the movement of the branch along the carbon backbone has a smaller increasing than decreasing effect. The size of the group in a branched …

Predicting The Viscosity Of Alkanes Using Nonequilibrium Molecular Dynamics: Evaluation Of Intermolecular Potential Models, Richard L. Rowley, William Allen

Faculty Publications

Nonequilibrium molecular dynamics (NEMD) viscosity simulations of branched and linear alkanes at liquid densities were performed using both united-atom (UA) and all-atom (AA) intermolecular potential models in order to study the relative efficacy of the models in predicting fluid viscosity. Both models were used in conjunction with fixed bond lengths and bond angles, but different torsional potentials were investigated. The commonly used Ryckaert—Bellemans intermolecular potential model, which accurately predicts viscosities for short straight-chain alkanes, produced values for branched and long-chain alkanes that were significantly below experimental values. Likewise, a more complex UA model that uses transferrable site potentials and is …

Note On The Number Dependence Of Nonequilibrium Molecular Dynamics Simulations Of The Viscosity Of Structured Molecules, Richard L. Rowley, James F. Ely

Faculty Publications

Nonequilibrium molecular dynamics simulations have been performed for a system of 512 four-site models representing n-butane molecules. The results are compared to simulations previously reported for 125 molecules to check a recently reported number dependence in such simulations. A small system size dependence was observed at low shear rates, but the rheological behavior is not affected. Considerably greater certainty is obtained using larger systems.