Engineering Commons^™

Study Of Amorphous Boron Carbide And Hydrogenated Boron Carbide Materials Using Molecular Dynamics And Hybrid Reverse Monte Carlo, Rajan Khadka

MSU Graduate Theses

We present a computational study of amorphous boron carbide (a-B_xC) models using Molecular Dynamics (MD) studied with Stillinger-Weber (SW) and ReaxFF potential. The atomic structure factor (S(Q)), radial distribution function (RDF) and bond lengths comparison with other experimental and ab initio models shows that a random arrangement of icosahedra (B₁₂, B₁₁C) interconnected by chains (CCC, CBC) are present in a-B_xC. Afterward, Hybrid Reverse Monte Carlo (HRMC) technique is used to recreate a-B_xC structures. The existing SW potential parameters of Boron are optimized for the α-rhombohedral (Icosahedral B_{12 …}

Molecular Dynamics Simulations Of Interaction Of Dna Nucleotides And Lignin Oligomers With Small Molecules And Interfaces, Xinjie Tong

LSU Doctoral Dissertations

Molecular dynamics (MD) simulations of interaction of DNA nucleotides with self-assembled monolayers (SAMs) provide valuable information that is critical to the development of a new DNA sequencing technique. We investigated the interactions and transport characteristics of mononucleotides moving through nanoslits with SAMs-covered surfaces. Our simulations focused on nanoslits in which the walls were composed of three different types of SAMs: methylformyl terminated, methyl terminated, and phenoxy terminated. The results demonstrated that the phenoxy terminated surfaces have the shortest required nanoslits length for nucleotides separation.

Using MD simulations, we also investigated the interaction of mono-lignin and oligo-lignols with lipid bilayers and …

Combined Molecular Dynamics And Phase Field Simulation Of Crystal Melt Interfacial Properties And Microstructure Evolution During Rapid Solidification Of Ti-Ni Alloys, Sepideh Kavousi

LSU Doctoral Dissertations

Phase field method has become a popular tool to investigate the microstructure evolution during the solidification. Quantitative predictions using this method is still limited, and in this dissertation, we try to study this problem from different perspectives.

Most of the phase field models consider the solid-liquid interface to be in local equilibrium. Solidification during some manufacturing processes like selective laser melting, and electron beam additive manufacturing is rapid and far from equilibrium which can result in supersaturated solid solutions, segregation-free crystals, or metastable phases. Before obtaining any conclusions from the phase field simulations, we must know the answer for “which …

Mechanical Properties Of Hydrogenated Amorphous Silicon (A-Si:H) Particles, Taizhi Jiang, Fardin Khabaz, Aniket Marne, Chenglin Wu, Raluca Gearba, Revanth Bodepudi, Roger T. Bonnecaze, Kenneth M. Liechti, Brian A. Korgel

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

A nanoindenter was used to compress individual particles of hydrogenated amorphous silicon (a-Si:H) ranging in diameter from 290 nm to 780 nm. The colloidal synthesis used to produce the particles enables the hydrogen content to be manipulated over a wide range, from about 5 at. % to 50 at. %, making these a-Si:H particles promising for applications in lithium ion batteries, hydrogen storage, and optical metamaterials. Force-displacement curves generated using a tungsten probe flattened with focused ion beam exhibited elastic and then plastic deformations, followed by fracture and crushing of the particles. For particles with 5% and 50% H, Young's …

Analysis Of Individual Molecular Dynamics Snapshots Simulating Wetting Of Surfaces Using Spheroidal Geometric Constructions, Aleksandr Abramov, Stefan Iglauer

Research outputs 2014 to 2021

Accurate characterization of wettability of minerals is important for efficient oil recovery and carbon geosequestration. In studies where molecular dynamics simulations are used to compute the contact angle, emphasis is often placed on results or theoretical details of the simulations themselves, overlooking potentially applicable methodologies for determination of the contact angle. In this manuscript, a concept of a method utilizing spheroidal geometric constructions to estimate the contact angle of a water droplet on a silica surface in carbon dioxide atmosphere is outlined and applied to the final snapshots of two molecular dynamics simulation runs. Two carbon dioxide pressures and two …

Computational Studies Of Thermal Properties And Desalination Performance Of Low-Dimensional Materials, Yang Hong

Department of Chemistry: Dissertations, Theses, and Student Research

During the last 30 years, microelectronic devices have been continuously designed and developed with smaller size and yet more functionalities. Today, hundreds of millions of transistors and complementary metal-oxide-semiconductor cells can be designed and integrated on a single microchip through 3D packaging and chip stacking technology. A large amount of heat will be generated in a limited space during the operation of microchips. Moreover, there is a high possibility of hot spots due to non-uniform integrated circuit design patterns as some core parts of a microchip work harder than other memory parts. This issue becomes acute as stacked microchips get …

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 Investigation Of The Interactions Between Bioactive Compounds And Biological Assemblies, Tye D. Martin

Biomedical Engineering ETDs

Small, biologically active molecules with unique properties and applications are potential solutions to a wide range of threats to global health including infectious agents and neurodegenerative disease. Experimental studies on a class of oligomeric p-phenylene ethynylenes (OPEs) have shown potential both as bioactive antimicrobials and fluorescent sensing agents for tracking amyloid-β (Aβ) aggregates found in Alzheimer’s Disease (AD). A second type of small molecule with potential applications in AD therapy, curcumin, has been found to interfere with Aβ fibril growth. Curcumin also attenuates Aβ-membrane interactions and Aβ toxicity. Our goal has been to use computational techniques to better understand the …

Predicting The Mechanical Properties Of Nanocomposites Reinforced With 1-D, 2-D And 3-D Nanomaterials, Scott Edward Muller

Graduate Theses and Dissertations

Materials with features at the nanoscale can provide unique mechanical properties and increased functionality when included as part of a nanocomposite. This dissertation utilizes computational methods at multiple scales, including molecular dynamics (MD) and density functional theory (DFT), and the coupled atomistic and discrete dislocation multiscale method (CADD), to predict the mechanical properties of nanocomposites possessing nanomaterials that are either 1-D (carbyne chains), 2-D (graphene sheets), or 3-D (Al/amorphous-Si core-shell nanorod).

The MD method is used to model Ni-graphene nanocomposites. The strength of a Ni-graphene nanocomposite is found to improve by increasing the gap between the graphene sheet and a …

Shock Compaction Of Graphene Doped Yttria Stabilized Zirconia: An Experimental And Computational Study, Christopher Rueben Johnson

Master's Theses (2009 -)

Yttria stabilized zirconia (YSZ) is a broadly used ceramic due to its impeccable hardness and thermal stability. Limitations of the material, however, subsist within its fracture toughness. Literature indicates that shock consolidation may enable production of composite YSZ and graphene mixtures with improved fracture toughness and other material properties while maintaining the material’s nanostructure dimensionality. Therefore, investigation of the compaction phenomena at non-equilibrium states will provide informative results to be used in the fabrication of bulk graphene-YSZ composites. Computational molecular dynamics (MD) simulations and impact experiments are conducted to explore and characterize the dynamic response of the YSZ variants. Molecular …

Wettability Of Fully Hydroxylated And Alkylated (001) Α-Quartz Surface In Carbon Dioxide Atmosphere, Aleksandr Abramov, Alireza Keshavarz, Stefan Iglauer

Research outputs 2014 to 2021

Wettability of alkylated quartz surfaces is of primary importance in several technological applications, including the development of oil and gas reservoirs and carbon geo-sequestration. It is intuitively understood and experimentally confirmed that hydroxylated quartz surfaces are hydrophilic. By gradually saturating a hydroxylated (001) α-quartz surface with pentyl groups, we show using molecular dynamics simulations that the surface can also exhibit extreme hydrophobicity. Within a range of surface pentyl group density from 0.29 to 3.18/nm², the contact angle of a water droplet under 10 MPa pressure of carbon dioxide at 300 K changes from 10–20 to 180°. This study …

Interactions Between Dislocations And Three-Dimensional Annealing Twins In Face Centered Cubic Metals, Yanxiang Liang, Xiaofang Yang, Mingyu Gong, Guisen Liu, Qing Liu, Jian Wang

Department of Mechanical and Materials Engineering: Faculty Publications

Annealing twins often form in metals with a face centered cubic structure during thermal and mechanical processing. Here, we conducted molecular dynamic (MD) simulations for copper and aluminum to study the interaction processes between {1 1 1}1/2 <1 1 0> dislocations and a three-dimensional annealing twin. Twin boundaries are characterized with Σ3{1 1 1} coherent twin boundaries (CTBs) and Σ3{1 1 2} incoherent twin boundaries (ITBs). MD results revealed that dislocation-ITB interactions affect slip transmission for a dislocation crossing CTBs, facilitating the nucleation of Lomer dislocation.

Tools For Understanding Static Structure Factors And Their Application To Simulations Of Liquids, Travis Mackoy

Graduate Research Theses & Dissertations

Molecular dynamics (MD) simulations can be used to compute static structure factors (��(��)) and provide an interpretation of the underlying periodic atomic ordering. MD simulations complement experimentally measured ��(��) by allowing qualitative assignment of peaks to various ordering, such as cation-anion ordering in ionic liquids, via decomposition of ��(��) into partial ��(��). Here we present a method for classifying interatomic distances that allows for quantitative peak assignment and visualization of atoms that contribute most to each peak in calculated ��(��) for soft materials. The method is illustrated by investigating ��(��) for the ionic liquid 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl)imide (C4C1pyrrTFSI), which shows two …

Direct Polymer Grafting As A Method Of Maintaining The Mechanical Properties Of Cellulose Nanocrystals In The Presence Of Moisture, Mary Elizabeth Breen-Lyles

Graduate Research Theses & Dissertations

Cellulose nanocrystals (CNCs) are a distinctive nanomaterial derived from cellulose, the most abundant natural polymer on Earth, and the primary reinforcing structural component of cellulose fibrils found within the plant cell wall. These nanocrystals exhibit mechanical properties comparable to synthetic aramid fibers but are advantageous as they are biodegradable, renewable, and can be produced sustainably as they are predominantly extracted from naturally occurring cellulosic materials. These qualities make it a sustainable, highly renewable and environmentally friendly material to be used in place of synthetic materials in a variety of applications. With their high surface area to volume ratio, low level …

Nanosecond Pulsed Electric Signals Can Affect Electrostatic Environment Of Protiens Below The Threshold Of Conformational Effects: The Case Study Of Sod1 With A Molecular Simulation Study, Elena Della Valle, Paolo Marracino, Olga Pakhomova, Micaela Liberti, Francesca Apollonio

Bioelectrics Publications

Electric fields can be a powerful tool to interact with enzymes or proteins, with an intriguing perspective to allow protein manipulation. Recently, researchers have focused the interest on intracellular enzyme modifications triggered by the application of nanosecond pulsed electric fields. These findings were also supported by theoretical predictions from molecular dynamics simulations focussing on significant variations in protein secondary structures. In this work, a theoretical study utilizing molecular dynamics simulations is proposed to explore effects of electric fields of high intensity and very short nanosecond duration applied to the superoxide dismutase (Cu/Zn-SOD or SOD-1), an important enzyme involved in the …

Wettability Of Quartz Surfaces Under Carbon Dioxide Geo-Sequestration Conditions. A Theoretical Study, Aleksandr Abramov

Theses: Doctorates and Masters

The wettability of rocks under reservoir conditions is important to ensure and secure long term underground storage of carbon dioxide. The composition of those rocks vary significantly and are influenced by the fact that quartz is the second most abundant mineral in the earth's continental crust. Thus, the CO2 wettability of quartz dominates the overall CO2 trapping performance of storage and cap rocks. If depleted oil or gas reservoirs are used for storage of CO2 quartz surfaces of rocks in reservoirs which have been previously exposed to hydrocarbons might be covered with chemisorpt hydrocarbon molecules. The CO2 wettability of these …

Impact Of Conformational Change, Solvation Environment, And Post-Translational Modification On Desulfurization Enzyme 2'-Hydroxybiphenyl-2-Sulfinate Desulfinase (Dszb) Stability And Activity, Landon C. Mills

Theses and Dissertations--Chemical and Materials Engineering

Naturally occurring enzymatic pathways enable highly specific, rapid thiophenic sulfur cleavage occurring at ambient temperature and pressure, which may be harnessed for the desulfurization of petroleum-based fuel. One pathway found in bacteria is a four-step catabolic pathway (the 4S pathway) converting dibenzothiophene (DBT), a common crude oil contaminant, into 2-hydroxybiphenyl (HBP) without disrupting the carbon-carbon bonds. 2’-Hydroxybiphenyl-2-sulfinate desulfinase (DszB), the rate-limiting enzyme in the enzyme cascade, is capable of selectively cleaving carbon-sulfur bonds. Accordingly, understanding the molecular mechanisms of DszB activity may enable development of the cascade as industrial biotechnology. Based on crystallographic evidence, we hypothesized that DszB …

Effect Of Turbostratic Orientations And Confined Fluid On Mechanical Strength Of Bi-Layer Graphene: A Molecular Dynamics Study, Nil B. Dhankecha

Theses

The rise of graphene as a reinforcement material in the last decade has been exponential owing to its superior mechanical properties. This one atom thick 2D material is applicable in many industries related to nanomechanical, nanoelectronics and optical devices. Despite its strength and superior properties, single-layer graphene tends to be unstable in a free-standing form. This led to active use of bi-layer and multilayered graphene in many of the above-stated applications. Though properties of single-layer graphene have been extensively investigated both computationally as well as experimentally for over a decade, bilayer graphene and its turbostratic form are still under research. …

Comparative Study Of Analytical Models Of The Gruneisen Parameter Of Metals As Function Of Pressure, Celia Garcia Amparan

Open Access Theses & Dissertations

Commonly used Gruneisen parameter (γ) models only hold accurate in limited regimes making them inapplicable for use over wide temperature-pressure conditions. The accuracy of these analytical models of γ and of the thermal expansion of solids are of particular interest as these are considered proxies for quantifying anharmonicity, which may be a significant contribution to the thermal pressure at high temperatures. This work reviews various definitions of γ and their relations to the equations of state and apply them to two simple metals: Tantalum (Ta) and Copper (Cu), for which a high body of experimental data exists. Classical Molecular Dynamics …

Modeling Cell Line-Specific Recruitment Of Signaling Proteins To The Insulin-Like Growth Factor 1 Receptor, Keesha E. Erickson, Dipak Barua, For Full List Of Authors, See Publisher's Website.

Chemical and Biochemical Engineering Faculty Research & Creative Works

Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common SLiM and vice versa. To investigate the effects of competition on RTK signaling, we used a rule-based modeling approach to develop and analyze models for ligand-induced recruitment of SH2/PTB domain-containing proteins to autophosphorylation sites in the insulin-like growth factor 1 …

Molecular Dynamics Study Of Creep Deformation In Nickel-Based Superalloy, Sabila Kader Pinky

MSU Graduate Theses

The present study employs molecular dynamics simulations of Ni-based superalloy to investigate the creep behavior under uniaxial compression test. Dislocation dynamics is analyzed for the nickel-based single crystal superalloy with the presence of void and with varying the distribution of gamma-prime phase The results show that multiple-void systems are more prone to yield than single-void systems and single-void systems are more prone to yield than the system without void. From the simulations, it has been determined that the creep mechanism in Ni/Ni3Al is subject to change on the applied stress depending on the distribution of gamma-prime phases change. Dislocation behavior …

Development Of Multicomponent Eam Potential For Ni-Based Superalloy, Muztoba Rabbani

MSU Graduate Theses

We initiated the development of multi-component EAM potentials for Aluminides and Carbides, key phases in Ni-based Superalloys. The goal is to utilize the MD simulation to understand the deformation dynamics that contribute to the formation of voids and creep initiation. For this purpose, we constructed the raw data from ab-initio (molecular dynamics) MD simulations fed into the potential development code and used Nickel as the base metal with the addition of a number of various elements including Aluminum, Chromium, Tungsten. We then developed the EAM potentials for the aluminide and carbide phases using the force-fitting code MEAMfit. Our generated potential …