Dynamics and Dynamical Systems Commons^™

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

An Analytical Framework For Quantifying Urban And Community Resilience To Natural Hazards From Cell-Phone Gps-Location And Traffic-Flow Data, Georgios Chatzikyriakidis

Civil and Environmental Engineering Theses and Dissertations

Urban areas are increasingly exposed to natural hazards while accommodating a growing share of the global population, yet a consistent science-based framework for quantifying urban and community resilience remains lacking. This dissertation develops a physics-based analytical framework grounded in statistical mechanics and the quantitative theory of Brownian motion. A city is conceptualized as a complex medium in which citizens move analogously to Brownian particles within a viscoelastic environment, influenced by socioeconomic interactions and infrastructure functionality.

A central premise is that urban resilience, interpreted as engineering resilience (an outcome), can be quantified through a single metric: the mean-square displacement MSD=⟨r²(t)⟩, of …

On The Exploration Of Crystallographic Anisotropy And Defects In Shock Loading Using Molecular Dynamics, Benjamin P. Helman

Theses and Dissertations

The impact of crystallographic orientation, grain boundaries, and vacancies on the shock behavior of aluminum was investigated using molecular dynamics simulations. Shock loading in the [001], [011], and [111] directions was explored, revealing anisotropic behavior in shock speed, melting, dislocation density, and unique phase changes. The Hugoniot elastic limit in the [100], [110], and [111] directions was calculated as 23.2 GPa, 24 GPa, and 18.4 GPa respectively. These results were found to be an order of magnitude larger than the compressive yield strength computed at equilibrium. Additionally, metastable melting in the [011] and [111] directions occurred roughly 1000 K below …

Towing Tank Trials Of Hydrokinetic Turbine Scale Model To Support Marine Energy System Verification, Shahab Rouhi

LSU New Orleans Theses and Dissertations

In response to the escalating demand for sustainable energy solutions and the critical reevaluation of conventional fossil fuels due to environmental concerns, this dissertation embarks on a comprehensive exploration of hydrokinetic energy as a promising alternative. The study delves into the underexplored domain of hydrokinetic energy, leveraging innovative methodologies for effective utilization and harnessing, particularly through the development and investigation of hydrokinetic turbines.

In the realm of hydrokinetic energy conversion, our research has exclusively concentrated on horizontal-axis turbines, distinct from other turbine configurations. Noteworthy is the adaptation of a conventional horizontal-axis wind turbine for water currents, revealing enhanced performance through …

Study Of Thermoelectric And Lattice Dynamics Properties Of 2d Layered Mx (M = Sn, Pb; X = S, Se, Te) And Zrs2 Compounds Using First-Principles Approach, Abhiyan Pandit

Graduate Theses and Dissertations

The aim of this dissertation is the investigation of thermoelectric and lattice dynamics properties of two-dimensional (2D) MX (M = Sn, Pb; X = S, Se, Te) and ZrS2 compounds based on the first-principles density functional theory. The dimensionality reduction (e.g., using 2D structure) of bulk materials is found to have enhanced thermoelectric efficiency. This enhancement is attributed to the increase of the Seebeck coefficient as a result of higher electronic density of states near the Fermi level in low-dimensional materials. In addition, lowering the dimensionality increases phonon scattering near interfaces and surfaces in 2D materials, which leads to a …

Design And Analysis Of Marangoni-Driven Robotic Surfers, Mitchel L. Timm

Dissertations, Master's Theses and Master's Reports

We designed and experimentally studied the dynamics of two robotic systems that surf along the water-air interface. The robots were self-propelled by means of creating and maintaining a surface tension gradient resulting from an asymmetric release of isopropyl alcohol (IPA). The imbalance in the distribution of surface tension surrounding the robots generates a propulsive force commonly referred to as Marangoni propulsion. First, we considered a single surfer, which was custom-made with novel control mechanisms that allow for both forward motion and steering to be remotely adjusted solely through the manipulation of local surface stresses. We analyzed the performance of this …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Study Of Static And Dynamical Properties Of Complex Antiferroelectrics Materials, Kinnary Yogeshbhai Patel

Graduate Theses and Dissertations

The aim of this dissertation is the investigation of the static and dynamical properties of the complex antiferroelectric materials using Effective Hamiltonian method and First principles calculations. In chapter 3, a novel elemental interatomic coupling in perovskite materials which bilinearly couples the antiferroelectric displacements of cations with the rotations of the oxygen octahedra. This new coupling explains a very complex crystal structure of prototypical antiferroelectric PbZrO3. My explanation provides a unified description of many other complex antipolar crystal structures in variety of perovskite materials, including the occurrence of incommensurate phases in some of them. In chapter 4, results and analysis …

Design And Control Of A Peristaltic Pump To Simulate Left Atrial Pressure In A Conductive Silicone Model, Jeremy Collins

Mechanical Engineering Undergraduate Honors Theses

According to the CDC, atrial fibrillation is responsible for more than 454,000 hospitalizations and approximately 158,000 deaths per year. A common treatment for atrial fibrillation is catheter ablation, a process in which a long flexible tube is guided through the femoral artery and to the source of arrhythmia in the heart, where it measures the electrical potential at various locations and converts problematic heart tissue to scar tissue via ablation. This paper details the design and control of a low-cost ($400) peristaltic pump system using repetitive control to replicate blood pressure in the left atrium in a conductive silicone model …

Numerical Simulation Of Nonlinear Vibrations Of Discrete Mass With Harmonic Force Perturbation, M. Yusupov, B. A. Akhmedov, Olga Karpova

Acta of Turin Polytechnic University in Tashkent

The problem of vibration of a single-mass system under the force excitation of vibration associated with a fixed base by a weightless nonlinear viscoelastic spring is considered. To take into account the rheological properties of the spring material, the Boltzmann-Volterra principle was used. Mathematical models of the problem under consideration are obtained, which are described by integro-differential equations. A solution method based on the use of quadrature formulas has been developed and a computer program has been compiled on its basis, the results obtained are presented in the form of graphs. The influence of nonlinear and rheological properties of a …

Adsorption And Reconfiguration Of Amphiphiles At Silica-Water Interfaces: Role Of Electrostatic Interactions, Van Der Waals Forces And Hydrogen Bonds, Yao Wu

LSU Doctoral Dissertations

The ability to explore and predict metastable structures of hybrid self-assemblies is of central importance for the next generation of advanced materials with novel properties. As compared to their thermodynamically stable forms, the kinetically stabilized materials show improved functionality potentially over their stable counterparts. The self-assembly processes usually originate from weak intermolecular interactions, involving a dynamic competition between attractive and repulsive interactions. These weak forces, including van der Waals (vdW), electrostatic interaction and the hydrogen bonding (H-bonding), can be tuned by external stimuli, e.g., confinement, temperature and ionization, and consequently driving hybrid materials into different configurations. It is challenging to …

Mechani-Kits Senior Design Project, Jake Utley, Sophie Carson, Vincent Seguin

Mechanical Engineering

Studies suggest that when designed and executed well, hands-on activities can enhance student understanding of key mechanics concepts. Current products are expensive and typically not designed to meet a variety of learning objectives. Through the Mechanics of Inclusion and Inclusivity in Mechanics grant, the Cal Poly Physics and Engineering Departments are seeking to incorporate new hands-on activities into their courses. Our team has designed three inexpensive ”MechaniKits” to be used in physics, statics and dynamics courses [1]. This Final Design Review outlines our findings, objectives, and final designs for this project. It also explains our manufacturing and design verification plans. …

Dual-Axis Solar Tracker, Bryan Kennedy

All Undergraduate Projects

Renewable energies, and fuels that are not fossil fuel-based, are one of the prolific topics of debate in modern society. With climate change now becoming a primary focus for scientists and innovators of today, one of the areas for the largest amount of potential and growth is that of the capturing and utilization of Solar Energy. This method involves using a mechanical system to track the progression of the sun as it traverses the sky throughout the day. A dual-axis solar tracker such as the one designed and built for this project, can follow the sun both azimuthally and in …

Investigation Of Fundamental Principles Of Rigid Body Impact Mechanics, Khalid Alluhydan

Mechanical Engineering Research Theses and Dissertations

In impact mechanics, the collision between two or more bodies is a common, yet a very challenging problem. Producing analytical solutions that can predict the post-collision motion of the colliding bodies require consistent modeling of the dynamics of the colliding bodies. This dissertation presents a new method for solving the two and multibody impact problems that can be used to predict the post-collision motion of the colliding bodies. Also, we solve the rigid body collision problem of planar kinematic chains with multiple contacts with external surfaces.

In the first part of this dissertation, we study planar collisions of Balls and …

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 …

Tracking Shock Movement On The Surface Of An Oscillating, Straked Semispan Delta Wing, Justin A. Pung

Theses and Dissertations

A recent research effort, sponsored by the Air Force Office of Scientific Research, numerically investigated the unsteady aerodynamic flow field around an oscillating, straked, delta wing. The study was centered on determining the importance of the unsteady aerodynamic forces acting as a driver for a nonlinear motion known as limit cycle oscillations. The current effort focused on creating a computational model to compare to the results of previous tests and modeling efforts and discover new information regarding the onset of LCO. The computational model was constructed using the Cartesian overset capabilities of the CREATE-AV™ fixed wing fluid dynamics solver Kestrel. …

Analytical Models And Control Design Approaches For A 6 Dof Motion Test Apparatus, Kyra L. Schmidt

Theses and Dissertations

Wind tunnels play an indispensable role in the process of aircraft design, providing a test bed to produce valuable, accurate data that can be extrapolated to actual flight conditions. Historically, time-averaged data has made up the bulk of wind tunnel research, but modern flight design necessitates the use of dynamic wind tunnel testing to provide time-accurate data for high frequency motion. This research explores the use of a 6 degree of freedom (DOF) motion test apparatus (MTA) in the form of a robotic arm to allow models inside a subsonic wind tunnel to track prescribed trajectories to obtain time-accurate force …

Current-Driven Production Of Vortex-Antivortex Pairs In Planar Josephson Junction Arrays And Phase Cracks In Long-Range Order, Francisco Estellés-Duart, Miguel Ortuño, Andrés M. Somoza, Valerii M. Vinokur, Alex Gurevich

Physics Faculty Publications

Proliferation of topological defects like vortices and dislocations plays a key role in the physics of systems with long-range order, particularly, superconductivity and superfluidity in thin films, plasticity of solids, and melting of atomic monolayers. Topological defects are characterized by their topological charge reflecting fundamental symmetries and conservation laws of the system. Conservation of topological charge manifests itself in extreme stability of static topological defects because destruction of a single defect requires overcoming a huge energy barrier proportional to the system size. However, the stability of driven topological defects remains largely unexplored. Here we address this issue and investigate numerically …

Experimental Building Demonstration Model With Viscous Fluid Dampers, Blake Thomas Reeve, Brianna Jean Kufa, Aden Malek Stepanians, Sophie Carmion Ratkovich

Architectural Engineering

The Architectural Engineering major places a heavy emphasis on structural dynamics and the role of wind and seismic loading in building analysis and design. Buildings of high importance that are critical to community function, such as hospitals, often utilize supplemental damping devices like supplemental viscous fluid dampers or base isolators to reduce the overall demands on the structural system. The design and analysis of these dampers are typically not taught at the undergraduate level, and is frequently performed by mechanical engineers, in lieu of structural engineers.

To better understand and research building behavior with supplemental damping devices, our multi-disciplinary team …

Viscosity Dependence Of Faraday Wave Formation Thresholds, Lisa M. Slaughter

Symposium

This experiment uses an electromagnetic shaker to produce standing wave patterns on the surface of a vertically oscillating sample of silicon liquid. These surface waves, known as Faraday waves, form shapes such as squares, lines, and hexagons. They are known to be dependent upon the frequency and amplitude of the forcing as well as on the viscosity and depth of the liquid in the dish. At a depth of 4mm and for various silicon liquids having kinematic viscosities of 10, 20, and 38 cSt, we determined the acceleration at which patterns form for frequencies between 10 and 60 Hz. For …

Active Optimal Control Strategies For Increasing The Efficiency Of Photovoltaic Cells, Sharif Aljoaba

Theses and Dissertations--Electrical and Computer Engineering

Energy consumption has increased drastically during the last century. Currently, the worldwide energy consumption is about 17.4 TW and is predicted to reach 25 TW by 2035. Solar energy has emerged as one of the potential renewable energy sources. Since its first physical recognition in 1887 by Adams and Day till nowadays, research in solar energy is continuously developing. This has lead to many achievements and milestones that introduced it as one of the most reliable and sustainable energy sources. Recently, the International Energy Agency declared that solar energy is predicted to be one of the major electricity production energy …

Dynamical Properties Of Ferroelectric Perovskites (Ba,Sr)Tio3 And Pb(Zr,Ti)O3 Systems From First Principles, Jeevaka Weerasinghe

Graduate Theses and Dissertations

A first-principles-based effective Hamiltonian scheme which incorporates coupling between ferroelectric (FE) and antiferrodistortive (AFD) motions is applied to Pb(Zr,Ti)O₃ alloys. It validates the existence of two modes of E symmetry (rather than the single E(1TO) soft mode) in the 50-75 cm^-1 range for temperatures smaller than 200 K and for compositions falling within the Rhombohedral R3c phase. Coupling between long-range-ordered FE and AFD motions is shown to be the cause of the additional mode and more insight into its nature is provided. This scheme is further used to reveal a field-induced anticrossing involving FE and AFD degrees of …

Simulation Of Temperature Distributions In Tissue Upon Laser Pulse Irradiation Including Water Mass Transfer, Deepthi Nagulapally

Electrical & Computer Engineering Theses & Dissertations

Lasers, due to their unique characteristics, have tremendous applications in the medical field. Generally all laser applications in hie-medicine involve the propagation of laser energy through tissue. Energy is deposited giving rise to many physical, hie-chemical, and mechanical effects. Among these are dynamical changes in the local temperature distributions within the tissue. Analysis of the temperature changes requires the creation of an appropriate optical transmission and heat flow model that incorporates user specified laser parameters. Here, a numerical simulation model was developed to study both steady state and time dependent temperature distributions due to pulsed laser radiation within user specified …

Hand-Held Flyback Driven Coaxial Dielectric Barrier Discharge: Development And Characterization, Victor J. Law, Vladimir Milosavljevic, Neil O’Connor, James F. Lalor, Steven Daniels

Articles

The development of a handheld single and triple chamber atmospheric pressure coaxial dielectric barrier discharge driven by Flyback circuitry for helium and argon discharges is described. The Flyback uses external metal-oxide-semiconductor field-effect transistor power switching technology and the transformer operates in the continuous current mode to convert a continuous dc power of 10–33 W to generate a 1.2–1.6 kV 3.5 μs pulse. An argon discharge breakdown voltage of ∼768 V is measured. With a 50 kHz, pulse repetition rate and an argon flow rate of 0.5–10 argon slm (slm denotes standard liters per minute), the electrical power density deposited in …

On Misorientation Distribution Evolution During Anisotropic Grain Growth, Elizabeth A. Holm, Gregory N. Hassold, Mark A. Miodownik

Physics Publications

In order to study the development of texture and boundary character during annealing, three-dimensional grain crystallography and crystallographically mediated grain boundary properties were incorporated into a finite temperature Monte Carlo model for grain growth. Randomly textured microstructures evolve normally, with growth exponent n=0.96. While texture remains random, the steady-state boundary misorientation distribution favors low-angle boundaries. To first order, low-angle boundaries increase by lengthening, not by proliferating. In contrast, microstructures with a strong single-component texture develop four-grain junctions and highly curved grain boundaries, which alter evolution. The boundary misorientation distribution narrows and shifts to low angles, and no steady state …

Studies Of Bistable Fluid Devices For Particle Flow Control, Gerald H. Hogland

Dissertations and Theses

This study was directed toward the development of a bistable wall attachment Flip-Flop device which was capable of directionally controlling particle flow. The particles were transported by a fluid stream which under the influence of wall attachment. The dominant criteria in the development of the device was the achievement of the highest recovery of particles at the active output, without destroying the wall attachment of the fluid stream The experiment was conducted in several distinct stages; each of which was concerned with at least one aspect of wa1l attachment or particle flow. Results derived from one test were used to …