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 …

Bifurcation Exploration Of Ion Acoustic Solitons Formation Of A Nonlinear Beta Fractional Kadomtsev-Petviashvili Burger Model In Plasma State, Mst. Razia Pervin, Alrazi Abdeljabbar, Fahad Sameer Alshammari, Mst. Shekha Khatun, Harun Or-Roshid

Mathematical Modelling and Numerical Simulation with Applications

This research presents an extensive investigation of Ion acoustic soliton dynamics governed by a Beta-fractional Kadomtsev-Petviashvili-Burgurs (KPB) model. By engaging the planar dynamical system scheme in aggregation with the extended $(\phi, \psi)$ expansion, Kudryashov expansion, and the NMKM analytic schemes, we create a broad class of exact nonlinear pattern wave solutions. The local stability edifice of the fractional plasma model is explored through bifurcation theory, enabling the far-reaching classification of all admissible phase diagrams. Conforming Ion acoustic wave structures allied with every detour alignment are systematically assembled. Owing to the fractional and dissipative appearances of the model, an all-embracing assortment …

Quantum Mechanics As A Framework For Data Assimilation And Its Application To Atmospheric Parameterization, David Freeman

Dartmouth College Ph.D Dissertations

Quantum mechanics, as a mathematical system, can be understood as a generalization of classical probability theory. Quantum Mechanical Data Assimilation (QMDA) is a method in which classical dynamical systems are embedded into a quantum mechanical setting, with an associated data assimilation scheme leveraging the operator algebraic setting. In this dissertation, the algebraic structure underlying the operator theoretic formulation of QMDA is discussed. A procedure for closure of dynamical systems based on QMDA, known as Quantum Mechanical Closure (QMCl), is then constructed, and the procedures for constructing the quantum embeddings and implementing QMCl in practice are laid out and implemented for …

Stability Analysis Of Thermohaline Convection With A Time-Varying Shear Flow Using The Lyapunov Method, Kalin Kochnev

Honors Scholar Theses

This work applies the Lyapunov method to identify instabilities and compute the growth rate of a linear time-varying system. The linear system studied describes cold fresh water on top of hot salty water with a periodically time-varying background shear flow. A time-dependent weighting matrix is employed to construct a Lyapunov function candidate. The resulting linear matrix inequalities are discretized in time using the forward Euler method. As the number of temporal discretization points increases, the growth rate predicted by the Lyapunov method or Floquet theory, used for comparison, will converge to the same value obtained from numerical simulations. Furthermore, the …

Modeling Synaptic Dysfunction As Neural Contagion: A Graph-Based Sedr Framework For Simulating Signal Spread, Michelle Marfo, Dr. Padmanabhan Seshaiyer, Alonso Ogueda-Oliva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Robust Spacecraft Autonomy For Deep Space Exploration In Special Euclidean Group Se(3), Matthew Wittal

Doctoral Dissertations and Master's Theses

Over the past half-century, humanity has gained extensive experience conducting manned spaceflight near Earth. Arguably, "near Earth" could even include the Moon — the most distant destination humans have reached. However, "near" in this work primarily refers low Earth orbit (LEO). One could argue that we have not truly left Earth since the Apollo, as spacecraft in some LEOs remain subject to atmospheric drag thus emphasizing their continued connection to Earth's immediate environment. Reflecting on this, it becomes clear that humanity has largely remained bound to Earth’s immediate vicinity since the Apollo missions reached the Moon. However, that is set …

Mathematics And Determinism: Chaos, Quantum Mechanics, And The Limits Of Predictive Structure, Jackson T. Salumbides

CMC Senior Theses

This thesis examines the relationship between mathematics and determinism by analyzing how chaos theory, quantum mechanics, and formal mathematical limits challenge traditional conceptions of predictability and causal structure. Chaos theory shows that deterministic systems can exhibit practical unpredictability due to sensitivity to initial conditions. Quantum mechanics introduces probabilistic outcomes that complicate deterministic interpretation, though alternative frameworks such as Bohmian mechanics and superdeterminism attempt to restore determinism at conceptual cost. Additionally, results from mathematical logic, including Gödel’s incompleteness theorems and Turing’s undecidability, demonstrate intrinsic limitations on what can be deduced or computed, even in fully deterministic systems. By synthesizing these areas, …

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

Leveraging Redundancy As A Link Between Spreading Dynamics On And Of Networks, Felipe Xavier Costa

Electronic Theses & Dissertations (2024 - present)

A constant quest in network science has been in the development of methods to identify the most relevant components in a dynamical system solely via the interaction structure amongst its subsystems. This information allows the development of control and intervention strategies in biochemical signaling and epidemic spreading. We highlight the relevant components in heterogeneous dynamical system by their patterns of redundancy, which can connect how dynamics affect network topology and which pathways are necessary to spreading phenomena on networks. In order to measure the redundancies in a large class of empirical systems, we develop the backbone of directed networks methodology, …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Wavelet Compression As An Observational Operator In Data Assimilation Systems For Sea Surface Temperature, Bradley J. Sciacca

LSU New Orleans Theses and Dissertations

The ocean remains severely under-observed, in part due to its sheer size. Containing nearly billion of water with most of the subsurface being invisible because water is extremely difficult to penetrate using electromagnetic radiation, as is typically used by satellite measuring instruments. For this reason, most observations of the ocean have very low spatial-temporal coverage to get a broad capture of the ocean’s features. However, recent “dense but patchy” data have increased the availability of high-resolution – low spatial coverage observations. These novel data sets have motivated research into multi-scale data assimilation methods. Here, we demonstrate a new assimilation approach …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Langevin Dynamic Models For Smfret Dynamic Shift, David Frost, Keisha Cook Dr, Hugo Sanabria Dr

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Effective Non-Hermiticity And Topology In Markovian Quadratic Bosonic Dynamics, Vincent Paul Flynn

Dartmouth College Ph.D Dissertations

Recently, there has been an explosion of interest in re-imagining many-body quantum phenomena beyond equilibrium. One such effort has extended the symmetry-protected topological (SPT) phase classification of non-interacting fermions to driven and dissipative settings, uncovering novel topological phenomena that are not known to exist in equilibrium which may have wide-ranging applications in quantum science. Similar physics in non-interacting bosonic systems has remained elusive. Even at equilibrium, an "effective non-Hermiticity" intrinsic to bosonic Hamiltonians poses theoretical challenges. While this non-Hermiticity has been acknowledged, its implications have not been explored in-depth. Beyond this dynamical peculiarity, major roadblocks have arisen in the search …

Photonic Sensors Based On Integrated Ring Resonators, Jaime Da Silva

Mechanical Engineering Research Theses and Dissertations

This thesis investigates the application of integrated ring resonators to different sensing applications. The sensors proposed here rely on the principle of optical whispering gallery mode (WGM) resonance shifts of the resonators. Three distinct sensing applications are investigated to demonstrate the concept: a photonic seismometer, an evanescent field sensor, and a zero-drift Doppler velocimeter. These concepts can be helpful in developing lightweight, compact, and highly sensitive sensors. Successful implementation of these sensors could potentially address sensing requirements for both space and Earth-bound applications. The feasibility of this class of sensors is assessed for seismic, proximity, and vibrational measurements.

Machine Learning-Based Data And Model Driven Bayesian Uncertanity Quantification Of Inverse Problems For Suspended Non-Structural System, Zhiyuan Qin

All Dissertations

Inverse problems involve extracting the internal structure of a physical system from noisy measurement data. In many fields, the Bayesian inference is used to address the ill-conditioned nature of the inverse problem by incorporating prior information through an initial distribution. In the nonparametric Bayesian framework, surrogate models such as Gaussian Processes or Deep Neural Networks are used as flexible and effective probabilistic modeling tools to overcome the high-dimensional curse and reduce computational costs. In practical systems and computer models, uncertainties can be addressed through parameter calibration, sensitivity analysis, and uncertainty quantification, leading to improved reliability and robustness of decision and …

Applying Hallgren’S Algorithm For Solving Pell’S Equation To Finding The Irrational Slope Of The Launch Of A Billiard Ball, Sangheon Choi

Mathematical Sciences Technical Reports (MSTR)

This thesis is an exploration of Quantum Computing applied to Pell’s equation in an attempt to find solutions to the Billiard Ball Problem. Pell’s equation is a Diophantine equation in the form of x² − ny² = 1, where n is a given positive nonsquare integer, and integer solutions are sought for x and y. We will be applying Hallgren’s algorithm for finding irrational periods in functions, in the context of billiard balls and their movement on a friction-less unit square billiard table. Our central research question has been the following: Given the cutting sequence of the billiard …

Nidus Idearum. Scilogs, Viii: Painting By Numbers, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In this eighth book of scilogs collected from my nest of ideas, one may find new and old questions and solutions, – in email messages to research colleagues, or replies, and personal notes handwritten on the planes to, and from international conferences, about all kind of topics, centered mostly on Paradoxism and Neutrosophy.

Exchanging ideas with: Robert Neil Boyd, Joseph Brenner, Ahmed Cevik, Victor Christianto, Adrian Curaj, Jean Dezert, Andrei-Lucian Drăgoi, Ervin Goldfain, Young Bae Jun, Yale Landsberg, Radu Munteanu, Paul Piștea, Viorel Roman, Ridvan Sahin, Said Broumi, Selcuk Topal, Eric W. Weisstein, Xiaohing Zhang.

The Kepler Problem On Complex And Pseudo-Riemannian Manifolds, Michael R. Astwood

Theses and Dissertations (Comprehensive)

The motion of objects in the sky has captured the attention of scientists and mathematicians since classical times. The problem of determining their motion has been dubbed the Kepler problem, and has since been generalized into an abstract problem of dynamical systems. In particular, the question of whether a classical system produces closed and bounded orbits is of importance even to modern mathematical physics, since these systems can often be analysed by hand. The aforementioned question was originally studied by Bertrand in the context of celestial mechanics, and is therefore referred to as the Bertrand problem. We investigate the qualitative …

Reduced-Order Dynamic Modeling And Robust Nonlinear Control Of Fluid Flow Velocity Fields, Anu Kossery Jayaprakash, William Mackunis, Vladimir Golubev, Oksana Stalnov

Publications

A robust nonlinear control method is developed for fluid flow velocity tracking, which formally addresses the inherent challenges in practical implementation of closed-loop active flow control systems. A key challenge being addressed here is flow control design to compensate for model parameter variations that can arise from actuator perturbations. The control design is based on a detailed reduced-order model of the actuated flow dynamics, which is rigorously derived to incorporate the inherent time-varying uncertainty in the both the model parameters and the actuator dynamics. To the best of the authors’ knowledge, this is the first robust nonlinear closed-loop active flow …

Entropic Dynamics Of Networks, Felipe Xavier Costa, Pedro Pessoa

Northeast Journal of Complex Systems (NEJCS)

Here we present the entropic dynamics formalism for networks. That is, a framework for the dynamics of graphs meant to represent a network derived from the principle of maximum entropy and the rate of transition is obtained taking into account the natural information geometry of probability distributions. We apply this framework to the Gibbs distribution of random graphs obtained with constraints on the node connectivity. The information geometry for this graph ensemble is calculated and the dynamical process is obtained as a diffusion equation. We compare the steady state of this dynamics to degree distributions found on real-world networks.

Towards A General Framework For Practical Quantum Network Protocols, Sumeet Khatri

LSU Doctoral Dissertations

The quantum internet is one of the frontiers of quantum information science. It will revolutionize the way we communicate and do other tasks, and it will allow for tasks that are not possible using the current, classical internet. The backbone of a quantum internet is entanglement distributed globally in order to allow for such novel applications to be performed over long distances. Experimental progress is currently being made to realize quantum networks on a small scale, but much theoretical work is still needed in order to understand how best to distribute entanglement and to guide the realization of large-scale quantum …

An Update On The Computational Theory Of Hamiltonian Period Functions, Bradley Joseph Klee

Graduate Theses and Dissertations

Lately, state-of-the-art calculation in both physics and mathematics has expanded to include the field of symbolic computing. The technical content of this dissertation centers on a few Creative Telescoping algorithms of our own design (Mathematica implementations are given as a supplement). These algorithms automate analysis of integral period functions at a level of difficulty and detail far beyond what is possible using only pencil and paper (unless, perhaps, you happen to have savant-level mental acuity). We can then optimize analysis in classical physics by using the algorithms to calculate Hamiltonian period functions as solutions to ordinary differential equations. The simple …

Mathematical Modelling Of Temperature Effects On The Afd Neuron Of Caenorhabditis Elegans, Zachary Mobille, Rosangela Follmann, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Period Estimation And Noise In A Neutrally Stable Stochastic Oscillator, Kevin R. Sanft, Ben F. M. Intoy

Spora: A Journal of Biomathematics

The periods of the orbits for the well-mixed cyclic three-species Lotka-Volterra model far away from the fixed point are studied. For finite system sizes, a discrete stochastic approach is employed and periods are found via wavelet analysis. As the system size is increased, a hierarchy of approximations ranging from Poisson noise to Gaussian noise to deterministic models are utilized. Based on the deterministic equations, a mathematical relationship between a conserved quantity of the model and the period of the population oscillations is found. Exploiting this property we then study the deterministic conserved quantity and period noise in finite size systems.

Optical Soliton Perturbation With Quadratic-Cubic Nonlinearity, Asma Mir

Student Works (2020-2029)

Solitons can be defined as wave packets that can travel undistorted across long distances even transcontinental and transoceanic. They serve as modern telecommunication means through cables and optical fibers for fast Internet activities. To maintain high-fidelity and time sensitive transmission, optical pulses manage the efficient flow of data. From the last few years, Nonlinear Schrödinger Equation (NLSE) has been a great attraction of research activities across the globe. The governing model is the Nonlinear Schrödinger Equation (NLSE). From a mathematical standpoint, NLSE is a nonlinear partial differential equation (PDE) that has been studied in a variety of other areas of …

Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese

Biology and Medicine Through Mathematics Conference

No abstract provided.

An Introduction To Shape Dynamics, Patrick R. Kerrigan

Physics

Shape Dynamics (SD) is a new fundamental framework of physics which seeks to remove any non-relational notions from its methodology. importantly it does away with a background space-time and replaces it with a conceptual framework meant to reflect direct observables and recognize how measurements are taken. It is a theory of pure relationalism, and is based on different first principles then General Relativity (GR). This paper investigates how SD assertions affect dynamics of the three body problem, then outlines the shape reduction framework in a general setting.

Fluids In Music: The Mathematics Of Pan’S Flutes, Bogdan Nita, Sajan Ramanathan

Department of Mathematics Faculty Scholarship and Creative Works

We discuss the mathematics behind the Pan’s flute. We analyze how the sound is created, the relationship between the notes that the pipes produce, their frequencies and the length of the pipes. We find an equation which models the curve that appears at the bottom of any Pan’s flute due to the different pipe lengths.

Wall Model Large Eddy Simulation Of A Diffusing Serpentine Inlet Duct, Ryan J. Thompson

Theses and Dissertations

The modeling focus on serpentine inlet ducts (S-duct), as with any inlet, is to quantify the total pressure recovery and ow distortion after the inlet, which directly impacts the performance of a turbine engine fed by the inlet. Accurate prediction of S-duct ow has yet to be achieved amongst the computational fluid dynamics (CFD) community to improve the reliance on modeling reducing costly testing. While direct numerical simulation of the turbulent ow in an S-duct is too cost prohibitive due to grid scaling with Reynolds number, wall-modeled large eddy simulation (WM-LES) serves as a tractable alternative. US3D, a hypersonic research …