Non-linear Dynamics Commons^™

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 …

Utilizing Non-Negative Least Squares For Data-Driven Discovery Of Dynamics, Tracey G. Oellerich

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Computational Modeling Using A Novel Continuum Approach Coupled With Pathway-Informed Neural Networks To Optimize Dynein-Mediated Centrosome Positioning In Polarized Cells, Arkaprovo Ghosal, Padmanabhan Seshaiyar Dr., Adriana Dawes Dr., General Genomics Inc.

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Using A Coupled Integral Projection Model To Investigate Interspecific Competition During An Invasion: An Application To Silver Carp (Hypophthalmichthys Molitrix) And Gizzard Shad (Dorosoma Cepedianum), James Peirce

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Critical Transitions In Mental Health: Van Gogh Case Study, Anna Singley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Effects Of Seasonal Birth And Predation On Disease Spread, Leah Shaw, Allison Introne

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Epidemic Conditions With Temporary Link Deactivation On A Network Sir Disease Model, John Gemmer

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Msis-Kadelka: Modularizing The Control Search For Biological Systems, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Msis-Kadelka: Canalization Reduces The Nonlinearity Of Regulation In Biological Networks, Claus Kadelka, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling The Communication Dynamics In Human-Autonomy Teams: Insights From Search And Rescue Scenarios, Carlos E. Bustamante Orellana, Lucero Rodriguez Rodriguez, Yun Kang

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Rigid Body Constrained Motion Optimization And Control On Lie Groups And Their Tangent Bundles, Brennan S. Mccann

Doctoral Dissertations and Master's Theses

Rigid body motion requires formulations where rotational and translational motion are accounted for appropriately. Two Lie groups, the special orthogonal group SO(3) and the space of quaternions H, are commonly used to represent attitude. When considering rigid body pose, that is spacecraft position and attitude, the special Euclidean group SE(3) and the space of dual quaternions DH are frequently utilized. All these groups are Lie groups and Riemannian manifolds, and these identifications have profound implications for dynamics and controls. The trajectory optimization and optimal control problem on Riemannian manifolds presents significant opportunities for theoretical development. Riemannian optimization is an attractive …

Exploring The Presence Of Nonlinear Deterministic Dynamics In Commodity Prices, Sagar Dahal

Department of Agricultural Economics: Dissertations, Theses, and Student Research

Determining whether commodity prices (and volatility) are driven by linear stochastic processes or low-dimensional nonlinear deterministic dynamics (“chaos”) is crucial for policymaking, forecasting, production, storage, investment, risk management, and hedging decisions. Previous studies that used Lyapunov exponents and correlation dimensions to identify chaotic structures in price series may be unreliable in practical applications because these methods rely on asymptotic properties that require large, noiseless data which is often not available. We applied nonlinear time series analysis approaches to empirically detect the underlying market dynamics using the daily futures prices of ten agricultural commodities. We used phase space reconstruction to reconstruct …

Pathogen Emergence As Complex Biological Invasion: Lessons From Dynamical Systems Modeling, Sudam Surasinghe, Marisabel Rodriguez, Victor Meszaros, Jane Molofsky, Salvador Almagro-Moreno, Brandon Ogbunugafor

Northeast Journal of Complex Systems (NEJCS)

Infectious disease emergence has become the target of cross-disciplinary efforts
that aim to understand and predict the shape of outbreaks. The many challenges
involved with the prediction of disease emergence events is a characteristic that in-
fectious diseases share with biological invasions in many subfields of ecology (e.g.,
how certain plants are able to successfully invade a new niche). Like infectious
diseases, biological invasions by plants and animals involve interactions between
agents (pathogens and plants in their respective cases) and a recipient niche. In
this study, we examine the problem of pathogen emergence through the lens of a
framework first …

Temporality-Induced Chaos In The Kuramoto Model, Keanu Mason Rock, Hamza Dirie, Sean P. Cornelius

Northeast Journal of Complex Systems (NEJCS)

Switched dynamical systems have been extensively studied in engineering literature in the context of system control. In these systems, the dynamical laws change between different subsystems depending on the environment, a process that is known to produce emergent behaviors---notably chaos. These dynamics are analogous to those of temporal networks, in which the network topology changes over time, thereby altering the dynamics on the network. It stands to reason that temporal networks may therefore produce emergent chaos and other exotic behaviors unanticipated in static networks, yet concrete examples remain elusive. Here, we present a minimal example of a networked system in …

Detecting Coherent Transport Structures In Ocean Surface Flows, Leah Hoogstra

Master's Theses

Ocean surface transport plays a critical role in marine ecosystems, influencing the complex spatiotemporal patterns of both marine species and pollutants. The theory of Lagrangian coherent structures (LCSs) aims to identify fundamental patterns within time-dependent, nonlinear fluid flows. LCSs are material surfaces that act as dividing lines which fluid does not cross for a relevant period of time. LCS theory is still under active development, and there are multiple proposed ways to mathematically determine an LCS. Each proposed mathematical definition aims to capture the same physical properties, and some capture those properties more successfully and consistently than others. Here we …

Deep Hybrid Modeling Of Neuronal Dynamics Using Generative Adversarial Networks, Soheil Saghafi

Dissertations

Mechanistic modeling and machine learning methods are powerful techniques for approximating biological systems and making accurate predictions from data. However, when used in isolation these approaches suffer from distinct shortcomings: model and parameter uncertainty limit mechanistic modeling, whereas machine learning methods disregard the underlying biophysical mechanisms. This dissertation constructs Deep Hybrid Models that address these shortcomings by combining deep learning with mechanistic modeling. In particular, this dissertation uses Generative Adversarial Networks (GANs) to provide an inverse mapping of data to mechanistic models and identifies the distributions of mechanistic model parameters coherent to the data.

Chapter 1 provides background information on …

Computing Brain Networks With Complex Dynamics, Anca R. Radulescu

Biology and Medicine Through Mathematics Conference

No abstract provided.

Modeling, Simulation And Control Of Microrobots For The Microfactory., Zhong Yang

Electronic Theses and Dissertations

Future assembly technologies will involve higher levels of automation in order to satisfy increased microscale or nanoscale precision requirements. Traditionally, assembly using a top-down robotic approach has been well-studied and applied to the microelectronics and MEMS industries, but less so in nanotechnology. With the boom of nanotechnology since the 1990s, newly designed products with new materials, coatings, and nanoparticles are gradually entering everyone’s lives, while the industry has grown into a billion-dollar volume worldwide. Traditionally, nanotechnology products are assembled using bottom-up methods, such as self-assembly, rather than top-down robotic assembly. This is due to considerations of volume handling of large …

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 …

Integrable Systems On Symmetric Spaces From A Quadratic Pencil Of Lax Operators, Rossen Ivanov

Conference papers

The article surveys the recent results on integrable systems arising from quadratic pencil of Lax operator L, with values in a Hermitian symmetric space. The counterpart operator M in the Lax pair defines positive, negative and rational flows. The results are illustrated with examples from the A.III symmetric space. The modeling aspect of the arising higher order nonlinear Schrödinger equations is briefly discussed.