Dynamic Systems Commons^™

Controlled Manipulation And Transport By Microswimmers In Stokes Flows, Jake Buzhardt

All Dissertations

Remotely actuated microscale swimming robots have the potential to revolutionize many aspects of biomedicine. However, for the longterm goals of this field of research to be achievable, it is necessary to develop modelling, simulation, and control strategies which effectively and efficiently account for not only the motion of individual swimmers, but also the complex interactions of such swimmers with their environment including other nearby swimmers, boundaries, other cargo and passive particles, and the fluid medium itself. The aim of this thesis is to study these problems in simulation from the perspective of controls and dynamical systems, with a particular focus …

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.

Effect Of Under-Reporting, Vaccine Efficiency And Social Behavior On Epidemic Progression, Samiran Ghosh, Samiran Ghosh

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Optimal Harvest Control Within A Predator-Prey System: A Case Study In Chesapeake Bay Fishes, Iordanka Panayotova

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.

Intracellular Transport And Filament Organization In Neurons, Maria-Veronica Ciocanel

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling The Long-Distance Effects Of Predation, Henry Ogu

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Msis-Kadelka: On The Uniqueness Of Network Identification, Alan Veliz-Cuba, Elena Dimitrova

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-Ledder: Empowering Future Physicians: Modeling Disease Transmission With Netlogo To Encourage Mathematical Reasoning, Anne E. Yust

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.

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems Program: Dissertations and Student Research

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Effect Of Under-Reporting, Vaccine Efficiency And Social Behavior On Epidemic Progression, Samiran Ghosh

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Deep Q-Learning Framework For Quantitative Climate Change Adaptation Policy For Florida Road Network Due To Extreme Precipitation, Orhun Aydin

I-GUIDE Forum

Climate change-induced extreme weather and increasing population are increasing the pressure on the global aging road networks. Adaptation requires designing interventions and alterations to the road networks that consider future dynamics of flooding and increased traffic due to the growing population. This paper introduces a reinforcement learning approach to designing interventions for Florida's road network under future traffic and climate projections. Three climate models and a tide and surge model are used to create flooding and coastal inundation projections, respectively. The optimal sequence of decisions for adapting Florida's road network to minimize flooding-related disruptions is solved by using a graph-based …

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 …

The Role Of Nanofluids In Renewable Energy Engineering, M. M. Bhatti, K. Vafai, Sara I. Abdelsalam

Basic Science Engineering

No abstract provided.

Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra

Research Symposium

Background: The textbook model of NNSV transcription predicts a gene expression gradient. However, multiple studies show non-gradient gene expression patterns or data inconsistent with a simple gradient. Regarding the latter, several studies show a dramatic decrease in gene expression over the last two genes of the respiratory syncytial virus (RSV) genome (a highly studied NNSV). The textbook model cannot explain these phenomena.

Methods: Computational models of RSV and vesicular stomatitis virus (VSV – another highly studied NNSV) transcription were written in the Python programming language using the Scientific Python Development Environment. The model code is freely available on GitHub: …

On Subset Labelings Of Trees, Gary Chartrand, Ebrahim Salehi, Ping Zhang

Mathematical Sciences Faculty Research

For a nontrivial graph G, a subset labeling of G is a labeling of the vertices of G with nonempty subsets of the set [r]={1, 2, ... , r} for a positive integer r such that two vertices of G have disjoint labels if and only if the vertices are adjacent. The subset index ρ(G) of G is the minimum positive integer r for which G has such a subset labeling from the set [r]. If T is a tree of diameter d, then ρ(Pd+1) ≤ ρ(T). It is shown that there are several classes of trees T of diameter …

An Implementation Of The Method Of Moments On Chemical Systems With Constant And Time-Dependent Rates, Emmanuel O. Adara, Roger B. Sidje

Northeast Journal of Complex Systems (NEJCS)

Among numerical techniques used to facilitate the analysis of biochemical reactions, we can use the method of moments to directly approximate statistics such as the mean numbers of molecules. The method is computationally viable in time and memory, compared to solving the chemical master equation (CME) which is notoriously expensive. In this study, we apply the method of moments to a chemical system with a constant rate representing a vascular endothelial growth factor (VEGF) model, as well as another system with time-dependent propensities representing the susceptible, infected, and recovered (SIR) model with periodic contact rate. We assess the accuracy of …

Flow Dynamics In Cardiovascular Devices: A Comprehensive Review, Venant Niyonkuru, Bosco Jean Ndayishimiye Dr, Anicet Barthélemy Sibomana

Digital Journal of Clinical Medicine

This review explores flow dynamics in cardiovascular devices, focusing on fundamental fluid mechanics principles and normal blood flow patterns. It discusses the role of different structures in maintaining flow dynamics and the importance of stents, heart valves, artificial hearts, and ventricular assist devices in cardiovascular interventions. The review emphasizes the need for optimized designs and further research to enhance knowledge of flow dynamics in cardiovascular devices, advancing the field and improving patient care in cardiovascular interventions.

Neural Network Learning For Pdes With Oscillatory Solutions And Causal Operators, Lizuo Liu

Mathematics Theses and Dissertations

In this thesis, we focus on developing neural networks algorithms for scientific computing. First, we proposed a phase shift deep neural network (PhaseDNN), which provides a uniform wideband convergence in approximating high frequency functions and solutions of wave equations. Several linearized learning schemes have been proposed for neural networks solving nonlinear Navier-Stokes equations. We also proposed a causality deep neural network (Causality-DeepONet) to learn the causal response of a physical system. An extension of the Causality-DeepONet to time-dependent PDE systems is also proposed. The PhaseDNN makes use of the fact that common DNNs often achieve convergence in the low frequency …

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 …

Analyzing Robustness Of An Agent Based Model On Action Potentials In Cardiac Tissue, Marion Jon Zollinger Lara

Master's Theses

An agent based model (ABM) is a computational model with ``agents'' that interact with each other in an ``environment.'' This paper analyzes a particular ABM simulating individual ions in cardiac tissue, with the goal of modelling the strength and consistency of the electrical signals needed for a healthy heartbeat. We build several frameworks based on work by M. A. Yereniuk and S. D. Olson to demonstrate robustness of the original model. We conclude a moderate level of robustness using those frameworks, through a combination of proofs and empirical evidence.

A Novel Family Of Chain Binomial Models To Investigate Correlated Vaccination And Infection Rates In Sveirs Epidemic Dynamics, Divine Wanduku

Biology and Medicine Through Mathematics Conference

No abstract provided.

Modeling The Immune Response To Immunotherapy And Triple Negative Breast Cancer In Mice, Dayton J. Syme, Angelica Davenport, Yun Lu, Anna G. Sorace, Nicholas G. Cogan

Biology and Medicine Through Mathematics Conference

No abstract provided.

Switching Between Synchronization And Desynchronization In Islets With Coupled Heterogenous Beta Cells: Finding Switch Cells, Zainab Almutawa

Biology and Medicine Through Mathematics Conference

No abstract provided.

Assorted Kerosene-Based Nanofluid Across A Dual-Zone Vertical Annulus With Electroosmosis, Sara I. Abdelsalam, A. M. Alsharif, Y. Abd Elmaboud, A. I. Abdellateef

Basic Science Engineering

The goal of this numerical simulation is to visualize the electroosmotic flow of immiscible fluids through a porous medium in vertical annular microtubes. The inner region (Region I) is filled with an electrically conducting hybrid nanofluid while an electrically conducting Jeffrey fluid is flowing in the second region (Region II). The chosen nanofluid is kerosene-based and the nanoparticles (Fe3O4-TiO2) are of a spherical shape. A strong zeta potential is taken into account and the electroosmotic velocity in the two layers is considered too. The annular microtubes are subjected to an external magnetic field and an electric field. The linked nonlinear …

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 …

Using Integral Projection Models To Explore Management Strategies For Silver Carp (Hypophthalmichthys Molitrix), Cameron Coles, Elizabeth Balas, James Peirce, Greg Sandland, Richard Erickson

Spora: A Journal of Biomathematics

Silver carp (Hypophthalmichthys molitrix) are planktivorous fish that were originally introduced to the United States for use in fish production ponds and have since escaped these enclosures and are invading the Mississippi River Basin. The silver carp invasion of the Illinois River has a myriad of negative effects on native ecosystems. In this paper, we introduce key dependencies that are likely important in the population dynamics of silver carp: length-dependent egg production and density-dependent growth. Using movement data between two adjacent pools of the Illinois River, we conduct numerical simulations to explore the theoretical effect of harvesting and …